Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network
Tài liệu tham khảo
Schwitzgebel, 2014, Many faces of monogenic diabetes, Journal of Diabetes Investigation, 5, 121, 10.1111/jdi.12197
Gu, 2002, Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors, Development, 129, 2447, 10.1242/dev.129.10.2447
Gradwohl, 2000, neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas, Proceedings of the National Academy of Sciences of the United States of America, 97, 1607, 10.1073/pnas.97.4.1607
Wang, 2006, Mutant neurogenin-3 in congenital malabsorptive diarrhea, New England Journal of Medicine, 355, 270, 10.1056/NEJMoa054288
Rubio-Cabezas, 2011, Permanent neonatal diabetes and enteric anendocrinosis associated with biallelic mutations in NEUROG3, Diabetes, 60, 1349, 10.2337/db10-1008
Pinney, 2011, Neonatal diabetes and congenital malabsorptive diarrhea attributable to a novel mutation in the human neurogenin-3 gene coding sequence, The Journal of Clinical Endocrinology and Metabolism, 96, 1960, 10.1210/jc.2011-0029
Hancili, 2017, A novel NEUROG3 mutation in neonatal diabetes associated with a neuro-intestinal syndrome, Pediatric Diabetes, 21, 464
Mellitzer, 2010, Loss of enteroendocrine cells in mice alters lipid absorption and glucose homeostasis and impairs postnatal survival, The Journal of Clinical Investigation, 120, 1708, 10.1172/JCI40794
McGrath, 2015, The basic helix-loop-helix transcription factor NEUROG3 is required for development of the human endocrine pancreas, Diabetes, 64, 2497, 10.2337/db14-1412
Zhu, 2016, Genome editing of lineage determinants in human pluripotent stem cells reveals mechanisms of pancreatic development and diabetes, Stem Cell, 1
Petri, 2006, The effect of neurogenin3 deficiency on pancreatic gene expression in embryonic mice, Journal of Molecular Endocrinology, 37, 301, 10.1677/jme.1.02096
Smith, 2004, Neurogenin3 activates the islet differentiation program while repressing its own expression, Molecular Endocrinology, 18, 142, 10.1210/me.2003-0037
Mellitzer, 2006, IA1 is NGN3-dependent and essential for differentiation of the endocrine pancreas, Embo Journal, 25, 1344, 10.1038/sj.emboj.7601011
Miyatsuka, 2011, Neurogenin3 inhibits proliferation in endocrine progenitors by inducing Cdkn1a, Proceedings of the National Academy of Sciences of the United States of America, 108, 185, 10.1073/pnas.1004842108
Huang, 2000, Regulation of the pancreatic islet-specific gene BETA2 (neuroD) by neurogenin 3, Molecular and Cellular Biology, 20, 3292, 10.1128/MCB.20.9.3292-3307.2000
Smith, 2003, Neurogenin3 and hepatic nuclear factor 1 cooperate in activating pancreatic expression of Pax4, The Journal of Biological Chemistry, 278, 38254, 10.1074/jbc.M302229200
Zhang, 2019, A comprehensive structure-function study of Neurogenin3 disease-causing alleles during human pancreas and intestinal organoid development, Developmental Cell, 50, 367, 10.1016/j.devcel.2019.05.017
Hainer, 2019, Profiling of pluripotency factors in single cells and early embryos, Cell, 177, 1319, 10.1016/j.cell.2019.03.014
Skene, 2017, An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites, eLife, 6, 576, 10.7554/eLife.21856
Skene, 2018, Targeted in situ genome-wide profiling with high efficiency for low cell numbers, Nature Protocols, 13, 1006, 10.1038/nprot.2018.015
Petersen, 2017, Single-cell gene expression analysis of a human ESC model of pancreatic endocrine development reveals different paths to β-cell differentiation, Stem Cell Reports, 1
Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635
Anders, 2015, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638
Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, 15, 550, 10.1186/s13059-014-0550-8
de Lichtenberg, 2018, Genome-wide identification of HES1 target genes uncover novel roles for HES1 in pancreatic development, BioRxiv
Anders, 2010, Differential expression analysis for sequence count data, Genome Biology, 11, R106, 10.1186/gb-2010-11-10-r106
Hainer, 2019, High-Resolution chromatin profiling using CUT&RUN, Current Protocols in Molecular Biology, 126, e85, 10.1002/cpmb.85
Schmid, 2004, ChIC and ChEC; genomic mapping of chromatin proteins, Molecular Cell, 16, 147
Ye, 2011, seqMINER: an integrated ChIP-seq data interpretation platform, Nucleic Acids Research, 39, e35, 10.1093/nar/gkq1287
Alvarez-Dominguez, 2020, Circadian entrainment triggers maturation of human in vitro islets, Cell Stem Cell, 26, 108, 10.1016/j.stem.2019.11.011
Cebola, 2015, TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors, Nature Cell Biology, 17, 615, 10.1038/ncb3160
Miguel-Escalada, 2019, Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes, Nat Genetics, 51, 1137, 10.1038/s41588-019-0457-0
Meers, 2019, Peak calling by Sparse enrichment analysis for CUT&RUN chromatin profiling, Epigenetics & Chromatin, 12, 42, 10.1186/s13072-019-0287-4
Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Molecular Cell, 38, 576, 10.1016/j.molcel.2010.05.004
McLean, 2010, GREAT improves functional interpretation of cis-regulatory regions, Nature Biotechnology, 28, 495, 10.1038/nbt.1630
Huang da, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, 4, 44, 10.1038/nprot.2008.211
Lambert, 2018, The human transcription factors, Cell, 175, 598, 10.1016/j.cell.2018.09.045
Cao, 2020, A human cell atlas of fetal gene expression, Science, 370, 10.1126/science.aba7721
Weng, 2020, Single-cell lineage analysis reveals extensive multimodal transcriptional control during directed beta-cell differentiation, Nature Metabolism, 2, 1443, 10.1038/s42255-020-00314-2
Shin, 2009, CEAS: cis-regulatory element annotation system, Bioinformatics, 25, 2605, 10.1093/bioinformatics/btp479
Rezania, 2014, Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells, Nature Biotechnology, 32, 1121, 10.1038/nbt.3033
van Arensbergen, 2017, A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element, PLoS One, 12, 10.1371/journal.pone.0171508
Mutoh, 1998, The basic helix-loop-helix protein BETA2 interacts with p300 to coordinate differentiation of secretin-expressing enteroendocrine cells, Genes & Development, 12, 820, 10.1101/gad.12.6.820
Kim, 2002, Pbx1 inactivation disrupts pancreas development and in Ipf1-deficient mice promotes diabetes mellitus, Nature Genetics, 30, 430, 10.1038/ng860
Piccand, 2014, Rfx6 maintains the functional identity of adult pancreatic β cells, Cell Reports, 9, 2219, 10.1016/j.celrep.2014.11.033
Ait-Lounis, 2010, The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression, Diabetes, 59, 1674, 10.2337/db09-0986
Andersson, 2020, Determinants of enhancer and promoter activities of regulatory elements, Nature Review Genetics, 21, 71, 10.1038/s41576-019-0173-8
Gao, 2008, Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development, Genes & Development, 22, 3435, 10.1101/gad.1752608
Lee, 2019, FOXA2 is required for enhancer priming during pancreatic differentiation, Cell Reports, 28, 382, 10.1016/j.celrep.2019.06.034
Churchill, 2017, Genetic evidence that Nkx2.2 acts primarily downstream of Neurog3 in pancreatic endocrine lineage development, eLife, 6, 10.7554/eLife.20010
Xu, 2015, SOX4 cooperates with neurogenin 3 to regulate endocrine pancreas formation in mouse models, Diabetologia, 58, 1013, 10.1007/s00125-015-3507-x
Collombat, 2003, Opposing actions of Arx and Pax4 in endocrine pancreas development, Genes & Development, 17, 2591, 10.1101/gad.269003
Schaffer, 2013, Nkx6.1 controls a gene regulatory network required for establishing and maintaining pancreatic Beta cell identity, PLoS Genetics, 9, 10.1371/journal.pgen.1003274
Muraro, 2016, A single-cell transcriptome atlas of the human pancreas, Cell Systems, 3, 385, 10.1016/j.cels.2016.09.002
Gage, 2015, The role of ARX in human pancreatic endocrine specification, PLoS One, 10, 10.1371/journal.pone.0144100
Lawlor, 2019, Multiomic profiling identifies cis-regulatory networks underlying human pancreatic beta cell identity and function, Cell Reports, 26, 788, 10.1016/j.celrep.2018.12.083
Zhang, 2014, The diabetes gene Hhex maintains delta-cell differentiation and islet function, Genes & Development, 28, 829, 10.1101/gad.235499.113
Huotari, 2002, ErbB signaling regulates lineage determination of developing pancreatic islet cells in embryonic organ culture, Endocrinology, 143, 4437, 10.1210/en.2002-220382
Han, 2016, Intrinsic HER4/4ICD transcriptional activation domains are required for STAT5A activated gene expression, Gene, 592, 221, 10.1016/j.gene.2016.07.071
Rorsman, 2018, Pancreatic beta-cell electrical activity and insulin secretion: of mice and men, Physiological Reviews, 98, 117, 10.1152/physrev.00008.2017
Krentz, 2020, Insights into pancreatic islet cell dysfunction from type 2 diabetes mellitus genetics, Nature Reviews Endocrinology, 16, 202, 10.1038/s41574-020-0325-0
