Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates
Tài liệu tham khảo
Ahlgren, 1996, The morphogenesis of the pancreatic mesenchyme is uncoupled from that of the pancreatic epithelium in IPF1/PDX1-deficient mice, Development, 122, 1409, 10.1242/dev.122.5.1409
Bernstein, 2006, A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, 125, 315, 10.1016/j.cell.2006.02.041
Boj, 2010, Epistasis of transcriptomes reveals synergism between transcriptional activators Hnf1alpha and Hnf4alpha, PLoS Genet., 6, e1000970, 10.1371/journal.pgen.1000970
Buecker, 2012, Enhancers as information integration hubs in development: lessons from genomics, Trends Genet., 28, 276, 10.1016/j.tig.2012.02.008
Carr, 1999, A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos, EMBO J., 18, 1598, 10.1093/emboj/18.6.1598
Creyghton, 2010, Histone H3K27ac separates active from poised enhancers and predicts developmental state, Proc. Natl. Acad. Sci. USA, 107, 21931, 10.1073/pnas.1016071107
Gao, 2008, Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development, Genes Dev., 22, 3435, 10.1101/gad.1752608
Hah, 2013, Enhancer transcripts mark active estrogen receptor binding sites, Genome Res., 23, 1210, 10.1101/gr.152306.112
Hawkins, 2010, Distinct epigenomic landscapes of pluripotent and lineage-committed human cells, Cell Stem Cell, 6, 479, 10.1016/j.stem.2010.03.018
Heintzman, 2009, Histone modifications at human enhancers reflect global cell-type-specific gene expression, Nature, 459, 108, 10.1038/nature07829
Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, 38, 576, 10.1016/j.molcel.2010.05.004
Heinz, 2013, Effect of natural genetic variation on enhancer selection and function, Nature, 503, 487, 10.1038/nature12615
Huang, 2011, Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors, Nature, 475, 386, 10.1038/nature10116
Huang, 2014, Efficient generation of lung and airway epithelial cells from human pluripotent stem cells, Nat. Biotechnol., 32, 84, 10.1038/nbt.2754
Iyer, 2001, Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF, Nature, 409, 533, 10.1038/35054095
Jin, 2011, PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers, Proc. Natl. Acad. Sci. USA, 108, 5290, 10.1073/pnas.1017214108
Jonsson, 1994, Insulin-promoter-factor 1 is required for pancreas development in mice, Nature, 371, 606, 10.1038/371606a0
Kim, 2010, Widespread transcription at neuronal activity-regulated enhancers, Nature, 465, 182, 10.1038/nature09033
Koch, 2007, The landscape of histone modifications across 1% of the human genome in five human cell lines, Genome Res., 17, 691, 10.1101/gr.5704207
Kroon, 2008, Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo, Nat. Biotechnol., 26, 443, 10.1038/nbt1393
Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25
Lango Allen, 2012, GATA6 haploinsufficiency causes pancreatic agenesis in humans, Nat. Genet., 44, 20, 10.1038/ng.1035
Lee, 2005, The initiation of liver development is dependent on Foxa transcription factors, Nature, 435, 944, 10.1038/nature03649
Lee, 2013, H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation, eLife, 2, e01503, 10.7554/eLife.01503
Li, 2000, Mammalian hepatocyte differentiation requires the transcription factor HNF-4alpha, Genes Dev., 14, 464, 10.1101/gad.14.4.464
Li, 2012, Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation, Cell, 151, 1608, 10.1016/j.cell.2012.11.018
Linker, 2004, Neural induction requires BMP inhibition only as a late step, and involves signals other than FGF and Wnt antagonists, Development, 131, 5671, 10.1242/dev.01445
Lupien, 2008, FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription, Cell, 132, 958, 10.1016/j.cell.2008.01.018
Martino, 2009, Reconstitution of yeast silent chromatin: multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro, Mol. Cell, 33, 323, 10.1016/j.molcel.2009.01.009
Mikkelsen, 2007, Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, 448, 553, 10.1038/nature06008
Rada-Iglesias, 2011, A unique chromatin signature uncovers early developmental enhancers in humans, Nature, 470, 279, 10.1038/nature09692
Rajagopal, 2013, RFECS: a random-forest based algorithm for enhancer identification from chromatin state, PLoS Comput. Biol., 9, e1002968, 10.1371/journal.pcbi.1002968
Schulz, 2012, A scalable system for production of functional pancreatic progenitors from human embryonic stem cells, PLoS ONE, 7, e37004, 10.1371/journal.pone.0037004
Shen, 2012, A map of the cis-regulatory sequences in the mouse genome, Nature, 488, 116, 10.1038/nature11243
Shih, 2013, Pancreas organogenesis: from lineage determination to morphogenesis, Annu. Rev. Cell Dev. Biol., 29, 81, 10.1146/annurev-cellbio-101512-122405
Shogren-Knaak, 2006, Histone H4-K16 acetylation controls chromatin structure and protein interactions, Science, 311, 844, 10.1126/science.1124000
Smith, 2010, Rfx6 directs islet formation and insulin production in mice and humans, Nature, 463, 775, 10.1038/nature08748
Soufi, 2012, Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome, Cell, 151, 994, 10.1016/j.cell.2012.09.045
Stoffers, 1997, Pancreatic agenesis attributable to a single nucleotide deletion in the human IPF1 gene coding sequence, Nat. Genet., 15, 106, 10.1038/ng0197-106
Storey, 1992, Neural induction and regionalisation in the chick embryo, Development, 114, 729, 10.1242/dev.114.3.729
van Hoek, 2008, Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study, Diabetes, 57, 3122, 10.2337/db08-0425
Visel, 2009, ChIP-seq accurately predicts tissue-specific activity of enhancers, Nature, 457, 854, 10.1038/nature07730
Waddington, 1940
Wang, 2012, Generating cells of the gastrointestinal system: current approaches and applications for the differentiation of human pluripotent stem cells, J. Mol. Med. (Berl), 90, 763, 10.1007/s00109-012-0923-y
Wang, 2011, Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA, Nature, 474, 390, 10.1038/nature10006
Wapinski, 2013, Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons, Cell, 155, 621, 10.1016/j.cell.2013.09.028
Watt, 2007, Development of the mammalian liver and ventral pancreas is dependent on GATA4, BMC Dev. Biol., 7, 37, 10.1186/1471-213X-7-37
Weedon, 2014, Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis, Nat. Genet., 46, 61, 10.1038/ng.2826
Wells, 2000, Early mouse endoderm is patterned by soluble factors from adjacent germ layers, Development, 127, 1563, 10.1242/dev.127.8.1563
Xie, 2013, Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells, Cell Stem Cell, 12, 224, 10.1016/j.stem.2012.11.023
Yang, 2006, Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells, Mol. Cell, 24, 593, 10.1016/j.molcel.2006.10.018
Zaret, 2011, Pioneer transcription factors: establishing competence for gene expression, Genes Dev., 25, 2227, 10.1101/gad.176826.111
Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137