gRNA_Cloning Vector Citations (332)
Originally described in: RNA-Guided Human Genome Engineering via Cas9.Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM Science. 2013 Feb 15;339(6121):823-6. doi: 10.1126/science.1232033 PubMed Journal
Articles Citing gRNA_Cloning Vector
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| Optimization of scarless human stem cell genome editing. Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Nucleic Acids Res. 2013 Oct;41(19):9049-61. doi: 10.1093/nar/gkt555. Epub 2013 Jul 31. PubMed |
An enChIP system for the analysis of bacterial genome functions.
Fujita T, Yuno M, Fujii H.
BMC Res Notes. 2018 Jun 14;11(1):387. doi: 10.1186/s13104-018-3486-3.
PubMed
Associated Plasmids |
| CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Sugano SS, Shirakawa M, Takagi J, Matsuda Y, Shimada T, Hara-Nishimura I, Kohchi T. Plant Cell Physiol. 2014 Mar;55(3):475-81. doi: 10.1093/pcp/pcu014. Epub 2014 Jan 18. PubMed |
| CRISPR-Cas-mediated targeted genome editing in human cells. Yang L, Mali P, Kim-Kiselak C, Church G. Methods Mol Biol. 2014;1114:245-67. doi: 10.1007/978-1-62703-761-7_16. PubMed |
| Validation of microinjection methods for generating knockout mice by CRISPR/Cas-mediated genome engineering. Horii T, Arai Y, Yamazaki M, Morita S, Kimura M, Itoh M, Abe Y, Hatada I. Sci Rep. 2014 Mar 28;4:4513. doi: 10.1038/srep04513. PubMed |
| Polyglutamine Disease Modeling: Epitope Based Screen for Homologous Recombination using CRISPR/Cas9 System. An MC, O'Brien RN, Zhang N, Patra BN, De La Cruz M, Ray A, Ellerby LM. PLoS Curr. 2014 Apr 15;6. pii: ecurrents.hd.0242d2e7ad72225efa72f6964589369a. doi: 10.1371/currents.hd.0242d2e7ad72225efa72f6964589369a. PubMed |
| A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation. van de Weijer ML, Bassik MC, Luteijn RD, Voorburg CM, Lohuis MA, Kremmer E, Hoeben RC, LeProust EM, Chen S, Hoelen H, Ressing ME, Patena W, Weissman JS, McManus MT, Wiertz EJ, Lebbink RJ. Nat Commun. 2014 May 8;5:3832. doi: 10.1038/ncomms4832. PubMed |
Adenoviral vector delivery of RNA-guided CRISPR/Cas9 nuclease complexes induces targeted mutagenesis in a diverse array of human cells.
Maggio I, Holkers M, Liu J, Janssen JM, Chen X, Goncalves MA.
Sci Rep. 2014 May 29;4:5105. doi: 10.1038/srep05105.
PubMed
Associated Plasmids |
Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Delta32 mutation confers resistance to HIV infection.
Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW.
Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9591-6. doi: 10.1073/pnas.1407473111. Epub 2014 Jun 9.
PubMed
Associated Plasmids |
| Biallelic targeting of expressed genes in mouse embryonic stem cells using the Cas9 system. Zhang Y, Vanoli F, LaRocque JR, Krawczyk PM, Jasin M. Methods. 2014 Sep;69(2):171-8. doi: 10.1016/j.ymeth.2014.05.003. Epub 2014 Jun 12. PubMed |
| Rapid generation of mouse models with defined point mutations by the CRISPR/Cas9 system. Inui M, Miyado M, Igarashi M, Tamano M, Kubo A, Yamashita S, Asahara H, Fukami M, Takada S. Sci Rep. 2014 Jun 23;4:5396. doi: 10.1038/srep05396. PubMed |
Allele-specific genome editing and correction of disease-associated phenotypes in rats using the CRISPR-Cas platform.
Yoshimi K, Kaneko T, Voigt B, Mashimo T.
Nat Commun. 2014 Jun 26;5:4240. doi: 10.1038/ncomms5240.
PubMed
Associated Plasmids |
| PVT1 dependence in cancer with MYC copy-number increase. Tseng YY, Moriarity BS, Gong W, Akiyama R, Tiwari A, Kawakami H, Ronning P, Reuland B, Guenther K, Beadnell TC, Essig J, Otto GM, O'Sullivan MG, Largaespada DA, Schwertfeger KL, Marahrens Y, Kawakami Y, Bagchi A. Nature. 2014 Aug 7;512(7512):82-6. doi: 10.1038/nature13311. Epub 2014 Jun 22. PubMed |
Expansion of the CRISPR-Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs.
Ranganathan V, Wahlin K, Maruotti J, Zack DJ.
Nat Commun. 2014 Aug 8;5:4516. doi: 10.1038/ncomms5516.
PubMed
Associated Plasmids |
| Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA. Long C, McAnally JR, Shelton JM, Mireault AA, Bassel-Duby R, Olson EN. Science. 2014 Sep 5;345(6201):1184-1188. doi: 10.1126/science.1254445. Epub 2014 Aug 14. PubMed |
| The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo. Lin SR, Yang HC, Kuo YT, Liu CJ, Yang TY, Sung KC, Lin YY, Wang HY, Wang CC, Shen YC, Wu FY, Kao JH, Chen DS, Chen PJ. Mol Ther Nucleic Acids. 2014 Aug 19;3:e186. doi: 10.1038/mtna.2014.38. PubMed |
Improving the specificity and efficacy of CRISPR/CAS9 and gRNA through target specific DNA reporter.
Zhang JH, Pandey M, Kahler JF, Loshakov A, Harris B, Dagur PK, Mo Y, Simonds WF.
J Biotechnol. 2014 Sep 2. pii: S0168-1656(14)00838-4. doi: 10.1016/j.jbiotec.2014.08.033.
PubMed
Associated Plasmids |
| Functional annotation of colon cancer risk SNPs. Yao L, Tak YG, Berman BP, Farnham PJ. Nat Commun. 2014 Sep 30;5:5114. doi: 10.1038/ncomms6114. PubMed |
| Simple knockout by electroporation of engineered endonucleases into intact rat embryos. Kaneko T, Sakuma T, Yamamoto T, Mashimo T. Sci Rep. 2014 Oct 1;4:6382. doi: 10.1038/srep06382. PubMed |
| Assaying break and nick-induced homologous recombination in mammalian cells using the DR-GFP reporter and Cas9 nucleases. Vriend LE, Jasin M, Krawczyk PM. Methods Enzymol. 2014;546:175-91. doi: 10.1016/B978-0-12-801185-0.00009-X. PubMed |
| Genome editing for human gene therapy. Meissner TB, Mandal PK, Ferreira LM, Rossi DJ, Cowan CA. Methods Enzymol. 2014;546:273-95. doi: 10.1016/B978-0-12-801185-0.00013-1. PubMed |
| A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential. Zhou HY, Katsman Y, Dhaliwal NK, Davidson S, Macpherson NN, Sakthidevi M, Collura F, Mitchell JA. Genes Dev. 2014 Dec 15;28(24):2699-711. doi: 10.1101/gad.248526.114. PubMed |
| CRISPR/Cas9-mediated genome modification in the mollusc, Crepidula fornicata. Perry KJ, Henry JQ. Genesis. 2015 Feb;53(2):237-44. doi: 10.1002/dvg.22843. Epub 2015 Jan 9. PubMed |
| Creating a monomeric endonuclease TALE-I-SceI with high specificity and low genotoxicity in human cells. Lin J, Chen H, Luo L, Lai Y, Xie W, Kee K. Nucleic Acids Res. 2015 Jan;43(2):1112-22. doi: 10.1093/nar/gku1339. Epub 2014 Dec 24. PubMed |
| Gene Targeting Through Homologous Recombination in Monkey Embryonic Stem Cells Using CRISPR/Cas9 System. Zhu S, Rong Z, Lu X, Xu Y, Fu X. Stem Cells Dev. 2015 May 15;24(10):1147-9. doi: 10.1089/scd.2014.0507. Epub 2015 Feb 25. PubMed |
| Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus. Zhen S, Hua L, Liu YH, Gao LC, Fu J, Wan DY, Dong LH, Song HF, Gao X. Gene Ther. 2015 May;22(5):404-12. doi: 10.1038/gt.2015.2. Epub 2015 Feb 5. PubMed |
| Production of Gene-Corrected Adult Beta Globin Protein in Human Erythrocytes Differentiated from Patient iPSCs After Genome Editing of the Sickle Point Mutation. Huang X, Wang Y, Yan W, Smith C, Ye Z, Wang J, Gao Y, Mendelsohn L, Cheng L. Stem Cells. 2015 May;33(5):1470-9. doi: 10.1002/stem.1969. PubMed |
| A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. O'Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ. Nucleic Acids Res. 2015 Mar 31;43(6):3389-404. doi: 10.1093/nar/gkv137. Epub 2015 Feb 20. PubMed |
| Isolation of specific genomic regions and identification of associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Fujita T, Fujii H. Methods Mol Biol. 2015;1288:43-52. doi: 10.1007/978-1-4939-2474-5_4. PubMed |
| Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries. Beaudoin M, Gupta RM, Won HH, Lo KS, Do R, Henderson CA, Lavoie-St-Amour C, Langlois S, Rivas D, Lehoux S, Kathiresan S, Tardif JC, Musunuru K, Lettre G. Arterioscler Thromb Vasc Biol. 2015 Jun;35(6):1472-1479. doi: 10.1161/ATVBAHA.115.305534. Epub 2015 Apr 2. PubMed |
| Cas9-mediated targeting of viral RNA in eukaryotic cells. Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. Proc Natl Acad Sci U S A. 2015 May 12;112(19):6164-9. doi: 10.1073/pnas.1422340112. Epub 2015 Apr 27. PubMed |
| An alternative pluripotent state confers interspecies chimaeric competency. Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC. Nature. 2015 May 21;521(7552):316-21. doi: 10.1038/nature14413. Epub 2015 May 6. PubMed |
| Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Hara S, Tamano M, Yamashita S, Kato T, Saito T, Sakuma T, Yamamoto T, Inui M, Takada S. Sci Rep. 2015 Jun 9;5:11221. doi: 10.1038/srep11221. PubMed |
| Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System. Grobarczyk B, Franco B, Hanon K, Malgrange B. Stem Cell Rev. 2015 Jun 10. PubMed |
| Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Martinez J, Malireddi RK, Lu Q, Cunha LD, Pelletier S, Gingras S, Orchard R, Guan JL, Tan H, Peng J, Kanneganti TD, Virgin HW, Green DR. Nat Cell Biol. 2015 Jul;17(7):893-906. doi: 10.1038/ncb3192. Epub 2015 Jun 22. PubMed |
| Haploid Genetic Screen Reveals a Profound and Direct Dependence on Cholesterol for Hantavirus Membrane Fusion. Kleinfelter LM, Jangra RK, Jae LT, Herbert AS, Mittler E, Stiles KM, Wirchnianski AS, Kielian M, Brummelkamp TR, Dye JM, Chandran K. MBio. 2015 Jun 30;6(4):e00801. doi: 10.1128/mBio.00801-15. PubMed |
Engineering Human Stem Cell Lines with Inducible Gene Knockout using CRISPR/Cas9.
Chen Y, Cao J, Xiong M, Petersen AJ, Dong Y, Tao Y, Huang CT, Du Z, Zhang SC.
Cell Stem Cell. 2015 Jul 1. pii: S1934-5909(15)00261-1. doi: 10.1016/j.stem.2015.06.001.
PubMed
Associated Plasmids |
| CCAR2/DBC1 is required for Chk2-dependent KAP1 phosphorylation and repair of DNA damage. Magni M, Ruscica V, Restelli M, Fontanella E, Buscemi G, Zannini L. Oncotarget. 2015 Jul 10;6(19):17817-31. PubMed |
| MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5. Nezich CL, Wang C, Fogel AI, Youle RJ. J Cell Biol. 2015 Aug 3;210(3):435-50. doi: 10.1083/jcb.201501002. PubMed |
| Transcriptomic Profiling and H3K27me3 Distribution Reveal Both Demethylase-Dependent and Independent Regulation of Developmental Gene Transcription in Cell Differentiation. Kang SC, Kim SK, Chai JC, Kim SH, Won KJ, Lee YS, Jung KH, Chai YG. PLoS One. 2015 Aug 11;10(8):e0135276. doi: 10.1371/journal.pone.0135276. eCollection 2015. PubMed |
| CRISPR mediated somatic cell genome engineering in the chicken. Veron N, Qu Z, Kipen PA, Hirst CE, Marcelle C. Dev Biol. 2015 Nov 1;407(1):68-74. doi: 10.1016/j.ydbio.2015.08.007. Epub 2015 Aug 13. PubMed |
| Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins. Fujii H, Fujita T. Int J Mol Sci. 2015 Sep 9;16(9):21802-12. doi: 10.3390/ijms160921802. PubMed |
| Generation of Hypertension-Associated STK39 Polymorphism Knockin Cell Lines With the Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 System. Mandai S, Mori T, Sohara E, Rai T, Uchida S. Hypertension. 2015 Dec;66(6):1199-206. doi: 10.1161/HYPERTENSIONAHA.115.05872. Epub 2015 Sep 28. PubMed |
| Use of the HPRT gene to study nuclease-induced DNA double-strand break repair. Gravells P, Ahrabi S, Vangala RK, Tomita K, Brash JT, Brustle LA, Chung C, Hong JM, Kaloudi A, Humphrey TC, Porter AC. Hum Mol Genet. 2015 Dec 15;24(24):7097-110. doi: 10.1093/hmg/ddv409. Epub 2015 Sep 30. PubMed |
| Monoclonal antibody profiling of cell surface proteins associated with the viral biofilms on HTLV-1 transformed cells. Tarasevich A, Filatov A, Pichugin A, Mazurov D. Acta Virol. 2015 Sep;59(3):247-56. PubMed |
| Glucocorticoid receptor antagonism reverts docetaxel resistance in human prostate cancer. Kroon J, Puhr M, Buijs JT, van der Horst G, Hemmer DM, Marijt KA, Hwang MS, Masood M, Grimm S, Storm G, Metselaar JM, Meijer OC, Culig Z, van der Pluijm G. Endocr Relat Cancer. 2016 Jan;23(1):35-45. doi: 10.1530/ERC-15-0343. Epub 2015 Oct 19. PubMed |
| Differentiation of human ESCs to retinal ganglion cells using a CRISPR engineered reporter cell line. Sluch VM, Davis CH, Ranganathan V, Kerr JM, Krick K, Martin R, Berlinicke CA, Marsh-Armstrong N, Diamond JS, Mao HQ, Zack DJ. Sci Rep. 2015 Nov 13;5:16595. doi: 10.1038/srep16595. PubMed |
| Mitochondrial E3 ubiquitin ligase MARCH5 controls mitochondrial fission and cell sensitivity to stress-induced apoptosis through regulation of MiD49 protein. Xu S, Cherok E, Das S, Li S, Roelofs BA, Ge SX, Polster BM, Boyman L, Lederer WJ, Wang C, Karbowski M. Mol Biol Cell. 2016 Jan 15;27(2):349-59. doi: 10.1091/mbc.E15-09-0678. Epub 2015 Nov 12. PubMed |
| A forward genetic screen reveals novel independent regulators of ULBP1, an activating ligand for natural killer cells. Gowen BG, Chim B, Marceau CD, Greene TT, Burr P, Gonzalez JR, Hesser CR, Dietzen PA, Russell T, Iannello A, Coscoy L, Sentman CL, Carette JE, Muljo SA, Raulet DH. Elife. 2015 Nov 13;4. pii: e08474. doi: 10.7554/eLife.08474. PubMed |
| De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly. Wang WJ, Acehan D, Kao CH, Jane WN, Uryu K, Tsou MF. Elife. 2015 Nov 26;4. pii: e10586. doi: 10.7554/eLife.10586. PubMed |
| Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis. Wassef M, Rodilla V, Teissandier A, Zeitouni B, Gruel N, Sadacca B, Irondelle M, Charruel M, Ducos B, Michaud A, Caron M, Marangoni E, Chavrier P, Le Tourneau C, Kamal M, Pasmant E, Vidaud M, Servant N, Reyal F, Meseure D, Vincent-Salomon A, Fre S, Margueron R. Genes Dev. 2015 Dec 15;29(24):2547-62. doi: 10.1101/gad.269522.115. Epub 2015 Dec 4. PubMed |
| Atg13 Is Essential for Autophagy and Cardiac Development in Mice. Kaizuka T, Mizushima N. Mol Cell Biol. 2015 Dec 7;36(4):585-95. doi: 10.1128/MCB.01005-15. PubMed |
| Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. Ng M, Ndungo E, Kaczmarek ME, Herbert AS, Binger T, Kuehne AI, Jangra RK, Hawkins JA, Gifford RJ, Biswas R, Demogines A, James RM, Yu M, Brummelkamp TR, Drosten C, Wang LF, Kuhn JH, Muller MA, Dye JM, Sawyer SL, Chandran K. Elife. 2015 Dec 23;4. pii: e11785. doi: 10.7554/eLife.11785. PubMed |
| Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O'Geen H, Segal DJ, Farnham PJ. Nucleic Acids Res. 2016 Jan 6. pii: gkv1530. PubMed |
| Redundant function of DNA ligase 1 and 3 in alternative end-joining during immunoglobulin class switch recombination. Masani S, Han L, Meek K, Yu K. Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1261-6. doi: 10.1073/pnas.1521630113. Epub 2016 Jan 19. PubMed |
| Ligase I and ligase III mediate the DNA double-strand break ligation in alternative end-joining. Lu G, Duan J, Shu S, Wang X, Gao L, Guo J, Zhang Y. Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1256-60. doi: 10.1073/pnas.1521597113. Epub 2016 Jan 19. PubMed |
| Nutrient-Regulated Phosphorylation of ATG13 Inhibits Starvation-Induced Autophagy. Puente C, Hendrickson RC, Jiang X. J Biol Chem. 2016 Jan 22. pii: jbc.M115.689646. PubMed |
| Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Alsafadi S, Houy A, Battistella A, Popova T, Wassef M, Henry E, Tirode F, Constantinou A, Piperno-Neumann S, Roman-Roman S, Dutertre M, Stern MH. Nat Commun. 2016 Feb 4;7:10615. doi: 10.1038/ncomms10615. PubMed |
| Direct Visualization of Ebola Virus Fusion Triggering in the Endocytic Pathway. Spence JS, Krause TB, Mittler E, Jangra RK, Chandran K. MBio. 2016 Feb 9;7(1):e01857-15. doi: 10.1128/mBio.01857-15. PubMed |
| Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair. Mianne J, Chessum L, Kumar S, Aguilar C, Codner G, Hutchison M, Parker A, Mallon AM, Wells S, Simon MM, Teboul L, Brown SD, Bowl MR. Genome Med. 2016 Feb 15;8(1):16. doi: 10.1186/s13073-016-0273-4. PubMed |
| Regulation of Transcription Factor Yin Yang 1 by SET7/9-mediated Lysine Methylation. Zhang WJ, Wu XN, Shi TT, Xu HT, Yi J, Shen HF, Huang MF, Shu XY, Wang FF, Peng BL, Xiao RQ, Gao WW, Ding JC, Liu W. Sci Rep. 2016 Feb 23;6:21718. doi: 10.1038/srep21718. PubMed |
| Transglutaminase 2 contributes to a TP53-induced autophagy program to prevent oncogenic transformation. Yeo SY, Itahana Y, Guo AK, Han R, Iwamoto K, Nguyen HT, Bao Y, Kleiber K, Wu YJ, Bay BH, Voorhoeve M, Itahana K. Elife. 2016 Mar 9;5:e07101. doi: 10.7554/eLife.07101. PubMed |
| Construction of a hybrid beta-hexosaminidase subunit capable of forming stable homodimers that hydrolyze GM2 ganglioside in vivo. Tropak MB, Yonekawa S, Karumuthil-Melethil S, Thompson P, Wakarchuk W, Gray SJ, Walia JS, Mark BL, Mahuran D. Mol Ther Methods Clin Dev. 2016 Mar 2;3:15057. doi: 10.1038/mtm.2015.57. eCollection 2016. PubMed |
| Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks. Vriend LE, Prakash R, Chen CC, Vanoli F, Cavallo F, Zhang Y, Jasin M, Krawczyk PM. Nucleic Acids Res. 2016 Jun 20;44(11):5204-17. doi: 10.1093/nar/gkw179. Epub 2016 Mar 21. PubMed |
| A Method for Genome Editing in Human Pluripotent Stem Cells. Smith C, Ye Z, Cheng L. Cold Spring Harb Protoc. 2016 Apr 1;2016(4):pdb.prot090217. doi: 10.1101/pdb.prot090217. PubMed |
| Genome Editing in Human Pluripotent Stem Cells. Smith C, Ye Z, Cheng L. Cold Spring Harb Protoc. 2016 Apr 1;2016(4):pdb.top086819. doi: 10.1101/pdb.top086819. PubMed |
| Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells. Moorthy SD, Mitchell JA. J Vis Exp. 2016 Apr 2;(110). doi: 10.3791/53552. PubMed |
| Testing the causality between CYP9M10 and pyrethroid resistance using the TALEN and CRISPR/Cas9 technologies. Itokawa K, Komagata O, Kasai S, Ogawa K, Tomita T. Sci Rep. 2016 Apr 20;6:24652. doi: 10.1038/srep24652. PubMed |
| Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage. Maure JF, Moser SC, Jaffray EG, F Alpi A, Hay RT. Sci Rep. 2016 May 17;6:26178. doi: 10.1038/srep26178. PubMed |
| Footprintless disruption of prosurvival genes in aneuploid cancer cells using CRISPR/Cas9 technology. Krachulec JM, Sedlmeier G, Thiele W, Sleeman JP. Biochem Cell Biol. 2016 Jun;94(3):289-96. doi: 10.1139/bcb-2015-0150. Epub 2016 Jun 2. PubMed |
Probing the impact of chromatin conformation on genome editing tools.
Chen X, Rinsma M, Janssen JM, Liu J, Maggio I, Goncalves MA.
Nucleic Acids Res. 2016 Jun 8. pii: gkw524.
PubMed
Associated Plasmids |
| Microinjection-based generation of mutant mice with a double mutation and a 0.5 Mb deletion in their genome by the CRISPR/Cas9 system. Hara S, Kato T, Goto Y, Kubota S, Tamano M, Terao M, Takada S. J Reprod Dev. 2016 Oct 18;62(5):531-536. doi: 10.1262/jrd.2016-058. Epub 2016 Jul 8. PubMed |
| ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects. Izumi K, Brett M, Nishi E, Drunat S, Tan ES, Fujiki K, Lebon S, Cham B, Masuda K, Arakawa M, Jacquinet A, Yamazumi Y, Chen ST, Verloes A, Okada Y, Katou Y, Nakamura T, Akiyama T, Gressens P, Foo R, Passemard S, Tan EC, El Ghouzzi V, Shirahige K. Am J Hum Genet. 2016 Aug 4;99(2):451-9. doi: 10.1016/j.ajhg.2016.06.011. Epub 2016 Jul 28. PubMed |
| Linear ubiquitination is involved in the pathogenesis of optineurin-associated amyotrophic lateral sclerosis. Nakazawa S, Oikawa D, Ishii R, Ayaki T, Takahashi H, Takeda H, Ishitani R, Kamei K, Takeyoshi I, Kawakami H, Iwai K, Hatada I, Sawasaki T, Ito H, Nureki O, Tokunaga F. Nat Commun. 2016 Aug 24;7:12547. doi: 10.1038/ncomms12547. PubMed |
Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions.
Morita S, Noguchi H, Horii T, Nakabayashi K, Kimura M, Okamura K, Sakai A, Nakashima H, Hata K, Nakashima K, Hatada I.
Nat Biotechnol. 2016 Aug 29. doi: 10.1038/nbt.3658.
PubMed
Associated Plasmids |
| Comprehensive protein tyrosine phosphatase mRNA profiling identifies new regulators in the progression of glioma. Bourgonje AM, Verrijp K, Schepens JT, Navis AC, Piepers JA, Palmen CB, van den Eijnden M, Hooft van Huijsduijnen R, Wesseling P, Leenders WP, Hendriks WJ. Acta Neuropathol Commun. 2016 Sep 1;4(1):96. doi: 10.1186/s40478-016-0372-x. PubMed |
| nc886, a non-coding RNA and suppressor of PKR, exerts an oncogenic function in thyroid cancer. Lee EK, Hong SH, Shin S, Lee HS, Lee JS, Park EJ, Choi SS, Min JW, Park D, Hwang JA, Johnson BH, Jeon SH, Kim IH, Lee YS, Lee YS. Oncotarget. 2016 Nov 15;7(46):75000-75012. doi: 10.18632/oncotarget.11852. PubMed |
| Targeted Gene Activation Using RNA-Guided Nucleases. Brown A, Woods WS, Perez-Pinera P. Methods Mol Biol. 2017;1468:235-50. doi: 10.1007/978-1-4939-4035-6_16. PubMed |
| IRGB10 Liberates Bacterial Ligands for Sensing by the AIM2 and Caspase-11-NLRP3 Inflammasomes. Man SM, Karki R, Sasai M, Place DE, Kesavardhana S, Temirov J, Frase S, Zhu Q, Malireddi RK, Kuriakose T, Peters JL, Neale G, Brown SA, Yamamoto M, Kanneganti TD. Cell. 2016 Oct 6;167(2):382-396.e17. doi: 10.1016/j.cell.2016.09.012. Epub 2016 Sep 29. PubMed |
| Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer. Harrod A, Fulton J, Nguyen VT, Periyasamy M, Ramos-Garcia L, Lai CF, Metodieva G, de Giorgio A, Williams RL, Santos DB, Gomez PJ, Lin ML, Metodiev MV, Stebbing J, Castellano L, Magnani L, Coombes RC, Buluwela L, Ali S. Oncogene. 2016 Oct 17. doi: 10.1038/onc.2016.382. PubMed |
| CRISPR-mediated targeting of HER2 inhibits cell proliferation through a dominant negative mutation. Wang H, Sun W. Cancer Lett. 2017 Jan 28;385:137-143. doi: 10.1016/j.canlet.2016.10.033. Epub 2016 Nov 1. PubMed |
| In Vitro and In Vivo Synergistic Therapeutic Effect of Cisplatin with Human Papillomavirus16 E6/E7 CRISPR/Cas9 on Cervical Cancer Cell Line. Zhen S, Lu JJ, Wang LJ, Sun XM, Zhang JQ, Li X, Luo WJ, Zhao L. Transl Oncol. 2016 Dec;9(6):498-504. doi: 10.1016/j.tranon.2016.10.002. Epub 2016 Oct 28. PubMed |
| Capturing the biology of disease severity in a PSC-based model of familial dysautonomia. Zeltner N, Fattahi F, Dubois NC, Saurat N, Lafaille F, Shang L, Zimmer B, Tchieu J, Soliman MA, Lee G, Casanova JL, Studer L. Nat Med. 2016 Dec;22(12):1421-1427. doi: 10.1038/nm.4220. Epub 2016 Nov 14. PubMed |
| A Simple and Efficient Approach to Construct Mutant Vaccinia Virus Vectors. Yuan M, Wang P, Chard LS, Lemoine NR, Wang Y. J Vis Exp. 2016 Oct 30;(116). doi: 10.3791/54171. PubMed |
In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration.
Suzuki K, Tsunekawa Y, Hernandez-Benitez R, Wu J, Zhu J, Kim EJ, Hatanaka F, Yamamoto M, Araoka T, Li Z, Kurita M, Hishida T, Li M, Aizawa E, Guo S, Chen S, Goebl A, Soligalla RD, Qu J, Jiang T, Fu X, Jafari M, Esteban CR, Berggren WT, Lajara J, Nunez-Delicado E, Guillen P, Campistol JM, Matsuzaki F, Liu GH, Magistretti P, Zhang K, Callaway EM, Zhang K, Belmonte JC.
Nature. 2016 Dec 1;540(7631):144-149. doi: 10.1038/nature20565. Epub 2016 Nov 16.
PubMed
Associated Plasmids |
| Targeted Inactivation of DNA Photolyase Genes in Medaka Fish (Oryzias latipes). Ishikawa-Fujiwara T, Shiraishi E, Fujikawa Y, Mori T, Tsujimura T, Todo T. Photochem Photobiol. 2017 Jan;93(1):315-322. doi: 10.1111/php.12658. Epub 2016 Dec 28. PubMed |
| Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. Moorthy SD, Davidson S, Shchuka VM, Singh G, Malek-Gilani N, Langroudi L, Martchenko A, So V, Macpherson NN, Mitchell JA. Genome Res. 2016 Nov 28. pii: gr.210930.116. PubMed |
| Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A, Jurkowski TP. Nucleic Acids Res. 2016 Nov 29. pii: gkw1112. PubMed |
| Deletion of conserved sequences in IG-DMR at Dlk1-Gtl2 locus suggests their involvement in expression of paternally expressed genes in mice. Saito T, Hara S, Tamano M, Asahara H, Takada S. J Reprod Dev. 2016 Dec 1. PubMed |
| ZEB1 is neither sufficient nor required for epithelial-mesenchymal transition in LS174T colorectal cancer cells. Jagle S, Dertmann A, Schrempp M, Hecht A. Biochem Biophys Res Commun. 2017 Jan 22;482(4):1226-1232. doi: 10.1016/j.bbrc.2016.12.017. Epub 2016 Dec 5. PubMed |
| Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion. Sokolova M, Turunen M, Mortusewicz O, Kivioja T, Herr P, Vaharautio A, Bjorklund M, Taipale M, Helleday T, Taipale J. Cell Cycle. 2017 Jan 17;16(2):189-199. doi: 10.1080/15384101.2016.1261765. Epub 2016 Dec 8. PubMed |
| Novel regulatory roles of Mff and Drp1 in E3 ubiquitin ligase MARCH5-dependent degradation of MiD49 and Mcl1 and control of mitochondrial dynamics. Cherok E, Xu S, Li S, Das S, Meltzer WA, Zalzman M, Wang C, Karbowski M. Mol Biol Cell. 2016 Dec 8. pii: mbc.E16-04-0208. PubMed |
| Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Hanzlikova H, Gittens W, Krejcikova K, Zeng Z, Caldecott KW. Nucleic Acids Res. 2016 Dec 13. pii: gkw1246. PubMed |
Simultaneous paralogue knockout using a CRISPR-concatemer in mouse small intestinal organoids.
Andersson-Rolf A, Merenda A, Mustata RC, Li T, Dietmann S, Koo BK.
Dev Biol. 2016 Oct 27. pii: S0012-1606(16)30479-1. doi: 10.1016/j.ydbio.2016.10.016.
PubMed
Associated Plasmids |
| XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Hoch NC, Hanzlikova H, Rulten SL, Tetreault M, Komulainen E, Ju L, Hornyak P, Zeng Z, Gittens W, Rey SA, Staras K, Mancini GM, McKinnon PJ, Wang ZQ, Wagner JD, Yoon G, Caldecott KW. Nature. 2017 Jan 5;541(7635):87-91. doi: 10.1038/nature20790. Epub 2016 Dec 21. PubMed |
| Inhibition of long non-coding RNA UCA1 by CRISPR/Cas9 attenuated malignant phenotypes of bladder cancer. Zhen S, Hua L, Liu YH, Sun XM, Jiang MM, Chen W, Zhao L, Li X. Oncotarget. 2017 Feb 7;8(6):9634-9646. doi: 10.18632/oncotarget.14176. PubMed |
| CRISPR/Cas9-Induced (CTGCAG)n Repeat Instability in the Myotonic Dystrophy Type 1 Locus: Implications for Therapeutic Genome Editing. van Agtmaal EL, Andre LM, Willemse M, Cumming SA, van Kessel IDG, van den Broek WJAA, Gourdon G, Furling D, Mouly V, Monckton DG, Wansink DG, Wieringa B. Mol Ther. 2017 Jan 4;25(1):24-43. doi: 10.1016/j.ymthe.2016.10.014. Epub 2017 Jan 4. PubMed |
One-step generation of conditional and reversible gene knockouts.
Andersson-Rolf A, Mustata RC, Merenda A, Kim J, Perera S, Grego T, Andrews K, Tremble K, Silva JC, Fink J, Skarnes WC, Koo BK.
Nat Methods. 2017 Jan 30. doi: 10.1038/nmeth.4156.
PubMed
Associated Plasmids |
| PRC2 is dispensable for HOTAIR-mediated transcriptional repression. Portoso M, Ragazzini R, Brencic Z, Moiani A, Michaud A, Vassilev I, Wassef M, Servant N, Sargueil B, Margueron R. EMBO J. 2017 Apr 13;36(8):981-994. doi: 10.15252/embj.201695335. Epub 2017 Feb 6. PubMed |
| ARID2 modulates DNA damage response in human hepatocellular carcinoma cells. Oba A, Shimada S, Akiyama Y, Nishikawaji T, Mogushi K, Ito H, Matsumura S, Aihara A, Mitsunori Y, Ban D, Ochiai T, Kudo A, Asahara H, Kaida A, Miura M, Tanabe M, Tanaka S. J Hepatol. 2017 May;66(5):942-951. doi: 10.1016/j.jhep.2016.12.026. Epub 2017 Feb 24. PubMed |
| Creation of mutant mice with megabase-sized deletions containing custom-designed breakpoints by means of the CRISPR/Cas9 system. Kato T, Hara S, Goto Y, Ogawa Y, Okayasu H, Kubota S, Tamano M, Terao M, Takada S. Sci Rep. 2017 Mar 3;7(1):59. doi: 10.1038/s41598-017-00140-9. PubMed |
| CREB Signaling Is Involved in Rett Syndrome Pathogenesis. Bu Q, Wang A, Hamzah H, Waldman A, Jiang K, Dong Q, Li R, Kim J, Turner D, Chang Q. J Neurosci. 2017 Mar 29;37(13):3671-3685. doi: 10.1523/JNEUROSCI.3735-16.2017. Epub 2017 Mar 7. PubMed |
| Pharmacological modulators of autophagy activate a parallel noncanonical pathway driving unconventional LC3 lipidation. Jacquin E, Leclerc-Mercier S, Judon C, Blanchard E, Fraitag S, Florey O. Autophagy. 2017 May 4;13(5):854-867. doi: 10.1080/15548627.2017.1287653. Epub 2017 Feb 15. PubMed |
Dual-utility NLS drives RNF169-dependent DNA damage responses.
An L, Jiang Y, Ng HH, Man EP, Chen J, Khoo US, Gong Q, Huen MS.
Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2872-E2881. doi: 10.1073/pnas.1616602114. Epub 2017 Mar 21.
PubMed
Associated Plasmids |
| cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent. Huang Y, Koues OI, Zhao JY, Liu R, Pyfrom SC, Payton JE, Oltz EM. Cell Rep. 2017 Mar 21;18(12):2918-2931. doi: 10.1016/j.celrep.2017.02.067. PubMed |
| Genome Editing in Human Pluripotent Stem Cells. Carlson-Stevermer J, Saha K. Methods Mol Biol. 2017;1590:165-174. doi: 10.1007/978-1-4939-6921-0_12. PubMed |
| Metformin inhibits SUV39H1-mediated migration of prostate cancer cells. Yu T, Wang C, Yang J, Guo Y, Wu Y, Li X. Oncogenesis. 2017 May 1;6(5):e324. doi: 10.1038/oncsis.2017.28. PubMed |
| Identification of physical interactions between genomic regions by enChIP-Seq. Fujita T, Yuno M, Suzuki Y, Sugano S, Fujii H. Genes Cells. 2017 Jun;22(6):506-520. doi: 10.1111/gtc.12492. Epub 2017 May 5. PubMed |
| SENP8 limits aberrant neddylation of NEDD8 pathway components to promote cullin-RING ubiquitin ligase function. Coleman KE, Bekes M, Chapman JR, Crist SB, Jones MJ, Ueberheide BM, Huang TT. Elife. 2017 May 5;6. doi: 10.7554/eLife.24325. PubMed |
| PD-L1 expression on malignant cells is no prerequisite for checkpoint therapy. Kleinovink JW, Marijt KA, Schoonderwoerd MJA, van Hall T, Ossendorp F, Fransen MF. Oncoimmunology. 2017 Feb 21;6(4):e1294299. doi: 10.1080/2162402X.2017.1294299. eCollection 2017. PubMed |
| Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. Dave K, Sur I, Yan J, Zhang J, Kaasinen E, Zhong F, Blaas L, Li X, Kharazi S, Gustafsson C, De Paepe A, Mansson R, Taipale J. Elife. 2017 Jun 6;6. pii: e23382. doi: 10.7554/eLife.23382. PubMed |
| Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line. Fujita T, Kitaura F, Yuno M, Suzuki Y, Sugano S, Fujii H. DNA Res. 2017 Jun 6. doi: 10.1093/dnares/dsx023. PubMed |
| Extensive Proliferation of Human Cancer Cells with Ever-Shorter Telomeres. Dagg RA, Pickett HA, Neumann AA, Napier CE, Henson JD, Teber ET, Arthur JW, Reynolds CP, Murray J, Haber M, Sobinoff AP, Lau LMS, Reddel RR. Cell Rep. 2017 Jun 20;19(12):2544-2556. doi: 10.1016/j.celrep.2017.05.087. PubMed |
| Genome Editing of Mouse by Cytoplasmic Injection. Horii T, Hatada I. Methods Mol Biol. 2017;1630:55-66. doi: 10.1007/978-1-4939-7128-2_5. PubMed |
| Entosis Is Induced by Glucose Starvation. Hamann JC, Surcel A, Chen R, Teragawa C, Albeck JG, Robinson DN, Overholtzer M. Cell Rep. 2017 Jul 5;20(1):201-210. doi: 10.1016/j.celrep.2017.06.037. PubMed |
Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics.
Rose JC, Stephany JJ, Valente WJ, Trevillian BM, Dang HV, Bielas JH, Maly DJ, Fowler DM.
Nat Methods. 2017 Jul 24. doi: 10.1038/nmeth.4368.
PubMed
Associated Plasmids |
| Ubiquitination of exposed glycoproteins by SCF(FBXO27) directs damaged lysosomes for autophagy. Yoshida Y, Yasuda S, Fujita T, Hamasaki M, Murakami A, Kawawaki J, Iwai K, Saeki Y, Yoshimori T, Matsuda N, Tanaka K. Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8574-8579. doi: 10.1073/pnas.1702615114. Epub 2017 Jul 25. PubMed |
| CRISPR/Cas9-Mediated Deletion of Foxn1 in NOD/SCID/IL2rg(-/-) Mice Results in Severe Immunodeficiency. Wei X, Lai Y, Li B, Qin L, Xu Y, Lin S, Wang S, Wu Q, Liang Q, Huang G, Deng Q, Liu P, Wu D, Lai L, Yao Y, Li P. Sci Rep. 2017 Aug 10;7(1):7720. doi: 10.1038/s41598-017-08337-8. PubMed |
| TH2A is phosphorylated at meiotic centromere by Haspin. Hada M, Kim J, Inoue E, Fukuda Y, Tanaka H, Watanabe Y, Okada Y. Chromosoma. 2017 Dec;126(6):769-780. doi: 10.1007/s00412-017-0638-5. Epub 2017 Aug 12. PubMed |
| Human microcephaly protein RTTN interacts with STIL and is required to build full-length centrioles. Chen HY, Wu CT, Tang CC, Lin YN, Wang WJ, Tang TK. Nat Commun. 2017 Aug 15;8(1):247. doi: 10.1038/s41467-017-00305-0. PubMed |
| CRISPR/Cas9 and piggyBac-mediated footprint-free LRRK2-G2019S knock-in reveals neuronal complexity phenotypes and alpha-Synuclein modulation in dopaminergic neurons. Qing X, Walter J, Jarazo J, Arias-Fuenzalida J, Hillje AL, Schwamborn JC. Stem Cell Res. 2017 Oct;24:44-50. doi: 10.1016/j.scr.2017.08.013. Epub 2017 Aug 18. PubMed |
| Mitochondrial fission facilitates the selective mitophagy of protein aggregates. Burman JL, Pickles S, Wang C, Sekine S, Vargas JNS, Zhang Z, Youle AM, Nezich CL, Wu X, Hammer JA, Youle RJ. J Cell Biol. 2017 Oct 2;216(10):3231-3247. doi: 10.1083/jcb.201612106. Epub 2017 Sep 11. PubMed |
| BRCA2 suppresses replication stress-induced mitotic and G1 abnormalities through homologous recombination. Feng W, Jasin M. Nat Commun. 2017 Sep 13;8(1):525. doi: 10.1038/s41467-017-00634-0. PubMed |
| CRISPR/Cas9-mediated simultaneous knockout of Dmrt1 and Dmrt3 does not recapitulate the 46,XY gonadal dysgenesis observed in 9p24.3 deletion patients. Inui M, Tamano M, Kato T, Takada S. Biochem Biophys Rep. 2017 Jan 9;9:238-244. doi: 10.1016/j.bbrep.2017.01.001. eCollection 2017 Mar. PubMed |
Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor alpha-Bound Enhancers.
Carleton JB, Berrett KC, Gertz J.
Cell Syst. 2017 Oct 25;5(4):333-344.e5. doi: 10.1016/j.cels.2017.08.011. Epub 2017 Sep 27.
PubMed
Associated Plasmids |
dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.
O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, Segal DJ.
Nucleic Acids Res. 2017 Sep 29;45(17):9901-9916. doi: 10.1093/nar/gkx578.
PubMed
Associated Plasmids |
| Multiplex CRISPR/Cas9-Based Genome Editing in Human Hematopoietic Stem Cells Models Clonal Hematopoiesis and Myeloid Neoplasia. Tothova Z, Krill-Burger JM, Popova KD, Landers CC, Sievers QL, Yudovich D, Belizaire R, Aster JC, Morgan EA, Tsherniak A, Ebert BL. Cell Stem Cell. 2017 Oct 5;21(4):547-555.e8. doi: 10.1016/j.stem.2017.07.015. PubMed |
| Methylation of transcription factor YY2 regulates its transcriptional activity and cell proliferation. Wu XN, Shi TT, He YH, Wang FF, Sang R, Ding JC, Zhang WJ, Shu XY, Shen HF, Yi J, Gao X, Liu W. Cell Discov. 2017 Oct 3;3:17035. doi: 10.1038/celldisc.2017.35. eCollection 2017. PubMed |
| Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance. Coggins NB, Stultz J, O'Geen H, Carvajal-Carmona LG, Segal DJ. Sci Rep. 2017 Nov 8;7(1):15044. doi: 10.1038/s41598-017-15407-4. PubMed |
| Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. Saunderson EA, Stepper P, Gomm JJ, Hoa L, Morgan A, Allen MD, Jones JL, Gribben JG, Jurkowski TP, Ficz G. Nat Commun. 2017 Nov 13;8(1):1450. doi: 10.1038/s41467-017-01078-2. PubMed |
| DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development. Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. Gut. 2019 Jan;68(1):49-61. doi: 10.1136/gutjnl-2017-314817. Epub 2017 Nov 15. PubMed |
| Mutations in RAB39B in individuals with intellectual disability, autism spectrum disorder, and macrocephaly. Woodbury-Smith M, Deneault E, Yuen RKC, Walker S, Zarrei M, Pellecchia G, Howe JL, Hoang N, Uddin M, Marshall CR, Chrysler C, Thompson A, Szatmari P, Scherer SW. Mol Autism. 2017 Nov 9;8:59. doi: 10.1186/s13229-017-0175-3. eCollection 2017. PubMed |
| SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells. Jagle S, Busch H, Freihen V, Beyes S, Schrempp M, Boerries M, Hecht A. PLoS Genet. 2017 Nov 20;13(11):e1007109. doi: 10.1371/journal.pgen.1007109. eCollection 2017 Nov. PubMed |
| A Universal Approach to Correct Various HBB Gene Mutations in Human Stem Cells for Gene Therapy of Beta-Thalassemia and Sickle Cell Disease. Cai L, Bai H, Mahairaki V, Gao Y, He C, Wen Y, Jin YC, Wang Y, Pan RL, Qasba A, Ye Z, Cheng L. Stem Cells Transl Med. 2018 Jan;7(1):87-97. doi: 10.1002/sctm.17-0066. Epub 2017 Nov 21. PubMed |
| Discovery of naturally occurring ESR1 mutations in breast cancer cell lines modelling endocrine resistance. Martin LA, Ribas R, Simigdala N, Schuster E, Pancholi S, Tenev T, Gellert P, Buluwela L, Harrod A, Thornhill A, Nikitorowicz-Buniak J, Bhamra A, Turgeon MO, Poulogiannis G, Gao Q, Martins V, Hills M, Garcia-Murillas I, Fribbens C, Patani N, Li Z, Sikora MJ, Turner N, Zwart W, Oesterreich S, Carroll J, Ali S, Dowsett M. Nat Commun. 2017 Nov 30;8(1):1865. doi: 10.1038/s41467-017-01864-y. PubMed |
| Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element. Zuin J, Casa V, Pozojevic J, Kolovos P, van den Hout MCGN, van Ijcken WFJ, Parenti I, Braunholz D, Baron Y, Watrin E, Kaiser FJ, Wendt KS. PLoS Genet. 2017 Dec 20;13(12):e1007137. doi: 10.1371/journal.pgen.1007137. eCollection 2017 Dec. PubMed |
| CCPG1 Is a Non-canonical Autophagy Cargo Receptor Essential for ER-Phagy and Pancreatic ER Proteostasis. Smith MD, Harley ME, Kemp AJ, Wills J, Lee M, Arends M, von Kriegsheim A, Behrends C, Wilkinson S. Dev Cell. 2018 Jan 22;44(2):217-232.e11. doi: 10.1016/j.devcel.2017.11.024. Epub 2017 Dec 28. PubMed |
| Human-Specific Adaptations in Vpu Conferring Anti-tetherin Activity Are Critical for Efficient Early HIV-1 Replication In Vivo. Yamada E, Nakaoka S, Klein L, Reith E, Langer S, Hopfensperger K, Iwami S, Schreiber G, Kirchhoff F, Koyanagi Y, Sauter D, Sato K. Cell Host Microbe. 2018 Jan 10;23(1):110-120.e7. doi: 10.1016/j.chom.2017.12.009. PubMed |
| Role of METTL20 in regulating beta-oxidation and heat production in mice under fasting or ketogenic conditions. Shimazu T, Furuse T, Balan S, Yamada I, Okuno S, Iwanari H, Suzuki T, Hamakubo T, Dohmae N, Yoshikawa T, Wakana S, Shinkai Y. Sci Rep. 2018 Jan 19;8(1):1179. doi: 10.1038/s41598-018-19615-4. PubMed |
| Ultraconserved Enhancers Are Required for Normal Development. Dickel DE, Ypsilanti AR, Pla R, Zhu Y, Barozzi I, Mannion BJ, Khin YS, Fukuda-Yuzawa Y, Plajzer-Frick I, Pickle CS, Lee EA, Harrington AN, Pham QT, Garvin TH, Kato M, Osterwalder M, Akiyama JA, Afzal V, Rubenstein JLR, Pennacchio LA, Visel A. Cell. 2018 Jan 25;172(3):491-499.e15. doi: 10.1016/j.cell.2017.12.017. Epub 2018 Jan 18. PubMed |
| Functional analysis after rapid degradation of condensins and 3D-EM reveals chromatin volume is uncoupled from chromosome architecture in mitosis. Samejima K, Booth DG, Ogawa H, Paulson JR, Xie L, Watson CA, Platani M, Kanemaki MT, Earnshaw WC. J Cell Sci. 2018 Feb 22;131(4). pii: jcs.210187. doi: 10.1242/jcs.210187. PubMed |
| Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly. Jacko M, Weyn-Vanhentenryck SM, Smerdon JW, Yan R, Feng H, Williams DJ, Pai J, Xu K, Wichterle H, Zhang C. Neuron. 2018 Feb 21;97(4):853-868.e6. doi: 10.1016/j.neuron.2018.01.020. Epub 2018 Feb 1. PubMed |
| T cells specific for a TAP-independent self-peptide remain naive in tumor-bearing mice and are fully exploitable for therapy. Doorduijn EM, Sluijter M, Marijt KA, Querido BJ, van der Burg SH, van Hall T. Oncoimmunology. 2017 Nov 20;7(3):e1382793. doi: 10.1080/2162402X.2017.1382793. eCollection 2018. PubMed |
| High Efficiency Gene Correction in Hematopoietic Cells by Donor-Template-Free CRISPR/Cas9 Genome Editing. Surun D, Schwable J, Tomasovic A, Ehling R, Stein S, Kurrle N, von Melchner H, Schnutgen F. Mol Ther Nucleic Acids. 2018 Mar 2;10:1-8. doi: 10.1016/j.omtn.2017.11.001. Epub 2017 Nov 10. PubMed |
| Editing of DNA Methylation Using dCas9-Peptide Repeat and scFv-TET1 Catalytic Domain Fusions. Morita S, Horii T, Hatada I. Methods Mol Biol. 2018;1767:419-428. doi: 10.1007/978-1-4939-7774-1_23. PubMed |
Conditional gene knockout and reconstitution in human iPSCs with an inducible Cas9 system.
Wu M, Liu S, Gao Y, Bai H, Machairaki V, Li G, Chen T, Cheng L.
Stem Cell Res. 2018 May;29:6-14. doi: 10.1016/j.scr.2018.03.003. Epub 2018 Mar 10.
PubMed
Associated Plasmids |
| Promoter-associated proteins of EPAS1 identified by enChIP-MS - A putative role of HDX as a negative regulator. Hamidian A, Vaapil M, von Stedingk K, Fujita T, Persson CU, Eriksson P, Veerla S, De Preter K, Speleman F, Fujii H, Pahlman S, Mohlin S. Biochem Biophys Res Commun. 2018 May 5;499(2):291-298. doi: 10.1016/j.bbrc.2018.03.150. Epub 2018 Mar 26. PubMed |
Unexpected binding behaviors of bacterial Argonautes in human cells cast doubts on their use as targetable gene regulators.
O'Geen H, Ren C, Coggins NB, Bates SL, Segal DJ.
PLoS One. 2018 Mar 27;13(3):e0193818. doi: 10.1371/journal.pone.0193818. eCollection 2018.
PubMed
Associated Plasmids |
| Efficient In Vivo Liver-Directed Gene Editing Using CRISPR/Cas9. Singh K, Evens H, Nair N, Rincon MY, Sarcar S, Samara-Kuko E, Chuah MK, VandenDriessche T. Mol Ther. 2018 May 2;26(5):1241-1254. doi: 10.1016/j.ymthe.2018.02.023. Epub 2018 Mar 6. PubMed |
| Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR. Grob A, Marbiah M, Isalan M. Methods Mol Biol. 2018;1766:285-301. doi: 10.1007/978-1-4939-7768-0_16. PubMed |
| Up-regulation of NOX1/NADPH oxidase following drug-induced myocardial injury promotes cardiac dysfunction and fibrosis. Iwata K, Matsuno K, Murata A, Zhu K, Fukui H, Ikuta K, Katsuyama M, Ibi M, Matsumoto M, Ohigashi M, Wen X, Zhang J, Cui W, Yabe-Nishimura C. Free Radic Biol Med. 2018 May 20;120:277-288. doi: 10.1016/j.freeradbiomed.2018.03.053. Epub 2018 Mar 31. PubMed |
| JMJD6 Licenses ERalpha-Dependent Enhancer and Coding Gene Activation by Modulating the Recruitment of the CARM1/MED12 Co-activator Complex. Gao WW, Xiao RQ, Zhang WJ, Hu YR, Peng BL, Li WJ, He YH, Shen HF, Ding JC, Huang QX, Ye TY, Li Y, Liu ZY, Ding R, Rosenfeld MG, Liu W. Mol Cell. 2018 Apr 19;70(2):340-357.e8. doi: 10.1016/j.molcel.2018.03.006. Epub 2018 Apr 5. PubMed |
| A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve. Law WD, Fogarty EA, Vester A, Antonellis A. BMC Genomics. 2018 May 2;19(1):311. doi: 10.1186/s12864-018-4692-z. PubMed |
| Detection of genome-edited cells by oligoribonucleotide interference-PCR. Fujita T, Yuno M, Kitaura F, Fujii H. DNA Res. 2018 Aug 1;25(4):395-407. doi: 10.1093/dnares/dsy012. PubMed |
| P53 and mTOR signalling determine fitness selection through cell competition during early mouse embryonic development. Bowling S, Di Gregorio A, Sancho M, Pozzi S, Aarts M, Signore M, D Schneider M, Martinez-Barbera JP, Gil J, Rodriguez TA. Nat Commun. 2018 May 2;9(1):1763. doi: 10.1038/s41467-018-04167-y. PubMed |
| Large-Scale Expansion of Human iPSC-Derived Skeletal Muscle Cells for Disease Modeling and Cell-Based Therapeutic Strategies. van der Wal E, Herrero-Hernandez P, Wan R, Broeders M, In 't Groen SLM, van Gestel TJM, van IJcken WFJ, Cheung TH, van der Ploeg AT, Schaaf GJ, Pijnappel WWMP. Stem Cell Reports. 2018 Jun 5;10(6):1975-1990. doi: 10.1016/j.stemcr.2018.04.002. Epub 2018 May 3. PubMed |
| A novel CHCHD10 mutation implicates a Mia40-dependent mitochondrial import deficit in ALS. Lehmer C, Schludi MH, Ransom L, Greiling J, Junghanel M, Exner N, Riemenschneider H, van der Zee J, Van Broeckhoven C, Weydt P, Heneka MT, Edbauer D. EMBO Mol Med. 2018 Jun;10(6). pii: emmm.201708558. doi: 10.15252/emmm.201708558. PubMed |
| Super-resolution architecture of mammalian centriole distal appendages reveals distinct blade and matrix functional components. Yang TT, Chong WM, Wang WJ, Mazo G, Tanos B, Chen Z, Tran TMN, Chen YD, Weng RR, Huang CE, Jane WN, Tsou MB, Liao JC. Nat Commun. 2018 May 22;9(1):2023. doi: 10.1038/s41467-018-04469-1. PubMed |
| Generation of Rat Monoclonal Antibodies Specific for DZIP3. Oikawa D, Shiota M, Tokunaga F, Wanibuchi H. Monoclon Antib Immunodiagn Immunother. 2018 Jun;37(3):153-157. doi: 10.1089/mab.2018.0005. Epub 2018 May 29. PubMed |
| Heterozygous IDH1(R132H/WT) created by "single base editing" inhibits human astroglial cell growth by downregulating YAP. Wei S, Wang J, Oyinlade O, Ma D, Wang S, Kratz L, Lal B, Xu Q, Liu S, Shah SR, Zhang H, Li Y, Quinones-Hinojosa A, Zhu H, Huang ZY, Cheng L, Qian J, Xia S. Oncogene. 2018 Sep;37(38):5160-5174. doi: 10.1038/s41388-018-0334-9. Epub 2018 May 30. PubMed |
| Naturally Occurring Variants in LRP1 (Low-Density Lipoprotein Receptor-Related Protein 1) Affect HDL (High-Density Lipoprotein) Metabolism Through ABCA1 (ATP-Binding Cassette A1) and SR-B1 (Scavenger Receptor Class B Type 1) in Humans. Oldoni F, van Capelleveen JC, Dalila N, Wolters JC, Heeren J, Sinke RJ, Hui DY, Dallinga-Thie GM, Frikke-Schmidt R, Hovingh KG, van de Sluis B, Tybjaerg-Hansen A, Kuivenhoven JA. Arterioscler Thromb Vasc Biol. 2018 Jul;38(7):1440-1453. doi: 10.1161/ATVBAHA.117.310309. Epub 2018 May 31. PubMed |
| Super-Resolution Imaging Reveals TCTN2 Depletion-Induced IFT88 Lumen Leakage and Ciliary Weakening. Weng RR, Yang TT, Huang CE, Chang CW, Wang WJ, Liao JC. Biophys J. 2018 Jul 17;115(2):263-275. doi: 10.1016/j.bpj.2018.04.051. Epub 2018 Jun 1. PubMed |
Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency.
Adachi K, Kopp W, Wu G, Heising S, Greber B, Stehling M, Arauzo-Bravo MJ, Boerno ST, Timmermann B, Vingron M, Scholer HR.
Cell Stem Cell. 2018 Aug 2;23(2):266-275.e6. doi: 10.1016/j.stem.2018.05.020. Epub 2018 Jun 14.
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| Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines. Carleton JB, Berrett KC, Gertz J. J Vis Exp. 2018 Jun 2;(136). doi: 10.3791/57883. PubMed |
| Straightforward Delivery of Linearized Double-Stranded DNA Encoding sgRNA and Donor DNA for the Generation of Single Nucleotide Variants Based on the CRISPR/Cas9 System. Jun S, Lim H, Jang H, Lee W, Ahn J, Lee JH, Bang D. ACS Synth Biol. 2018 Jul 20;7(7):1651-1659. doi: 10.1021/acssynbio.7b00345. Epub 2018 Jul 2. PubMed |
| A tandem repeat array in IG-DMR is essential for imprinting of paternal allele at the Dlk1-Dio3 domain during embryonic development. Saito T, Hara S, Kato T, Tamano M, Muramatsu A, Asahara H, Takada S. Hum Mol Genet. 2018 Sep 15;27(18):3283-3292. doi: 10.1093/hmg/ddy235. PubMed |
| The E3 ubiquitin ligase SMURF1 regulates cell-fate specification and outflow tract septation during mammalian heart development. Koefoed K, Skat-Rordam J, Andersen P, Warzecha CB, Pye M, Andersen TA, Ajbro KD, Bendsen E, Narimatsu M, Vilhardt F, Pedersen LB, Wrana JL, Anderson RH, Mollgard K, Christensen ST, Larsen LA. Sci Rep. 2018 Jun 22;8(1):9542. doi: 10.1038/s41598-018-27854-8. PubMed |
| Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk. Dudek AM, Vermeulen SH, Kolev D, Grotenhuis AJ, Kiemeney LALM, Verhaegh GW. Cell Oncol (Dordr). 2018 Oct;41(5):555-568. doi: 10.1007/s13402-018-0393-5. Epub 2018 Jun 28. PubMed |
| Optimized Plasmid Construction Strategy for Cas9. Xu J, Li W, Hossen MM, Jia Y, Li L, Huang Z. Cell Physiol Biochem. 2018;48(1):131-137. doi: 10.1159/000491669. Epub 2018 Jul 12. PubMed |
| Species-independent contribution of ZBP1/DAI/DLM-1-triggered necroptosis in host defense against HSV1. Guo H, Gilley RP, Fisher A, Lane R, Landsteiner VJ, Ragan KB, Dovey CM, Carette JE, Upton JW, Mocarski ES, Kaiser WJ. Cell Death Dis. 2018 Jul 26;9(8):816. doi: 10.1038/s41419-018-0868-3. PubMed |
| Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways. Olson HC, Davis L, Kiianitsa K, Khoo KJ, Liu Y, Knijnenburg TA, Maizels N. Nucleic Acids Res. 2018 Oct 12;46(18):9496-9509. doi: 10.1093/nar/gky727. PubMed |
| Confirming TDP2 mutation in spinocerebellar ataxia autosomal recessive 23 (SCAR23). Zagnoli-Vieira G, Bruni F, Thompson K, He L, Walker S, de Brouwer APM, Taylor R, Niyazov D, Caldecott KW. Neurol Genet. 2018 Aug 1;4(4):e262. doi: 10.1212/NXG.0000000000000262. eCollection 2018 Aug. PubMed |
| PPP1R35 ensures centriole homeostasis by promoting centriole-to-centrosome conversion. Fong CS, Ozaki K, Tsou MB. Mol Biol Cell. 2018 Nov 15;29(23):2801-2808. doi: 10.1091/mbc.E18-08-0525. Epub 2018 Sep 19. PubMed |
NONO Detects the Nuclear HIV Capsid to Promote cGAS-Mediated Innate Immune Activation.
Lahaye X, Gentili M, Silvin A, Conrad C, Picard L, Jouve M, Zueva E, Maurin M, Nadalin F, Knott GJ, Zhao B, Du F, Rio M, Amiel J, Fox AH, Li P, Etienne L, Bond CS, Colleaux L, Manel N.
Cell. 2018 Oct 4;175(2):488-501.e22. doi: 10.1016/j.cell.2018.08.062. Epub 2018 Sep 27.
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| Highly Efficient CRISPR-Cas9-Mediated Genome Editing in Human Pluripotent Stem Cells. Maguire JA, Cardenas-Diaz FL, Gadue P, French DL. Curr Protoc Stem Cell Biol. 2019 Feb;48(1):e64. doi: 10.1002/cpsc.64. Epub 2018 Oct 24. PubMed |
| Protocadherin-1 is essential for cell entry by New World hantaviruses. Jangra RK, Herbert AS, Li R, Jae LT, Kleinfelter LM, Slough MM, Barker SL, Guardado-Calvo P, Roman-Sosa G, Dieterle ME, Kuehne AI, Muena NA, Wirchnianski AS, Nyakatura EK, Fels JM, Ng M, Mittler E, Pan J, Bharrhan S, Wec AZ, Lai JR, Sidhu SS, Tischler ND, Rey FA, Moffat J, Brummelkamp TR, Wang Z, Dye JM, Chandran K. Nature. 2018 Nov;563(7732):559-563. doi: 10.1038/s41586-018-0702-1. Epub 2018 Nov 21. PubMed |
| NKG2A Blockade Potentiates CD8 T Cell Immunity Induced by Cancer Vaccines. van Montfoort N, Borst L, Korrer MJ, Sluijter M, Marijt KA, Santegoets SJ, van Ham VJ, Ehsan I, Charoentong P, Andre P, Wagtmann N, Welters MJP, Kim YJ, Piersma SJ, van der Burg SH, van Hall T. Cell. 2018 Dec 13;175(7):1744-1755.e15. doi: 10.1016/j.cell.2018.10.028. Epub 2018 Nov 29. PubMed |
| Mapping of a responsible region for sex reversal upstream of Sox9 by production of mice with serial deletion in a genomic locus. Ogawa Y, Terao M, Hara S, Tamano M, Okayasu H, Kato T, Takada S. Sci Rep. 2018 Nov 30;8(1):17514. doi: 10.1038/s41598-018-35746-0. PubMed |
| Exocyst dynamics during vesicle tethering and fusion. Ahmed SM, Nishida-Fukuda H, Li Y, McDonald WH, Gradinaru CC, Macara IG. Nat Commun. 2018 Dec 3;9(1):5140. doi: 10.1038/s41467-018-07467-5. PubMed |
| Interleukin 34 (IL-34) cell-surface localization regulated by the molecular chaperone 78-kDa glucose-regulated protein facilitates the differentiation of monocytic cells. Ogawa S, Matsuoka Y, Takada M, Matsui K, Yamane F, Kubota E, Yasuhara S, Hieda K, Kanayama N, Hatano N, Tokumitsu H, Magari M. J Biol Chem. 2019 Feb 15;294(7):2386-2396. doi: 10.1074/jbc.RA118.006226. Epub 2018 Dec 20. PubMed |
| Upf1 regulates neurite outgrowth and branching by transcriptional and post-transcriptional modulation of Arc. Ryu HG, Seo JY, Jung Y, Kim SW, Kim E, Jang SK, Kim KT. J Cell Sci. 2019 Jan 18;132(2). pii: jcs.224055. doi: 10.1242/jcs.224055. PubMed |
| Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3. Villegas F, Lehalle D, Mayer D, Rittirsch M, Stadler MB, Zinner M, Olivieri D, Vabres P, Duplomb-Jego L, De Bont ESJM, Duffourd Y, Duijkers F, Avila M, Genevieve D, Houcinat N, Jouan T, Kuentz P, Lichtenbelt KD, Thauvin-Robinet C, St-Onge J, Thevenon J, van Gassen KLI, van Haelst M, van Koningsbruggen S, Hess D, Smallwood SA, Riviere JB, Faivre L, Betschinger J. Cell Stem Cell. 2019 Feb 7;24(2):257-270.e8. doi: 10.1016/j.stem.2018.11.021. Epub 2018 Dec 27. PubMed |
| NOX1/NADPH oxidase regulates the expression of multidrug resistance-associated protein 1 and maintains intracellular glutathione levels. Wen X, Iwata K, Ikuta K, Zhang X, Zhu K, Ibi M, Matsumoto M, Asaoka N, Liu J, Katsuyama M, Yabe-Nishimura C. FEBS J. 2019 Feb;286(4):678-687. doi: 10.1111/febs.14753. Epub 2019 Feb 6. PubMed |
| FOXO3-Engineered Human ESC-Derived Vascular Cells Promote Vascular Protection and Regeneration. Yan P, Li Q, Wang L, Lu P, Suzuki K, Liu Z, Lei J, Li W, He X, Wang S, Ding J, Chan P, Zhang W, Song M, Izpisua Belmonte JC, Qu J, Tang F, Liu GH. Cell Stem Cell. 2019 Mar 7;24(3):447-461.e8. doi: 10.1016/j.stem.2018.12.002. Epub 2019 Jan 17. PubMed |
| Design and Assembly of CRISPR/Cas9 Lentiviral and rAAV Vectors for Targeted Genome Editing. Sandoval IM, Collier TJ, Manfredsson FP. Methods Mol Biol. 2019;1937:29-45. doi: 10.1007/978-1-4939-9065-8_2. PubMed |
| Telomere-dependent and telomere-independent roles of RAP1 in regulating human stem cell homeostasis. Zhang X, Liu Z, Liu X, Wang S, Zhang Y, He X, Sun S, Ma S, Shyh-Chang N, Liu F, Wang Q, Wang X, Liu L, Zhang W, Song M, Liu GH, Qu J. Protein Cell. 2019 Feb 22. pii: 10.1007/s13238-019-0610-7. doi: 10.1007/s13238-019-0610-7. PubMed |
| Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements. Hwang B, Lee W, Yum SY, Jeon Y, Cho N, Jang G, Bang D. Nat Commun. 2019 Mar 15;10(1):1234. doi: 10.1038/s41467-019-09203-z. PubMed |
| A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation. Saadi W, Kermezli Y, Dao LTM, Mathieu E, Santiago-Algarra D, Manosalva I, Torres M, Belhocine M, Pradel L, Loriod B, Aribi M, Puthier D, Spicuglia S. Sci Rep. 2019 Mar 18;9(1):4707. doi: 10.1038/s41598-019-41247-5. PubMed |
| TMEPAI/PMEPA1 inhibits Wnt signaling by regulating beta-catenin stability and nuclear accumulation in triple negative breast cancer cells. Amalia R, Abdelaziz M, Puteri MU, Hwang J, Anwar F, Watanabe Y, Kato M. Cell Signal. 2019 Jul;59:24-33. doi: 10.1016/j.cellsig.2019.03.016. Epub 2019 Mar 16. PubMed |
| SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons. Zaslavsky K, Zhang WB, McCready FP, Rodrigues DC, Deneault E, Loo C, Zhao M, Ross PJ, El Hajjar J, Romm A, Thompson T, Piekna A, Wei W, Wang Z, Khattak S, Mufteev M, Pasceri P, Scherer SW, Salter MW, Ellis J. Nat Neurosci. 2019 Apr;22(4):556-564. doi: 10.1038/s41593-019-0365-8. Epub 2019 Mar 25. PubMed |
| Maintenance of Nucleolar Homeostasis by CBX4 Alleviates Senescence and Osteoarthritis. Ren X, Hu B, Song M, Ding Z, Dang Y, Liu Z, Zhang W, Ji Q, Ren R, Ding J, Chan P, Jiang C, Ye K, Qu J, Tang F, Liu GH. Cell Rep. 2019 Mar 26;26(13):3643-3656.e7. doi: 10.1016/j.celrep.2019.02.088. PubMed |
| Up-regulation of FOXD1 by YAP alleviates senescence and osteoarthritis. Fu L, Hu Y, Song M, Liu Z, Zhang W, Yu FX, Wu J, Wang S, Izpisua Belmonte JC, Chan P, Qu J, Tang F, Liu GH. PLoS Biol. 2019 Apr 1;17(4):e3000201. doi: 10.1371/journal.pbio.3000201. eCollection 2019 Apr. PubMed |
PCNA-Mediated Degradation of p21 Coordinates the DNA Damage Response and Cell Cycle Regulation in Individual Cells.
Sheng C, Mendler IH, Rieke S, Snyder P, Jentsch M, Friedrich D, Drossel B, Loewer A.
Cell Rep. 2019 Apr 2;27(1):48-58.e7. doi: 10.1016/j.celrep.2019.03.031.
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| DNA Damage Signaling-Induced Cancer Cell Reprogramming as a Driver of Tumor Relapse. Filipponi D, Emelyanov A, Muller J, Molina C, Nichols J, Bulavin DV. Mol Cell. 2019 May 16;74(4):651-663.e8. doi: 10.1016/j.molcel.2019.03.002. Epub 2019 Apr 3. PubMed |
| Crumbs3 is a critical factor that regulates invasion and metastasis of colon adenocarcinoma via the specific interaction with FGFR1. Iioka H, Saito K, Sakaguchi M, Tachibana T, Homma K, Kondo E. Int J Cancer. 2019 Apr 13. doi: 10.1002/ijc.32336. PubMed |
| CEP120 interacts with C2CD3 and Talpid3 and is required for centriole appendage assembly and ciliogenesis. Tsai JJ, Hsu WB, Liu JH, Chang CW, Tang TK. Sci Rep. 2019 Apr 15;9(1):6037. doi: 10.1038/s41598-019-42577-0. PubMed |
Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.
O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ.
Epigenetics Chromatin. 2019 May 3;12(1):26. doi: 10.1186/s13072-019-0275-8.
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| Indirect activation of constitutive androstane receptor in three-dimensionally cultured HepG2 cells. Yokobori K, Azuma I, Chiba K, Akita H, Furihata T, Kobayashi K. Biochem Pharmacol. 2019 Jun 13;168:26-37. doi: 10.1016/j.bcp.2019.06.011. PubMed |
| Noncoding deletions reveal a gene that is critical for intestinal function. Oz-Levi D, Olender T, Bar-Joseph I, Zhu Y, Marek-Yagel D, Barozzi I, Osterwalder M, Alkelai A, Ruzzo EK, Han Y, Vos ESM, Reznik-Wolf H, Hartman C, Shamir R, Weiss B, Shapiro R, Pode-Shakked B, Tatarskyy P, Milgrom R, Schvimer M, Barshack I, Imai DM, Coleman-Derr D, Dickel DE, Nord AS, Afzal V, van Bueren KL, Barnes RM, Black BL, Mayhew CN, Kuhar MF, Pitstick A, Tekman M, Stanescu HC, Wells JM, Kleta R, de Laat W, Goldstein DB, Pras E, Visel A, Lancet D, Anikster Y, Pennacchio LA. Nature. 2019 Jul;571(7763):107-111. doi: 10.1038/s41586-019-1312-2. Epub 2019 Jun 19. PubMed |
KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control.
Dhaliwal NK, Abatti LE, Mitchell JA.
Genes Dev. 2019 Jun 20. pii: gad.324319.119. doi: 10.1101/gad.324319.119.
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| HSF2BP Interacts with a Conserved Domain of BRCA2 and Is Required for Mouse Spermatogenesis. Brandsma I, Sato K, van Rossum-Fikkert SE, van Vliet N, Sleddens E, Reuter M, Odijk H, van den Tempel N, Dekkers DHW, Bezstarosti K, Demmers JAA, Maas A, Lebbink J, Wyman C, Essers J, van Gent DC, Baarends WM, Knipscheer P, Kanaar R, Zelensky AN. Cell Rep. 2019 Jun 25;27(13):3790-3798.e7. doi: 10.1016/j.celrep.2019.05.096. PubMed |
| Adhesion G-protein coupled receptor 56 is required for 3T3-L1 adipogenesis. Al Hasan M, Roy P, Dolan S, Martin PE, Patterson S, Bartholomew C. J Cell Physiol. 2020 Feb;235(2):1601-1614. doi: 10.1002/jcp.29079. Epub 2019 Jul 15. PubMed |
| Stabilizing heterochromatin by DGCR8 alleviates senescence and osteoarthritis. Deng L, Ren R, Liu Z, Song M, Li J, Wu Z, Ren X, Fu L, Li W, Zhang W, Guillen P, Izpisua Belmonte JC, Chan P, Qu J, Liu GH. Nat Commun. 2019 Jul 26;10(1):3329. doi: 10.1038/s41467-019-10831-8. PubMed |
| Modeling Monogenic Diabetes using Human ESCs Reveals Developmental and Metabolic Deficiencies Caused by Mutations in HNF1A. Cardenas-Diaz FL, Osorio-Quintero C, Diaz-Miranda MA, Kishore S, Leavens K, Jobaliya C, Stanescu D, Ortiz-Gonzalez X, Yoon C, Chen CS, Haliyur R, Brissova M, Powers AC, French DL, Gadue P. Cell Stem Cell. 2019 Aug 1;25(2):273-289.e5. doi: 10.1016/j.stem.2019.07.007. PubMed |
| Genome-wide mapping of DNA-binding sites identifies stemness-related genes as directly repressed targets of SNAIL1 in colorectal cancer cells. Beyes S, Andrieux G, Schrempp M, Aicher D, Wenzel J, Anton-Garcia P, Boerries M, Hecht A. Oncogene. 2019 Oct;38(40):6647-6661. doi: 10.1038/s41388-019-0905-4. Epub 2019 Aug 7. PubMed |
| Precise in vivo genome editing via single homology arm donor mediated intron-targeting gene integration for genetic disease correction. Suzuki K, Yamamoto M, Hernandez-Benitez R, Li Z, Wei C, Soligalla RD, Aizawa E, Hatanaka F, Kurita M, Reddy P, Ocampo A, Hishida T, Sakurai M, Nemeth AN, Nunez Delicado E, Campistol JM, Magistretti P, Guillen P, Rodriguez Esteban C, Gong J, Yuan Y, Gu Y, Liu GH, Lopez-Otin C, Wu J, Zhang K, Izpisua Belmonte JC. Cell Res. 2019 Oct;29(10):804-819. doi: 10.1038/s41422-019-0213-0. Epub 2019 Aug 23. PubMed |
| Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders. Wang X, Ye F, Wen Z, Guo Z, Yu C, Huang WK, Rojas Ringeling F, Su Y, Zheng W, Zhou G, Christian KM, Song H, Zhang M, Ming GL. Mol Psychiatry. 2019 Aug 23. pii: 10.1038/s41380-019-0485-2. doi: 10.1038/s41380-019-0485-2. PubMed |
Targeting of early endosomes by autophagy facilitates EGFR recycling and signalling.
Fraser J, Simpson J, Fontana R, Kishi-Itakura C, Ktistakis NT, Gammoh N.
EMBO Rep. 2019 Oct 4;20(10):e47734. doi: 10.15252/embr.201947734. Epub 2019 Aug 26.
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| Phosphorylation of CEP83 by TTBK2 is necessary for cilia initiation. Lo CH, Lin IH, Yang TT, Huang YC, Tanos BE, Chou PC, Chang CW, Tsay YG, Liao JC, Wang WJ. J Cell Biol. 2019 Oct 7;218(10):3489-3505. doi: 10.1083/jcb.201811142. Epub 2019 Aug 27. PubMed |
| SNAIL1 employs beta-Catenin-LEF1 complexes to control colorectal cancer cell invasion and proliferation. Freihen V, Ronsch K, Mastroianni J, Frey P, Rose K, Boerries M, Zeiser R, Busch H, Hecht A. Int J Cancer. 2020 Apr 15;146(8):2229-2242. doi: 10.1002/ijc.32644. Epub 2019 Sep 18. PubMed |
Multi-input chemical control of protein dimerization for programming graded cellular responses.
Foight GW, Wang Z, Wei CT, Jr Greisen P, Warner KM, Cunningham-Bryant D, Park K, Brunette TJ, Sheffler W, Baker D, Maly DJ.
Nat Biotechnol. 2019 Sep 9. pii: 10.1038/s41587-019-0242-8. doi: 10.1038/s41587-019-0242-8.
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| In vivo epigenetic editing of Sema6a promoter reverses transcallosal dysconnectivity caused by C11orf46/Arl14ep risk gene. Peter CJ, Saito A, Hasegawa Y, Tanaka Y, Nagpal M, Perez G, Alway E, Espeso-Gil S, Fayyad T, Ratner C, Dincer A, Gupta A, Devi L, Pappas JG, Lalonde FM, Butman JA, Han JC, Akbarian S, Kamiya A. Nat Commun. 2019 Sep 11;10(1):4112. doi: 10.1038/s41467-019-12013-y. PubMed |
| Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A. Vazquez C, Tan CY, Horner SM. J Virol. 2019 Nov 13;93(23). pii: JVI.00725-19. doi: 10.1128/JVI.00725-19. Print 2019 Dec 1. PubMed |
| Deletion of a Seminal Gene Cluster Reinforces a Crucial Role of SVS2 in Male Fertility. Shindo M, Inui M, Kang W, Tamano M, Tingwei C, Takada S, Hibino T, Yoshida M, Yoshida K, Okada H, Iwamoto T, Miyado K, Kawano N. Int J Mol Sci. 2019 Sep 14;20(18). pii: ijms20184557. doi: 10.3390/ijms20184557. PubMed |
| Coordinated removal of repressive epigenetic modifications during induced reversal of cell identity. Tran KA, Dillingham CM, Sridharan R. EMBO J. 2019 Nov 15;38(22):e101681. doi: 10.15252/embj.2019101681. Epub 2019 Oct 4. PubMed |
| Nuclear localization of Desmoplakin and its involvement in telomere maintenance. Li P, Meng Y, Wang Y, Li J, Lam M, Wang L, Di LJ. Int J Biol Sci. 2019 Aug 24;15(11):2350-2362. doi: 10.7150/ijbs.34450. eCollection 2019. PubMed |
| Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells. Cardenas-Diaz FL, Maguire JA, Gadue P, French DL. J Vis Exp. 2019 Sep 25;(151). doi: 10.3791/60085. PubMed |
| PODXL1 promotes metastasis of the pancreatic ductal adenocarcinoma by activating the C5aR/C5a axis from the tumor microenvironment. Saito K, Iioka H, Maruyama S, Sumardika IW, Sakaguchi M, Kondo E. Neoplasia. 2019 Dec;21(12):1121-1132. doi: 10.1016/j.neo.2019.09.003. Epub 2019 Nov 20. PubMed |
| Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2. Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J. EMBO J. 2020 Jan 15;39(2):e102591. doi: 10.15252/embj.2019102591. Epub 2019 Nov 29. PubMed |
Precise and broad scope genome editing based on high-specificity Cas9 nickases.
Wang Q, Liu J, Janssen JM, Le Bouteiller M, Frock RL, Goncalves MAFV.
Nucleic Acids Res. 2021 Jan 25;49(2):1173-1198. doi: 10.1093/nar/gkaa1236.
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| Antibody Therapy Targeting RAN Proteins Rescues C9 ALS/FTD Phenotypes in C9orf72 Mouse Model. Nguyen L, Montrasio F, Pattamatta A, Tusi SK, Bardhi O, Meyer KD, Hayes L, Nakamura K, Banez-Coronel M, Coyne A, Guo S, Laboissonniere LA, Gu Y, Narayanan S, Smith B, Nitsch RM, Kankel MW, Rushe M, Rothstein J, Zu T, Grimm J, Ranum LPW. Neuron. 2019 Dec 4. pii: S0896-6273(19)30970-5. doi: 10.1016/j.neuron.2019.11.007. PubMed |
| Efficient production and transmission of CRISPR/Cas9-mediated mutant alleles at the IG-DMR via generation of mosaic mice using a modified 2CC method. Hara S, Terao M, Muramatsu A, Takada S. Sci Rep. 2019 Dec 27;9(1):20202. doi: 10.1038/s41598-019-56676-5. PubMed |
| Integrating gene delivery and gene-editing technologies by adenoviral vector transfer of optimized CRISPR-Cas9 components. Maggio I, Zittersteijn HA, Wang Q, Liu J, Janssen JM, Ojeda IT, van der Maarel SM, Lankester AC, Hoeben RC, Goncalves MAFV. Gene Ther. 2020 May;27(5):209-225. doi: 10.1038/s41434-019-0119-y. Epub 2020 Jan 3. PubMed |
Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects.
Hofacker D, Broche J, Laistner L, Adam S, Bashtrykov P, Jeltsch A.
Int J Mol Sci. 2020 Jan 13;21(2). pii: ijms21020502. doi: 10.3390/ijms21020502.
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| Degradation of the Tumor Suppressor PDCD4 Is Impaired by the Suppression of p62/SQSTM1 and Autophagy. Manirujjaman M, Ozaki I, Murata Y, Guo J, Xia J, Nishioka K, Perveen R, Takahashi H, Anzai K, Matsuhashi S. Cells. 2020 Jan 15;9(1). pii: cells9010218. doi: 10.3390/cells9010218. PubMed |
| TUG1 Is a Regulator of AFP and Serves as Prognostic Marker in Non-Hepatitis B Non-Hepatitis C Hepatocellular Carcinoma. Lin YH, Wu MH, Huang YH, Yeh CT, Lin KH. Cells. 2020 Jan 21;9(2). pii: cells9020262. doi: 10.3390/cells9020262. PubMed |
| Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation. Holmes AC, Zagnoli-Vieira G, Caldecott KW, Semler BL. Viruses. 2020 Jan 31;12(2). pii: v12020166. doi: 10.3390/v12020166. PubMed |
| Temporal and rheostatic control of genome editing with a chemically-inducible Cas9. Wei CT, Maly DJ, Fowler DM. Methods Enzymol. 2020;633:119-141. doi: 10.1016/bs.mie.2019.11.001. Epub 2019 Nov 22. PubMed |
| TGF-beta-Induced TMEPAI Attenuates the Response of Triple-Negative Breast Cancer Cells to Doxorubicin and Paclitaxel. Wardhani BW, Puteri MU, Watanabe Y, Louisa M, Setiabudy R, Kato M. J Exp Pharmacol. 2020 Jan 23;12:17-26. doi: 10.2147/JEP.S235233. eCollection 2020. PubMed |
| PMEPA1/TMEPAI isoforms function via its PY and Smad-interaction motifs for tumorigenic activities of breast cancer cells. Puteri MU, Watanabe Y, Wardhani BWK, Amalia R, Abdelaziz M, Kato M. Genes Cells. 2020 Jun;25(6):375-390. doi: 10.1111/gtc.12766. Epub 2020 Apr 29. PubMed |
FGF6 and FGF9 regulate UCP1 expression independent of brown adipogenesis.
Shamsi F, Xue R, Huang TL, Lundh M, Liu Y, Leiria LO, Lynes MD, Kempf E, Wang CH, Sugimoto S, Nigro P, Landgraf K, Schulz T, Li Y, Emanuelli B, Kothakota S, Williams LT, Jessen N, Pedersen SB, Bottcher Y, Bluher M, Korner A, Goodyear LJ, Mohammadi M, Kahn CR, Tseng YH.
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| Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome. Horii T, Morita S, Hino S, Kimura M, Hino Y, Kogo H, Nakao M, Hatada I. Genome Biol. 2020 Apr 1;21(1):77. doi: 10.1186/s13059-020-01991-8. PubMed |
| Super-resolution microscopy reveals coupling between mammalian centriole subdistal appendages and distal appendages. Chong WM, Wang WJ, Lo CH, Chiu TY, Chang TJ, Liu YP, Tanos B, Mazo G, Tsou MB, Jane WN, Yang TT, Liao JC. Elife. 2020 Apr 3;9. pii: 53580. doi: 10.7554/eLife.53580. PubMed |
| A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. Xi H, Langerman J, Sabri S, Chien P, Young CS, Younesi S, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K, Pyle AD. Cell Stem Cell. 2020 Jul 2;27(1):158-176.e10. doi: 10.1016/j.stem.2020.04.017. Epub 2020 May 11. PubMed |
| Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene. Alomairi J, Molitor AM, Sadouni N, Hussain S, Torres M, Saadi W, Dao LTM, Charbonnier G, Santiago-Algarra D, Andrau JC, Puthier D, Sexton T, Spicuglia S. PLoS One. 2020 May 26;15(5):e0233191. doi: 10.1371/journal.pone.0233191. eCollection 2020. PubMed |
| Suppression of unwanted CRISPR-Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs. Rose JC, Popp NA, Richardson CD, Stephany JJ, Mathieu J, Wei CT, Corn JE, Maly DJ, Fowler DM. Nat Commun. 2020 Jun 1;11(1):2697. doi: 10.1038/s41467-020-16542-9. PubMed |
| Transcriptional consequences of MBD5 disruption in mouse brain and CRISPR-derived neurons. Seabra CM, Aneichyk T, Erdin S, Tai DJC, De Esch CEF, Razaz P, An Y, Manavalan P, Ragavendran A, Stortchevoi A, Abad C, Young JI, Maciel P, Talkowski ME, Gusella JF. Mol Autism. 2020 Jun 5;11(1):45. doi: 10.1186/s13229-020-00354-1. PubMed |
| A caveolin binding motif in Na/K-ATPase is required for stem cell differentiation and organogenesis in mammals and C. elegans. Wang X, Cai L, Xie JX, Cui X, Zhang J, Wang J, Chen Y, Larre I, Shapiro JI, Pierre SV, Wu D, Zhu GZ, Xie Z. Sci Adv. 2020 May 27;6(22):eaaw5851. doi: 10.1126/sciadv.aaw5851. eCollection 2020 May. PubMed |
| Standardized Reporter Systems for Purification and Imaging of Human Pluripotent Stem Cell-derived Motor Neurons and Other Cholinergic Cells. Garcia-Diaz A, Efe G, Kabra K, Patel A, Lowry ER, Shneider NA, Corneo B, Wichterle H. Neuroscience. 2020 Jun 30. pii: S0306-4522(20)30404-8. doi: 10.1016/j.neuroscience.2020.06.028. PubMed |
| Analysis of CRISPR/Cas9 Guide RNA Efficiency and Specificity Against Genetically Diverse HIV-1 Isolates. Sessions KJ, Chen YY, Hodge CA, Hudson TR, Eszterhas SK, Hayden MS, Howell AL. AIDS Res Hum Retroviruses. 2020 Aug 26. doi: 10.1089/AID.2020.0055. PubMed |
| Profiling APOL1 Nephropathy Risk Variants in Genome-Edited Kidney Organoids with Single-Cell Transcriptomics. Liu E, Radmanesh B, Chung BH, Donnan MD, Yi D, Dadi A, Smith KD, Himmelfarb J, Li M, Freedman BS, Lin J. Kidney360. 2020 Mar;1(3):203-215. doi: 10.34067/kid.0000422019. PubMed |
| Tumors induce de novo steroid biosynthesis in T cells to evade immunity. Mahata B, Pramanik J, van der Weyden L, Polanski K, Kar G, Riedel A, Chen X, Fonseca NA, Kundu K, Campos LS, Ryder E, Duddy G, Walczak I, Okkenhaug K, Adams DJ, Shields JD, Teichmann SA. Nat Commun. 2020 Jul 17;11(1):3588. doi: 10.1038/s41467-020-17339-6. PubMed |
| APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis. Maciejowski J, Chatzipli A, Dananberg A, Chu K, Toufektchan E, Klimczak LJ, Gordenin DA, Campbell PJ, de Lange T. Nat Genet. 2020 Sep;52(9):884-890. doi: 10.1038/s41588-020-0667-5. Epub 2020 Jul 27. PubMed |
| Stabilization of heterochromatin by CLOCK promotes stem cell rejuvenation and cartilage regeneration. Liang C, Liu Z, Song M, Li W, Wu Z, Wang Z, Wang Q, Wang S, Yan K, Sun L, Hishida T, Cai Y, Belmonte JCI, Guillen P, Chan P, Zhou Q, Zhang W, Qu J, Liu GH. Cell Res. 2021 Feb;31(2):187-205. doi: 10.1038/s41422-020-0385-7. Epub 2020 Jul 31. PubMed |
| Lamin A-mediated nuclear lamina integrity is required for proper ciliogenesis. Fan JR, You LR, Wang WJ, Huang WS, Chu CT, Chi YH, Chen HC. EMBO Rep. 2020 Oct 5;21(10):e49680. doi: 10.15252/embr.201949680. Epub 2020 Aug 19. PubMed |
| Interhomolog Homologous Recombination in Mouse Embryonic Stem Cells. Vanoli F, Prakash R, White T, Jasin M. Methods Mol Biol. 2021;2153:127-143. doi: 10.1007/978-1-0716-0644-5_10. PubMed |
| Identification of Differentially Methylated Regions Associated with a Knockout of SUV39H1 in Prostate Cancer Cells. Yan W, Guo Y, Xu F, Saxena D, Li X. Genes (Basel). 2020 Oct 13;11(10). pii: genes11101188. doi: 10.3390/genes11101188. PubMed |
| A cell cycle-dependent CRISPR-Cas9 activation system based on an anti-CRISPR protein shows improved genome editing accuracy. Matsumoto D, Tamamura H, Nomura W. Commun Biol. 2020 Oct 23;3(1):601. doi: 10.1038/s42003-020-01340-2. PubMed |
| Cellular and Mathematical Analyses of LUBAC Involvement in T Cell Receptor-Mediated NF-kappaB Activation Pathway. Oikawa D, Hatanaka N, Suzuki T, Tokunaga F. Front Immunol. 2020 Nov 23;11:601926. doi: 10.3389/fimmu.2020.601926. eCollection 2020. PubMed |
| Effects of activation of the LINE-1 antisense promoter on the growth of cultured cells. Honda T, Nishikawa Y, Nishimura K, Teng D, Takemoto K, Ueda K. Sci Rep. 2020 Dec 17;10(1):22136. doi: 10.1038/s41598-020-79197-y. PubMed |
| CRISPR/Cas9-mediated generation and analysis of N terminus polymorphic models of beta2AR in isogenic hPSC-derived cardiomyocytes. Kondrashov A, Mohd Yusof NAN, Hasan A, Goulding J, Kodagoda T, Hoang DM, Vo NTN, Melarangi T, Dolatshad N, Gorelik J, Hill SJ, Harding SE, Denning C. Mol Ther Methods Clin Dev. 2020 Oct 27;20:39-53. doi: 10.1016/j.omtm.2020.10.019. eCollection 2021 Mar 12. PubMed |
| Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. Tothova Z, Valton AL, Gorelov RA, Vallurupalli M, Krill-Burger JM, Holmes A, Landers CC, Haydu JE, Malolepsza E, Hartigan C, Donahue M, Popova KD, Koochaki S, Venev SV, Rivera J, Chen E, Lage K, Schenone M, D'Andrea AD, Carr SA, Morgan EA, Dekker J, Ebert BL. JCI Insight. 2021 Feb 8;6(3). pii: 142149. doi: 10.1172/jci.insight.142149. PubMed |
Generation of PAX7 Reporter Cells to Investigate Skeletal Myogenesis from Human Pluripotent Stem Cells.
Xi H, Young CS, Pyle AD.
STAR Protoc. 2020 Nov 5;1(3):100158. doi: 10.1016/j.xpro.2020.100158. eCollection 2020 Dec 18.
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| Transcriptionally active enhancers in human cancer cells. Lidschreiber K, Jung LA, von der Emde H, Dave K, Taipale J, Cramer P, Lidschreiber M. Mol Syst Biol. 2021 Jan;17(1):e9873. doi: 10.15252/msb.20209873. PubMed |
| Type III Collagen is Required for Adipogenesis and Actin Stress Fibre Formation in 3T3-L1 Preadipocytes. Al Hasan M, Martin PE, Shu X, Patterson S, Bartholomew C. Biomolecules. 2021 Jan 25;11(2). pii: biom11020156. doi: 10.3390/biom11020156. PubMed |
| A Cellular Stress Response Induced by the CRISPR-dCas9 Activation System Is Not Heritable Through Cell Divisions. Johnston AD, Abdulrazak A, Sato H, Maqbool SB, Suzuki M, Greally JM, Simoes-Pires CA. CRISPR J. 2020 Jun;3(3):188-197. doi: 10.1089/crispr.2019.0077. PubMed |
| The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. Davydova E, Shimazu T, Schuhmacher MK, Jakobsson ME, Willemen HLDM, Liu T, Moen A, Ho AYY, Malecki J, Schroer L, Pinto R, Suzuki T, Gronsberg IA, Sohtome Y, Akakabe M, Weirich S, Kikuchi M, Olsen JV, Dohmae N, Umehara T, Sodeoka M, Siino V, McDonough MA, Eijkelkamp N, Schofield CJ, Jeltsch A, Shinkai Y, Falnes PO. Nat Commun. 2021 Feb 9;12(1):891. doi: 10.1038/s41467-020-20670-7. PubMed |
| Cooperative genetic networks drive embryonic stem cell transition from naive to formative pluripotency. Lackner A, Sehlke R, Garmhausen M, Giuseppe Stirparo G, Huth M, Titz-Teixeira F, van der Lelij P, Ramesmayer J, Thomas HF, Ralser M, Santini L, Galimberti E, Sarov M, Stewart AF, Smith A, Beyer A, Leeb M. EMBO J. 2021 Apr 15;40(8):e105776. doi: 10.15252/embj.2020105776. Epub 2021 Mar 9. PubMed |
| A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells. Singh G, Mullany S, Moorthy SD, Zhang R, Mehdi T, Tian R, Duncan AG, Moses AM, Mitchell JA. Genome Res. 2021 Apr;31(4):564-575. doi: 10.1101/gr.272468.120. Epub 2021 Mar 12. PubMed |
| The alternative initiation factor eIF2A plays key role in RAN translation of myotonic dystrophy type 2 CCUG*CAGG repeats. Tusi SK, Nguyen L, Thangaraju K, Li J, Cleary JD, Zu T, Ranum LPW. Hum Mol Genet. 2021 May 31;30(11):1020-1029. doi: 10.1093/hmg/ddab098. PubMed |
| PLOD2-driven IL-6/STAT3 signaling promotes the invasion and metastasis of oral squamous cell carcinoma via activation of integrin beta1. Saito K, Mitsui A, Sumardika IW, Yokoyama Y, Sakaguchi M, Kondo E. Int J Oncol. 2021 Jun;58(6). pii: 29. doi: 10.3892/ijo.2021.5209. Epub 2021 Apr 23. PubMed |
| Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells. Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J. EMBO J. 2021 Jun 15;40(12):e106818. doi: 10.15252/embj.2020106818. Epub 2021 Apr 28. PubMed |
Modeling plasticity and dysplasia of pancreatic ductal organoids derived from human pluripotent stem cells.
Breunig M, Merkle J, Wagner M, Melzer MK, Barth TFE, Engleitner T, Krumm J, Wiedenmann S, Cohrs CM, Perkhofer L, Jain G, Kruger J, Hermann PC, Schmid M, Madacsy T, Varga A, Griger J, Azoitei N, Muller M, Wessely O, Robey PG, Heller S, Dantes Z, Reichert M, Gunes C, Bolenz C, Kuhn F, Maleth J, Speier S, Liebau S, Sipos B, Kuster B, Seufferlein T, Rad R, Meier M, Hohwieler M, Kleger A.
Cell Stem Cell. 2021 Jun 3;28(6):1105-1124.e19. doi: 10.1016/j.stem.2021.03.005. Epub 2021 Apr 28.
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| Novel vertebrate- and brain-specific driver of neuronal outgrowth. Jansen EJR, van Bakel NHM, Benedict B, Olde Loohuis NFM, Hafmans TGM, Chim SM, Xu J, Kolk SM, Martens GJM. Prog Neurobiol. 2021 Jul;202:102069. doi: 10.1016/j.pneurobio.2021.102069. Epub 2021 Apr 29. PubMed |
| Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer. Rosier F, Brisebarre A, Dupuis C, Baaklini S, Puthier D, Brun C, Pradel LC, Rihet P, Payen D. Int J Mol Sci. 2021 May 29;22(11). pii: ijms22115852. doi: 10.3390/ijms22115852. PubMed |
| A first-in-class Polymerase Theta Inhibitor selectively targets Homologous-Recombination-Deficient Tumors. Zhou J, Gelot C, Pantelidou C, Li A, Yucel H, Davis RE, Farkkila A, Kochupurakkal B, Syed A, Shapiro GI, Tainer JA, Blagg BSJ, Ceccaldi R, D'Andrea AD. Nat Cancer. 2021 Jun;2(6):598-610. doi: 10.1038/s43018-021-00203-x. Epub 2021 Jun 17. PubMed |
| The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J. J Biol Chem. 2021 Aug;297(2):100947. doi: 10.1016/j.jbc.2021.100947. Epub 2021 Jul 13. PubMed |
| The structurally conserved TELR region on shelterin protein TPP1 is essential for telomerase processivity but not recruitment. Sandhu R, Sharma M, Wei D, Xu L. Proc Natl Acad Sci U S A. 2021 Jul 27;118(30). pii: 2024889118. doi: 10.1073/pnas.2024889118. PubMed |
| Condensation of pericentrin proteins in human cells illuminates phase separation in centrosome assembly. Jiang X, Ho DBT, Mahe K, Mia J, Sepulveda G, Antkowiak M, Jiang L, Yamada S, Jao LE. J Cell Sci. 2021 Jul 15;134(14). pii: 271045. doi: 10.1242/jcs.258897. Epub 2021 Jul 26. PubMed |
| Tyrosine phosphorylation of lamin A by Src promotes disassembly of nuclear lamina in interphase. Chu CT, Chen YH, Chiu WT, Chen HC. Life Sci Alliance. 2021 Aug 12;4(10). pii: 4/10/e202101120. doi: 10.26508/lsa.202101120. Print 2021 Oct. PubMed |
| Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain. Playfoot CJ, Duc J, Sheppard S, Dind S, Coudray A, Planet E, Trono D. Genome Res. 2021 Sep;31(9):1531-1545. doi: 10.1101/gr.275133.120. Epub 2021 Aug 16. PubMed |
| USP7 facilitates SMAD3 autoregulation to repress cancer progression in p53-deficient lung cancer. Huang YT, Cheng AC, Tang HC, Huang GC, Cai L, Lin TH, Wu KJ, Tseng PH, Wang GG, Chen WY. Cell Death Dis. 2021 Sep 27;12(10):880. doi: 10.1038/s41419-021-04176-8. PubMed |
| A novel AST2 mutation generated upon whole-genome transformation of Saccharomyces cerevisiae confers high tolerance to 5-Hydroxymethylfurfural (HMF) and other inhibitors. Vanmarcke G, Deparis Q, Vanthienen W, Peetermans A, Foulquie-Moreno MR, Thevelein JM. PLoS Genet. 2021 Oct 8;17(10):e1009826. doi: 10.1371/journal.pgen.1009826. eCollection 2021 Oct. PubMed |
| Mutations and variants of ONECUT1 in diabetes. Philippi A, Heller S, Costa IG, Senee V, Breunig M, Li Z, Kwon G, Russell R, Illing A, Lin Q, Hohwieler M, Degavre A, Zalloua P, Liebau S, Schuster M, Krumm J, Zhang X, Geusz R, Benthuysen JR, Wang A, Chiou J, Gaulton K, Neubauer H, Simon E, Klein T, Wagner M, Nair G, Besse C, Dandine-Roulland C, Olaso R, Deleuze JF, Kuster B, Hebrok M, Seufferlein T, Sander M, Boehm BO, Oswald F, Nicolino M, Julier C, Kleger A. Nat Med. 2021 Nov;27(11):1928-1940. doi: 10.1038/s41591-021-01502-7. Epub 2021 Oct 18. PubMed |
| K2P18.1 translates T cell receptor signals into thymic regulatory T cell development. Ruck T, Bock S, Pfeuffer S, Schroeter CB, Cengiz D, Marciniak P, Lindner M, Herrmann A, Liebmann M, Kovac S, Gola L, Rolfes L, Pawlitzki M, Opel N, Hahn T, Dannlowski U, Pap T, Luessi F, Schreiber JA, Wunsch B, Kuhlmann T, Seebohm G, Tackenberg B, Seja P, Doring F, Wischmeyer E, Chasan AI, Roth J, Klotz L, Meyer Zu Horste G, Wiendl H, Marschall T, Floess S, Huehn J, Budde T, Bopp T, Bittner S, Meuth SG. Cell Res. 2022 Jan;32(1):72-88. doi: 10.1038/s41422-021-00580-z. Epub 2021 Oct 26. PubMed |
| A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals. Holoch D, Wassef M, Lovkvist C, Zielinski D, Aflaki S, Lombard B, Hery T, Loew D, Howard M, Margueron R. Nat Genet. 2021 Dec;53(12):1686-1697. doi: 10.1038/s41588-021-00964-2. Epub 2021 Nov 15. PubMed |
| Epromoters function as a hub to recruit key transcription factors required for the inflammatory response. Santiago-Algarra D, Souaid C, Singh H, Dao LTM, Hussain S, Medina-Rivera A, Ramirez-Navarro L, Castro-Mondragon JA, Sadouni N, Charbonnier G, Spicuglia S. Nat Commun. 2021 Nov 18;12(1):6660. doi: 10.1038/s41467-021-26861-0. PubMed |
| Two distinct mechanisms underlie estrogen-receptor-negative breast cancer susceptibility at the 2p23.2 locus. Mendoza-Fandino G, Lyra PCM Jr, Nepomuceno TC, Harro CM, Woods NT, Li X, Rangel LB, Carvalho MA, Couch FJ, Monteiro ANA. Eur J Hum Genet. 2022 Apr;30(4):465-473. doi: 10.1038/s41431-021-01005-6. Epub 2021 Nov 22. PubMed |
| Evaluation of the OsTIR1 and AtAFB2 AID Systems for Genome Architectural Protein Degradation in Mammalian Cells. Yunusova A, Smirnov A, Shnaider T, Lukyanchikova V, Afonnikova S, Battulin N. Front Mol Biosci. 2021 Nov 4;8:757394. doi: 10.3389/fmolb.2021.757394. eCollection 2021. PubMed |
| CRISPR Generated SIX6 and POU4F2 Reporters Allow Identification of Brain and Optic Transcriptional Differences in Human PSC-Derived Organoids. Wahlin KJ, Cheng J, Jurlina SL, Jones MK, Dash NR, Ogata A, Kibria N, Ray S, Eldred KC, Kim C, Heng JS, Phillips J, Johnston RJ Jr, Gamm DM, Berlinicke C, Zack DJ. Front Cell Dev Biol. 2021 Nov 16;9:764725. doi: 10.3389/fcell.2021.764725. eCollection 2021. PubMed |
| Antagonistic Roles of the Tumor Suppressor miR-210-3p and Oncomucin MUC4 Forming a Negative Feedback Loop in Pancreatic Adenocarcinoma. Boukrout N, Souidi M, Lahdaoui F, Duchene B, Neve B, Coppin L, Leteurtre E, Torrisani J, Van Seuningen I, Jonckheere N. Cancers (Basel). 2021 Dec 9;13(24). pii: cancers13246197. doi: 10.3390/cancers13246197. PubMed |
| Bex1 is essential for ciliogenesis and harbours biomolecular condensate-forming capacity. Hibino E, Ichiyama Y, Tsukamura A, Senju Y, Morimune T, Ohji M, Maruo Y, Nishimura M, Mori M. BMC Biol. 2022 Feb 10;20(1):42. doi: 10.1186/s12915-022-01246-x. PubMed |
| Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing. O'Geen H, Tomkova M, Combs JA, Tilley EK, Segal DJ. Nucleic Acids Res. 2022 Apr 8;50(6):3239-3253. doi: 10.1093/nar/gkac123. PubMed |
| NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Huth M, Santini L, Galimberti E, Ramesmayer J, Titz-Teixeira F, Sehlke R, Oberhuemer M, Stummer S, Herzog V, Garmhausen M, Romeike M, Chugunova A, Leesch F, Holcik L, Weipoltshammer K, Lackner A, Schoefer C, von Haeseler A, Buecker C, Pauli A, Ameres SL, Smith A, Beyer A, Leeb M. Genes Dev. 2022 Mar 1;36(5-6):348-367. doi: 10.1101/gad.347690.120. Epub 2022 Mar 3. PubMed |
| TFEB- and TFE3-dependent autophagy activation supports cancer proliferation in the absence of centrosomes. Kao CH, Su TY, Huang WS, Lu XY, Jane WN, Huang CY, Huang HH, Wang WJ. Autophagy. 2022 Mar 22:1-21. doi: 10.1080/15548627.2022.2051880. PubMed |
| Generating Somatic Knockout Cell Lines with CRISPR-Cas9 Technology to Investigate SMAD Signaling. Huang Z, Loewer A. Methods Mol Biol. 2022;2488:81-97. doi: 10.1007/978-1-0716-2277-3_7. PubMed |
| Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor. Heath NG, O'Geen H, Halmai NB, Corn JE, Segal DJ. Front Genome Ed. 2022 Mar 25;4:867390. doi: 10.3389/fgeed.2022.867390. eCollection 2022. PubMed |
Aberrant promoter methylation contributes to LRIG1 silencing in basal/triple-negative breast cancer.
Umeh-Garcia M, O'Geen H, Simion C, Gephart MH, Segal DJ, Sweeney CA.
Br J Cancer. 2022 Apr 19. pii: 10.1038/s41416-022-01812-8. doi: 10.1038/s41416-022-01812-8.
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Associated Plasmids |
| Evaluation of the alpha-casein (CSN1S1) locus as a potential target for a site-specific transgene integration. Smirnov AV, Kontsevaya GV, Shnaider TA, Yunusova AM, Feofanova NA, Gerlinskaya LA, Serova IA, Serov OL, Battulin NR. Sci Rep. 2022 May 14;12(1):7983. doi: 10.1038/s41598-022-12071-1. PubMed |
| Gelatin nanofiber mats with Lipofectamine/plasmid DNA complexes for in vitro genome editing. Furuno K, Suzuki K, Sakai S. Colloids Surf B Biointerfaces. 2022 Aug;216:112561. doi: 10.1016/j.colsurfb.2022.112561. Epub 2022 May 11. PubMed |
| Cell Engineering and Cultivation of Chinese Hamster Ovary Cells for the Development of Orthogonal Eukaryotic Cell-free Translation Systems. Schlosshauer JL, Cavak N, Zemella A, Thoring L, Kubick S. Front Mol Biosci. 2022 Apr 14;9:832379. doi: 10.3389/fmolb.2022.832379. eCollection 2022. PubMed |
| Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus. Taylor T, Sikorska N, Shchuka VM, Chahar S, Ji C, Macpherson NN, Moorthy SD, de Kort MAC, Mullany S, Khader N, Gillespie ZE, Langroudi L, Tobias IC, Lenstra TL, Mitchell JA, Sexton T. Genes Dev. 2022 Jun 1;36(11-12):699-717. doi: 10.1101/gad.349489.122. Epub 2022 Jun 16. PubMed |
| Inhibition of RNA Binding in SND1 Increases the Levels of miR-1-3p and Sensitizes Cancer Cells to Navitoclax. Lehmusvaara S, Haikarainen T, Saarikettu J, Martinez Nieto G, Silvennoinen O. Cancers (Basel). 2022 Jun 24;14(13). pii: cancers14133100. doi: 10.3390/cancers14133100. PubMed |
| Reduced calcium levels and accumulation of abnormal insulin granules in stem cell models of HNF1A deficiency. Gonzalez BJ, Zhao H, Niu J, Williams DJ, Lee J, Goulbourne CN, Xing Y, Wang Y, Oberholzer J, Blumenkrantz MH, Chen X, LeDuc CA, Chung WK, Colecraft HM, Gromada J, Shen Y, Goland RS, Leibel RL, Egli D. Commun Biol. 2022 Aug 2;5(1):779. doi: 10.1038/s42003-022-03696-z. PubMed |
| BRAT1 links Integrator and defective RNA processing with neurodegeneration. Cihlarova Z, Kubovciak J, Sobol M, Krejcikova K, Sachova J, Kolar M, Stanek D, Barinka C, Yoon G, Caldecott KW, Hanzlikova H. Nat Commun. 2022 Aug 26;13(1):5026. doi: 10.1038/s41467-022-32763-6. PubMed |
| Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis. Aguilar C, Pauzuolis M, Pompaiah M, Vafadarnejad E, Arampatzi P, Fischer M, Narres D, Neyazi M, Kayisoglu O, Sell T, Bluthgen N, Morkel M, Wiegering A, Germer CT, Kircher S, Rosenwald A, Saliba AE, Bartfeld S. Nat Commun. 2022 Oct 5;13(1):5878. doi: 10.1038/s41467-022-33165-4. PubMed |
| Colon tumour cell death causes mTOR dependence by paracrine P2X4 stimulation. Schmitt M, Ceteci F, Gupta J, Pesic M, Bottger TW, Nicolas AM, Kennel KB, Engel E, Schewe M, Callak Kirisozu A, Petrocelli V, Dabiri Y, Varga J, Ramakrishnan M, Karimova M, Ablasser A, Sato T, Arkan MC, de Sauvage FJ, Greten FR. Nature. 2022 Dec;612(7939):347-353. doi: 10.1038/s41586-022-05426-1. Epub 2022 Nov 16. PubMed |
| Targeting PEA3 transcription factors to mitigate small cell lung cancer progression. Shia DW, Choi W, Vijayaraj P, Vuong V, Sandlin JM, Lu MM, Aziz A, Marin C, Aros CJ, Sen C, Durra A, Lund AJ, Purkayastha A, Rickabaugh TM, Graeber TG, Gomperts BN. Oncogene. 2023 Feb;42(6):434-448. doi: 10.1038/s41388-022-02558-6. Epub 2022 Dec 13. PubMed |
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| A mitochondrial quality control mechanism reverses the phagosome maturation arrest caused by Mycobacterium tuberculosis. Verma S, Das M, Sharma RD, Yadav V, Thakur S, Sharma P, Marzuki M, Foo S, Piperno GM, Khan MZ, Mathew B, Bajpai M, Maras JS, Howland S, Sarkar S, Benvenuti F, Singh A, Nandicoori V, Singhal A, Kumar D. bioRxiv [Preprint]. 2023 Dec 1:2023.12.01.569475. doi: 10.1101/2023.12.01.569475. PubMed |
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| Evolution of a novel regulatory mechanism of hypoxia inducible factor in hypoxia-tolerant electric fishes. Elbassiouny AA, Buck LT, Abatti LE, Mitchell JA, Crampton WGR, Lovejoy NR, Chang BSW. J Biol Chem. 2024 Mar;300(3):105727. doi: 10.1016/j.jbc.2024.105727. Epub 2024 Feb 5. PubMed |
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| Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2alpha. Schlosshauer JL, Tholen L, Korner A, Kubick S, Chatzopoulou S, Honow A, Zemella A. Synth Syst Biotechnol. 2024 Mar 27;9(3):416-424. doi: 10.1016/j.synbio.2024.03.011. eCollection 2024 Sep. PubMed |
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| The pRb/RBL2-E2F1/4-GCN5 axis regulates cancer stem cell formation and G0 phase entry/exit by paracrine mechanisms. Chang CH, Liu F, Militi S, Hester S, Nibhani R, Deng S, Dunford J, Rendek A, Soonawalla Z, Fischer R, Oppermann U, Pauklin S. Nat Commun. 2024 Apr 27;15(1):3580. doi: 10.1038/s41467-024-47680-z. PubMed |
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| ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway. Veronese M, Kallabis S, Kaczmarek AT, Das A, Robers L, Schumacher S, Lofrano A, Brodesser S, Muller S, Hofmann K, Kruger M, Rugarli EI. Life Sci Alliance. 2024 May 23;7(8):e202402620. doi: 10.26508/lsa.202402620. Print 2024 Aug. PubMed |
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