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For: Genga RMJ, Kernfeld EM, Parsi KM, Parsons TJ, Ziller MJ, Maehr R. Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development. Cell Rep 2019;27:708-718.e10. [PMID: 30995470 PMCID: PMC6525305 DOI: 10.1016/j.celrep.2019.03.076] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/22/2019] [Accepted: 03/20/2019] [Indexed: 12/22/2022]  Open
Number Cited by Other Article(s)
1
Li Y, Meng Z, Fan C, Rong H, Xi Y, Liao Q. Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer. Biochem Biophys Rep 2025;41:101938. [PMID: 40034256 PMCID: PMC11874739 DOI: 10.1016/j.bbrep.2025.101938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 01/19/2025] [Accepted: 01/28/2025] [Indexed: 03/05/2025]  Open
2
Hogrebe NJ, Schmidt MD, Augsornworawat P, Gale SE, Shunkarova M, Millman JR. Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.21.618465. [PMID: 39484596 PMCID: PMC11526947 DOI: 10.1101/2024.10.21.618465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
3
Su C, Pastor WA, Emad A. Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP. Brief Bioinform 2024;25:bbae592. [PMID: 39535258 PMCID: PMC11558691 DOI: 10.1093/bib/bbae592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 10/09/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024]  Open
4
Barrero M, Lazarenkov A, Blanco E, Palma LG, López-Rubio AV, Bauer M, Bigas A, Di Croce L, Sardina JL, Payer B. The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogramming. SCIENCE ADVANCES 2024;10:eadj8862. [PMID: 39110794 PMCID: PMC11305397 DOI: 10.1126/sciadv.adj8862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
5
Madrigal A, Lu T, Soto LM, Najafabadi HS. A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. Nat Commun 2024;15:6573. [PMID: 39097589 PMCID: PMC11298001 DOI: 10.1038/s41467-024-50963-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 07/23/2024] [Indexed: 08/05/2024]  Open
6
Zhou H, Ye P, Xiong W, Duan X, Jing S, He Y, Zeng Z, Wei Y, Ye Q. Genome-scale CRISPR-Cas9 screening in stem cells: theories, applications and challenges. Stem Cell Res Ther 2024;15:218. [PMID: 39026343 PMCID: PMC11264826 DOI: 10.1186/s13287-024-03831-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]  Open
7
Edenhofer FC, Térmeg A, Ohnuki M, Jocher J, Kliesmete Z, Briem E, Hellmann I, Enard W. Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi. iScience 2024;27:110090. [PMID: 38947524 PMCID: PMC11214527 DOI: 10.1016/j.isci.2024.110090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/28/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024]  Open
8
Barry T, Mason K, Roeder K, Katsevich E. Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection. Genome Biol 2024;25:124. [PMID: 38760839 PMCID: PMC11100084 DOI: 10.1186/s13059-024-03254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024]  Open
9
Barry T, Mason K, Roeder K, Katsevich E. Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.15.540875. [PMID: 38659821 PMCID: PMC11042176 DOI: 10.1101/2023.05.15.540875] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
10
Xing M, Yao B, Xu J, Lu P, Li Q, Wu D, Chen B, Wei J, Su L, Zhao Q. NatD epigenetically activates FOXA2 expression to promote breast cancer progression by facilitating MMP14 expression. iScience 2024;27:108840. [PMID: 38303717 PMCID: PMC10830889 DOI: 10.1016/j.isci.2024.108840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/09/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024]  Open
11
Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024;84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
12
Yang C, Lei Y, Ren T, Yao M. The Current Situation and Development Prospect of Whole-Genome Screening. Int J Mol Sci 2024;25:658. [PMID: 38203828 PMCID: PMC10779205 DOI: 10.3390/ijms25010658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]  Open
13
Li Q, Li J, Wang P, He X, Hong M, Liu F. A Comparative Study of Endoderm Differentiation Between Activin A and Small Molecules. Exp Clin Endocrinol Diabetes 2023;131:667-675. [PMID: 38056491 DOI: 10.1055/a-2182-8936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
14
Rummel CK, Gagliardi M, Ahmad R, Herholt A, Jimenez-Barron L, Murek V, Weigert L, Hausruckinger A, Maidl S, Hauger B, Raabe FJ, Fürle C, Trastulla L, Turecki G, Eder M, Rossner MJ, Ziller MJ. Massively parallel functional dissection of schizophrenia-associated noncoding genetic variants. Cell 2023;186:5165-5182.e33. [PMID: 37852259 DOI: 10.1016/j.cell.2023.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/12/2023] [Accepted: 09/14/2023] [Indexed: 10/20/2023]
15
Kolvenbach CM, Shril S, Hildebrandt F. The genetics and pathogenesis of CAKUT. Nat Rev Nephrol 2023;19:709-720. [PMID: 37524861 DOI: 10.1038/s41581-023-00742-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2023] [Indexed: 08/02/2023]
16
Meyers S, Demeyer S, Cools J. CRISPR screening in hematology research: from bulk to single-cell level. J Hematol Oncol 2023;16:107. [PMID: 37875911 PMCID: PMC10594891 DOI: 10.1186/s13045-023-01495-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/21/2023] [Indexed: 10/26/2023]  Open
17
Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S. Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nat Commun 2023;14:6519. [PMID: 37845234 PMCID: PMC10579264 DOI: 10.1038/s41467-023-42274-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023]  Open
18
Kearns NA, Lobo M, Genga RMJ, Abramowitz RG, Parsi KM, Min J, Kernfeld EM, Huey JD, Kady J, Hennessy E, Brehm MA, Ziller MJ, Maehr R. Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm. Dev Cell 2023;58:1801-1818.e15. [PMID: 37751684 PMCID: PMC10637111 DOI: 10.1016/j.devcel.2023.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/15/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
19
Yi Y, Lan X, Li Y, Yan C, Lv J, Zhang T, Jiang W. Fatty acid synthesis and oxidation regulate human endoderm differentiation by mediating SMAD3 nuclear localization via acetylation. Dev Cell 2023;58:1670-1687.e4. [PMID: 37516106 DOI: 10.1016/j.devcel.2023.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/02/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
20
Yu Q, Van Minsel P, Galle E, Thienpont B. GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens. Commun Biol 2023;6:975. [PMID: 37741886 PMCID: PMC10518011 DOI: 10.1038/s42003-023-05351-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023]  Open
21
Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023;597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
22
Armendariz DA, Sundarrajan A, Hon GC. Breaking enhancers to gain insights into developmental defects. eLife 2023;12:e88187. [PMID: 37497775 PMCID: PMC10374278 DOI: 10.7554/elife.88187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]  Open
23
Rummel CK, Gagliardi M, Herholt A, Ahmad R, Murek V, Weigert L, Hausruckinger A, Maidl S, Jimenez-Barron L, Trastulla L, Eder M, Rossner M, Ziller MJ. Cell type and condition specific functional annotation of schizophrenia associated non-coding genetic variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.545266. [PMID: 37425902 PMCID: PMC10326990 DOI: 10.1101/2023.06.27.545266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
24
Armendariz DA, Goetsch SC, Sundarrajan A, Sivakumar S, Wang Y, Xie S, Munshi NV, Hon GC. CHD-associated enhancers shape human cardiomyocyte lineage commitment. eLife 2023;12:e86206. [PMID: 37096669 PMCID: PMC10156167 DOI: 10.7554/elife.86206] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/10/2023] [Indexed: 04/26/2023]  Open
25
Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 2023;12:e83077. [PMID: 36719724 PMCID: PMC9889090 DOI: 10.7554/elife.83077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023]  Open
26
Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023;14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023]  Open
27
Yu C, Li X, Zhao Y, Hu Y. The role of FOXA family transcription factors in glucolipid metabolism and NAFLD. Front Endocrinol (Lausanne) 2023;14:1081500. [PMID: 36798663 PMCID: PMC9927216 DOI: 10.3389/fendo.2023.1081500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023]  Open
28
Warren I, Moeller MM, Guiggey D, Chiang A, Maloy M, Ogoke O, Groth T, Mon T, Meamardoost S, Liu X, Thompson S, Szeglowski A, Thompson R, Chen P, Paulmurugan R, Yarmush ML, Kidambi S, Parashurama N. FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells. FASEB J 2023;37:e22652. [PMID: 36515690 DOI: 10.1096/fj.202101506rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022]
29
Yamatani Y, Nakai K. Comprehensive comparison of gene expression diversity among a variety of human stem cells. NAR Genom Bioinform 2022;4:lqac087. [PMID: 36458020 PMCID: PMC9706419 DOI: 10.1093/nargab/lqac087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022]  Open
30
Medina-Cano D, Corrigan EK, Glenn RA, Islam MT, Lin Y, Kim J, Cho H, Vierbuchen T. Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids. Development 2022;149:dev200561. [PMID: 35899604 PMCID: PMC10655922 DOI: 10.1242/dev.200561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
31
An artificial LAMA2-GelMA hydrogel microenvironment for the development of pancreatic endocrine progenitors. Biomaterials 2022;291:121882. [DOI: 10.1016/j.biomaterials.2022.121882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/15/2022] [Accepted: 10/23/2022] [Indexed: 11/21/2022]
32
Zheng B, Seltzsam S, Wang C, Schierbaum L, Schneider S, Wu CHW, Dai R, Connaughton DM, Nakayama M, Mann N, Stajic N, Mane S, Bauer SB, Tasic V, Nam HJ, Shril S, Hildebrandt F. Whole-exome sequencing identifies FOXL2, FOXA2 and FOXA3 as candidate genes for monogenic congenital anomalies of the kidneys and urinary tract. Nephrol Dial Transplant 2022;37:1833-1843. [PMID: 34473308 PMCID: PMC9755999 DOI: 10.1093/ndt/gfab253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Indexed: 11/14/2022]  Open
33
Loss of FOXA2 induces ER stress and hepatic steatosis and alters developmental gene expression in human iPSC-derived hepatocytes. Cell Death Dis 2022;13:713. [PMID: 35973994 PMCID: PMC9381545 DOI: 10.1038/s41419-022-05158-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 01/21/2023]
34
Application of Gene Editing Technology in Resistance Breeding of Livestock. LIFE (BASEL, SWITZERLAND) 2022;12:life12071070. [PMID: 35888158 PMCID: PMC9325061 DOI: 10.3390/life12071070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023]
35
Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Ranking reprogramming factors for cell differentiation. Nat Methods 2022;19:812-822. [PMID: 35710610 PMCID: PMC10460539 DOI: 10.1038/s41592-022-01522-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2022] [Indexed: 12/16/2022]
36
Yang D, Cho H, Tayyebi Z, Shukla A, Luo R, Dixon G, Ursu V, Stransky S, Tremmel DM, Sackett SD, Koche R, Kaplan SJ, Li QV, Park J, Zhu Z, Rosen BP, Pulecio J, Shi ZD, Bram Y, Schwartz RE, Odorico JS, Sidoli S, Wright CV, Leslie CS, Huangfu D. CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction. Nat Cell Biol 2022;24:1064-1076. [PMID: 35787684 PMCID: PMC9283336 DOI: 10.1038/s41556-022-00946-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/25/2022] [Indexed: 01/07/2023]
37
Zhang SY, Zhao J, Ni JJ, Li H, Quan ZZ, Qing H. Application and prospects of high-throughput screening for in vitro neurogenesis. World J Stem Cells 2022;14:393-419. [PMID: 35949394 PMCID: PMC9244953 DOI: 10.4252/wjsc.v14.i6.393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/07/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023]  Open
38
Haellman V, Pirkl M, Akmammedov A, Saxena P, Beerenwinkel N, Paro R, Teixeira AP, Fussenegger M. dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation. Metab Eng 2022;73:70-81. [PMID: 35724832 DOI: 10.1016/j.ymben.2022.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
39
Fang F, Iaquinta PJ, Xia N, Liu L, Diao L, Reijo Pera RA. Transcriptional control of human gametogenesis. Hum Reprod Update 2022;28:313-345. [PMID: 35297982 PMCID: PMC9071081 DOI: 10.1093/humupd/dmac002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/22/2021] [Indexed: 11/14/2022]  Open
40
Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y. Single-cell RNA sequencing technologies and applications: A brief overview. Clin Transl Med 2022;12:e694. [PMID: 35352511 PMCID: PMC8964935 DOI: 10.1002/ctm2.694] [Citation(s) in RCA: 514] [Impact Index Per Article: 171.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 12/19/2022]  Open
41
Su EY, Spangler A, Bian Q, Kasamoto JY, Cahan P. Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification. Stem Cell Reports 2022;17:427-442. [PMID: 35090587 PMCID: PMC8828556 DOI: 10.1016/j.stemcr.2021.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/21/2021] [Accepted: 12/26/2021] [Indexed: 11/17/2022]  Open
42
Metabolic and epigenetic regulation of endoderm differentiation. Trends Cell Biol 2022;32:151-164. [PMID: 34607773 PMCID: PMC8760149 DOI: 10.1016/j.tcb.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/31/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023]
43
Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nat Commun 2021;12:6636. [PMID: 34789735 PMCID: PMC8599738 DOI: 10.1038/s41467-021-26950-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/28/2021] [Indexed: 01/15/2023]  Open
44
Haswell JR, Mattioli K, Gerhardinger C, Maass PG, Foster DJ, Peinado P, Wang X, Medina PP, Rinn JL, Slack FJ. Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PLoS One 2021;16:e0252848. [PMID: 34731163 PMCID: PMC8565776 DOI: 10.1371/journal.pone.0252848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/26/2021] [Indexed: 12/26/2022]  Open
45
Pioneer factors in development and cancer. iScience 2021;24:103132. [PMID: 34632331 PMCID: PMC8487031 DOI: 10.1016/j.isci.2021.103132] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
46
Li B, Hon GC. Single-Cell Genomics: Catalyst for Cell Fate Engineering. Front Bioeng Biotechnol 2021;9:748942. [PMID: 34733831 PMCID: PMC8558416 DOI: 10.3389/fbioe.2021.748942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022]  Open
47
Rankin SA, Steimle JD, Yang XH, Rydeen AB, Agarwal K, Chaturvedi P, Ikegami K, Herriges MJ, Moskowitz IP, Zorn AM. Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development. eLife 2021;10:69288. [PMID: 34643182 PMCID: PMC8555986 DOI: 10.7554/elife.69288] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022]  Open
48
Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods 2021;18:1046-1055. [PMID: 34480151 PMCID: PMC8446342 DOI: 10.1038/s41592-021-01248-7] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/18/2021] [Indexed: 01/05/2023]
49
Hertzano R, Gwilliam K, Rose K, Milon B, Matern MS. Cell Type-Specific Expression Analysis of the Inner Ear: A Technical Report. Laryngoscope 2021;131 Suppl 5:S1-S16. [PMID: 32579737 PMCID: PMC8996438 DOI: 10.1002/lary.28765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 01/11/2023]
50
Hammelman J, Gifford DK. Discovering differential genome sequence activity with interpretable and efficient deep learning. PLoS Comput Biol 2021;17:e1009282. [PMID: 34370721 PMCID: PMC8376110 DOI: 10.1371/journal.pcbi.1009282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/19/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022]  Open
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