Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency (original) (raw)
Plath, K. & Lowry, W. E. Progress in understanding reprogramming to the induced pluripotent state. Nat. Rev. Genet.12, 253–265 (2011). ArticleCAS Google Scholar
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell126, 663–676 (2006). ArticleCAS Google Scholar
Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature454, 49–55 (2008). ArticleCAS Google Scholar
Ang, Y-S. et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell145, 183–197 (2011). ArticleCAS Google Scholar
Gaspar-Maia, A. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature460, 863–868 (2009). ArticleCAS Google Scholar
Singhal, N. et al. Chromatin-remodeling components of the baf complex facilitate reprogramming. Cell141, 943–955 (2010). ArticleCAS Google Scholar
Wang, T. et al. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell9, 575–587 (2011). ArticleCAS Google Scholar
Liang, G., He, J. & Zhang, Y. Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nat. Cell Biol.14, 457–466 (2012). ArticleCAS Google Scholar
Onder, T. T. et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature483, 598–602 (2012). ArticleCAS Google Scholar
Chen, J. et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nature Genet.45, 34–42 (2013). ArticleCAS Google Scholar
Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell151, 994–1004 (2012). ArticleCAS Google Scholar
Mattout, A., Biran, A. & Meshorer, E. Global epigenetic changes during somatic cell reprogramming to iPS cells. J. Mol. Cell Biol.3, 341–350 (2011). Article Google Scholar
Maherali, N. et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell1, 55–70 (2007). ArticleCAS Google Scholar
Chin, M. H. et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell5, 111–123 (2009). ArticleCAS Google Scholar
Sridharan, R. et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell136, 364–377 (2009). ArticleCAS Google Scholar
Garcia, B. A. et al. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc.2, 933–938 (2007). ArticleCAS Google Scholar
Plazas-Mayorca, M. D. et al. One-pot shotgun quantitative mass spectrometry characterization of histones. J. Proteome Res.8, 5367–5374 (2009). ArticleCAS Google Scholar
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet.40, 897–903 (2008). ArticleCAS Google Scholar
Karmodiya, K. et al. H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genom.13, 424 (2013). Article Google Scholar
Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature470, 279–283 (2011). ArticleCAS Google Scholar
Xie, W. et al. Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol. Cell33, 417–427 (2009). ArticleCAS Google Scholar
Wang, Y. et al. Histone H3 lysine 14 acetylation is required for activation of a DNA damage checkpoint in fission yeast. J. Biol. Chem.287, 4386–4393 (2012). ArticleCAS Google Scholar
Meshorer, E. et al. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell10, 105–116 (2006). ArticleCAS Google Scholar
Hiratani, I. et al. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Gen. Res.20, 155–169 (2010). ArticleCAS Google Scholar
Steger, D. J. et al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol. Cell. Biol.28, 2825–2839 (2008). ArticleCAS Google Scholar
Krogan, N. J. et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol.23, 4207–4218 (2003). ArticleCAS Google Scholar
Zee, B. M. et al. In vivo residue-specific histone methylation dynamics. J. Biol. Chem.285, 3341–3350 (2010). ArticleCAS Google Scholar
Efroni, S. et al. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell2, 437–447 (2008). ArticleCAS Google Scholar
Golipour, A. et al. A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network. Stem Cell11, 769–782 (2012). CAS Google Scholar
Polo, J. M. et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell151, 1617–1632 (2012). ArticleCAS Google Scholar
Silva, J. et al. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol.6, e253 (2008). Article Google Scholar
Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature410, 120–124 (2001). ArticleCAS Google Scholar
Lachner, M., O’Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature410, 116–120 (2001). ArticleCAS Google Scholar
Kwon, S. H. & Workman, J. L. The changing faces of HP1: from heterochromatin formation and gene silencing to euchromatic gene expression. Bioessays33, 280–289 (2011). ArticleCAS Google Scholar
Smallwood, A. et al. CBX3 regulates efficient RNA processing genome-wide. Genome Res.22, 1426–1436 (2012). ArticleCAS Google Scholar
Bilodeau, S., Kagey, M. H., Frampton, G. M., Rahl, P. B. & Young, R. A. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev.23, 2484–2489 (2009). ArticleCAS Google Scholar
Yuan, P. et al. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev.23, 2507–2520 (2009). ArticleCAS Google Scholar
Cloos, P. A. C. et al. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature442, 307–311 (2006). ArticleCAS Google Scholar
Loh, Y. H., Zhang, W., Chen, X., George, J. & Ng, H. H. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev.21, 2545–2557 (2007). ArticleCAS Google Scholar
Ma, D. K., Chiang, C-H. J., Ponnusamy, K., Ming, G-L. & Song, H. G9a and Jhdm2a regulate embryonic stem cell fusion-induced reprogramming of adult neural stem cells. Stem Cell.26, 2131–2141 (2008). ArticleCAS Google Scholar
Li, R. et al. A mesenchymal-to-epithelial transition initiates and is requiredfor the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell7, 51–63 (2010). ArticleCAS Google Scholar
Ichida, J. K. et al. A small-molecule inhibitor of Tgf-β; signaling replaces Sox2 in reprogramming by inducing nanog. Cell Stem Cell5, 491–503 (2009). ArticleCAS Google Scholar
Silva, J. et al. Nanog is the gateway to the pluripotent ground state. Cell138, 722–737 (2009). ArticleCAS Google Scholar
Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature462, 595–601 (2009). ArticleCAS Google Scholar
Thomas, M. C. & Chiang, C-M. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol.41, 105–178 (2006). ArticleCAS Google Scholar
Griffiths, D. S. et al. LIF-independent JAK signalling to chromatin in embryonic stem cells uncovered from an adult stem cell disease. Nat. Cell Biol.13, 13–21 (2010). Article Google Scholar
Stadtfeld, M., Maherali, N., Breault, D. T. & Hochedlinger, K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell2, 230–240 (2008). ArticleCAS Google Scholar
Yin, H., Sweeney, S., Raha, D., Snyder, M. & Lin, H. A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. PLoS Genet.7, e1002380 (2011). ArticleCAS Google Scholar
Szabó, P. E., Hübner, K., Schöler, H. & Mann, J. R. Allele-specific expression of imprinted genes in mouse migratory primordial germ cells. Mech. Dev.115, 157–160 (2002). Article Google Scholar
Stadtfeld, M., Maherali, N., Borkent, M. & Hochedlinger, K. A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nature Meth.7, 53–55 (2009). Article Google Scholar
Beard, C., Hochedlinger, K., Plath, K., Wutz, A. & Jaenisch, R. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis44, 23–28 (2006). ArticleCAS Google Scholar
Okabe, S., Forsberg-Nilsson, K., Spiro, A. C., Segal, M. & McKay, R. D. Development of neuronal precursor cells and functional postmitotic neurons from embryonic stem cells in vitro. Mech. Dev.59, 89–102 (1996). ArticleCAS Google Scholar
Chen, X-F. et al. Mediator and SAGA have distinct roles in pol ii preinitiation complex assembly and function. Cell Rep.2, 1061–1067 (2012). ArticleCAS Google Scholar
Lin, J. J. et al. Mediator coordinates PIC assembly with recruitment of CHD1. Genes Dev.25, 2198–2209 (2011). ArticleCAS Google Scholar