Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

Adenot, 1997, Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos, Development, 124, 4615, 10.1242/dev.124.22.4615 Ahmed, 2010, Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo, PLoS One, 5, e10531, 10.1371/journal.pone.0010531 Blakeley, 2015, Defining the three cell lineages of the human blastocyst by single-cell RNA-seq, Development, 142, 3151, 10.1242/dev.123547 Boroviak, 2014, The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification, Nat. Cell Biol., 16, 516, 10.1038/ncb2965 Boroviak, 2015, Lineage-specific profiling delineates the emergence and progression of naive pluripotency in mammalian embryogenesis, Dev. Cell, 35, 366, 10.1016/j.devcel.2015.10.011 Chan, 2013, Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast, Cell Stem Cell, 13, 663, 10.1016/j.stem.2013.11.015 Chen, 2012, Where PI3K/Akt meets smads: the crosstalk determines human embryonic stem cell fate, Cell Stem Cell, 10, 231, 10.1016/j.stem.2012.02.008 Collier, 2017, Comprehensive cell surface protein profiling identifies specific markers of human naive and primed pluripotent states, Cell Stem Cell, 20, 874, 10.1016/j.stem.2017.02.014 Crane, 2015, Condensin-driven remodelling of X chromosome topology during dosage compensation, Nature, 523, 240, 10.1038/nature14450 Creyghton, 2010, Histone H3K27ac separates active from poised enhancers and predicts developmental state, Proc. Natl. Acad. Sci. U S A, 107, 21931, 10.1073/pnas.1016071107 Dahl, 2016, Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition, Nature, 537, 548, 10.1038/nature19360 Deng, 2015, Bipartite structure of the inactive mouse X chromosome, Genome Biol., 16, 152, 10.1186/s13059-015-0728-8 Dixon, 2012, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 485, 376, 10.1038/nature11082 Dixon, 2015, Chromatin architecture reorganization during stem cell differentiation, Nature, 518, 331, 10.1038/nature14222 Du, 2017, Allelic reprogramming of 3D chromatin architecture during early mammalian development, Nature, 547, 232, 10.1038/nature23263 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 Forneris, 2005, Human histone demethylase LSD1 reads the histone code, J. Biol. Chem., 280, 41360, 10.1074/jbc.M509549200 Gafni, 2013, Derivation of novel human ground state naive pluripotent stem cells, Nature, 504, 282, 10.1038/nature12745 Giorgetti, 2016, Structural organization of the inactive X chromosome in the mouse, Nature, 535, 575, 10.1038/nature18589 Guo, 2014, The DNA methylation landscape of human early embryos, Nature, 511, 606, 10.1038/nature13544 Guo, 2016, Naive pluripotent stem cells derived directly from isolated cells of the human inner cell mass, Stem Cell Reports, 6, 437, 10.1016/j.stemcr.2016.02.005 Hanna, 2010, Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs, Proc. Natl. Acad. Sci. U S A, 107, 9222, 10.1073/pnas.1004584107 Hawkins, 2010, Distinct epigenomic landscapes of pluripotent and lineage-committed human cells, Cell Stem Cell, 6, 479, 10.1016/j.stem.2010.03.018 Hawkins, 2011, Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency, Cell Res., 21, 1393, 10.1038/cr.2011.146 Hawkins, 2013, Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization, Immunity, 38, 1271, 10.1016/j.immuni.2013.05.011 Heintzman, 2007, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat. Genet., 39, 311, 10.1038/ng1966 Heintzman, 2009, Histone modifications at human enhancers reflect global cell-type-specific gene expression, Nature, 459, 108, 10.1038/nature07829 Ji, 2016, 3D chromosome regulatory landscape of human pluripotent cells, Cell Stem Cell, 18, 262, 10.1016/j.stem.2015.11.007 Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Lee, 2006, Functional interplay between histone demethylase and deacetylase enzymes, Mol. Cell. Biol., 26, 6395, 10.1128/MCB.00723-06 Lepikhov, 2004, Differential dynamics of histone H3 methylation at positions K4 and K9 in the mouse zygote, BMC Dev. Biol., 4, 12, 10.1186/1471-213X-4-12 Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289, 10.1126/science.1181369 Liu, 2004, Regulation of histone H3 lysine 9 methylation in oocytes and early pre-implantation embryos, Development, 131, 2269, 10.1242/dev.01116 Meshorer, 2006, Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells, Dev. Cell, 10, 105, 10.1016/j.devcel.2005.10.017 Moody, 2017, First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor, Proc. Natl. Acad. Sci. U S A, 114, 10125, 10.1073/pnas.1706907114 Niakan, 2013, Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse, Dev. Biol., 375, 54, 10.1016/j.ydbio.2012.12.008 Nichols, 2009, Naive and primed pluripotent states, Cell Stem Cell, 4, 487, 10.1016/j.stem.2009.05.015 Ooi, 2007, DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA, Nature, 448, 714, 10.1038/nature05987 Parker, 2013, Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants, Proc. Natl. Acad. Sci. U S A, 110, 17921, 10.1073/pnas.1317023110 Rada-Iglesias, 2011, A unique chromatin signature uncovers early developmental enhancers in humans, Nature, 470, 279, 10.1038/nature09692 Rao, 2014, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, 159, 1665, 10.1016/j.cell.2014.11.021 Rossant, 2015, Mouse and human blastocyst-derived stem cells: vive les differences, Development, 142, 9, 10.1242/dev.115451 Sarmento, 2004, Dynamic alterations of specific histone modifications during early murine development, J. Cell Sci., 117, 4449, 10.1242/jcs.01328 Shin, 2016, TopDom: an efficient and deterministic method for identifying topological domains in genomes, Nucleic Acids Res., 44, e70, 10.1093/nar/gkv1505 Silva, 2008, Capturing pluripotency, Cell, 132, 532, 10.1016/j.cell.2008.02.006 Sperber, 2015, The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition, Nat. Cell Biol., 17, 1523, 10.1038/ncb3264 Takashima, 2014, Resetting transcription factor control circuitry toward ground-state pluripotency in human, Cell, 158, 1254, 10.1016/j.cell.2014.08.029 Theunissen, 2014, Systematic identification of culture conditions for induction and maintenance of naive human pluripotency, Cell Stem Cell, 15, 471, 10.1016/j.stem.2014.07.002 Theunissen, 2016, Molecular criteria for defining the naive human pluripotent state, Cell Stem Cell, 19, 502, 10.1016/j.stem.2016.06.011 Trapnell, 2010, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621 Valamehr, 2014, Platform for induction and maintenance of transgene-free hiPSCs resembling ground state pluripotent stem cells, Stem Cell Reports, 2, 366, 10.1016/j.stemcr.2014.01.014 van der Heijden, 2005, Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote, Mech. Dev., 122, 1008, 10.1016/j.mod.2005.04.009 Ware, 2016, Concise review: lessons from naïve human pluripotent cells, Stem Cells, 35, 35, 10.1002/stem.2507 Ware, 2014, Derivation of naive human embryonic stem cells, Proc. Natl. Acad. Sci. U S A, 111, 4484, 10.1073/pnas.1319738111 Whyte, 2012, Enhancer decommissioning by LSD1 during embryonic stem cell differentiation, Nature, 482, 221, 10.1038/nature10805 Whyte, 2013, Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, 153, 307, 10.1016/j.cell.2013.03.035 Wiekowski, 1997, Changes in histone synthesis and modification at the beginning of mouse development correlate with the establishment of chromatin mediated repression of transcription, J. Cell Sci., 110, 1147, 10.1242/jcs.110.10.1147 Wu, 2015, Dynamic pluripotent stem cell states and their applications, Cell Stem Cell, 17, 509, 10.1016/j.stem.2015.10.009 Yan, 2013, Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells, Nat. Struct. Mol. Biol., 20, 1131, 10.1038/nsmb.2660 Zhang, 2015, AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors, Nucleic Acids Res., 43, D76, 10.1093/nar/gku887 Zhou, 2012, HIF1alpha induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition, EMBO J., 31, 2103, 10.1038/emboj.2012.71 Zimmerlin, 2017, Capturing human naive pluripotency in the embryo and in the dish, Stem Cells Dev., 26, 1141, 10.1089/scd.2017.0055