Histone Variant H2A.X Deposition Pattern Serves as a Functional Epigenetic Mark for Distinguishing the Developmental Potentials of iPSCs

Adachi, 2013, Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells, Mol. Cell, 52, 380, 10.1016/j.molcel.2013.09.002 Banaszynski, 2010, Histone variants in metazoan development, Dev. Cell, 19, 662, 10.1016/j.devcel.2010.10.014 Bassing, 2002, Increased ionizing radiation sensitivity and genomic instability in the absence of histone H2AX, Proc. Natl. Acad. Sci. USA, 99, 8173, 10.1073/pnas.122228699 Bilodeau, 2009, SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state, Genes Dev., 23, 2484, 10.1101/gad.1837309 Bracken, 2006, Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions, Genes Dev., 20, 1123, 10.1101/gad.381706 Brinkman, 2012, Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk, Genome Res., 22, 1128, 10.1101/gr.133728.111 Buganim, 2013, Mechanisms and models of somatic cell reprogramming, Nat. Rev. Genet., 14, 427, 10.1038/nrg3473 Cahan, 2013, Origins and implications of pluripotent stem cell variability and heterogeneity, Nat. Rev. Mol. Cell Biol., 14, 357, 10.1038/nrm3584 Celeste, 2002, Genomic instability in mice lacking histone H2AX, Science, 296, 922, 10.1126/science.1069398 Fragola, 2013, Cell reprogramming requires silencing of a core subset of polycomb targets, PLoS Genet., 9, e1003292, 10.1371/journal.pgen.1003292 González, 2013, Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state, Cell Reports, 3, 651, 10.1016/j.celrep.2013.02.005 Haffner-Krausz, 1999, Expression of Fgfr2 in the early mouse embryo indicates its involvement in preimplantation development, Mech. Dev., 85, 167, 10.1016/S0925-4773(99)00082-9 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 Ivanova, 2006, Dissecting self-renewal in stem cells with RNA interference, Nature, 442, 533, 10.1038/nature04915 Koh, 2011, Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells, Cell Stem Cell, 8, 200, 10.1016/j.stem.2011.01.008 Liu, 2010, Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells, J. Biol. Chem., 285, 19483, 10.1074/jbc.M110.131995 Mager, 2003, Genome imprinting regulated by the mouse Polycomb group protein Eed, Nat. Genet., 33, 502, 10.1038/ng1125 Mahony, 2007, STAMP: a web tool for exploring DNA-binding motif similarities, Nucleic Acids Res., 35, W253, 10.1093/nar/gkm272 Marión, 2009, A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity, Nature, 460, 1149, 10.1038/nature08287 Matsui, 2010, Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET, Nature, 464, 927, 10.1038/nature08858 Micsinai, 2012, Picking ChIP-seq peak detectors for analyzing chromatin modification experiments, Nucleic Acids Res., 40, e70, 10.1093/nar/gks048 Müller, 2012, Overcoming reprogramming resistance of Fanconi anemia cells, Blood, 119, 5449, 10.1182/blood-2012-02-408674 Narsinh, 2011, Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells, J. Clin. Invest., 121, 1217, 10.1172/JCI44635 Ng, 2008, Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5, Nat. Cell Biol., 10, 1280, 10.1038/ncb1786 Nishiyama, 2009, Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors, Cell Stem Cell, 5, 420, 10.1016/j.stem.2009.07.012 Niwa, 2000, Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells, Nat. Genet., 24, 372, 10.1038/74199 Niwa, 2005, Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation, Cell, 123, 917, 10.1016/j.cell.2005.08.040 Oda, 2006, Trophoblast stem cells, Methods Enzymol., 419, 387, 10.1016/S0076-6879(06)19015-1 Orkin, 2011, Chromatin connections to pluripotency and cellular reprogramming, Cell, 145, 835, 10.1016/j.cell.2011.05.019 Rada-Iglesias, 2011, A unique chromatin signature uncovers early developmental enhancers in humans, Nature, 470, 279, 10.1038/nature09692 Ralston, 2010, Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2, Development, 137, 395, 10.1242/dev.038828 Redon, 2002, Histone H2A variants H2AX and H2AZ, Curr. Opin. Genet. Dev., 12, 162, 10.1016/S0959-437X(02)00282-4 Rossant, 2007, Stem cells and lineage development in the mammalian blastocyst, Reprod. Fertil. Dev., 19, 111, 10.1071/RD06125 Song, 2011, Identifying dispersed epigenomic domains from ChIP-Seq data, Bioinformatics, 27, 870, 10.1093/bioinformatics/btr030 Stadtfeld, 2010, Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells, Nature, 465, 175, 10.1038/nature09017 Stadtfeld, 2010, A reprogrammable mouse strain from gene-targeted embryonic stem cells, Nat. Methods, 7, 53, 10.1038/nmeth.1409 Strumpf, 2005, Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst, Development, 132, 2093, 10.1242/dev.01801 Yuan, 2009, Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells, Genes Dev., 23, 2507, 10.1101/gad.1831909