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Evidence that gene activation and silencing during stem cell differentiation requires a transcriptionally paused intermediate state.

Golob JL, Kumar RM, Guenther MG, Pabon LM, Pratt GA, Loring JF, Laurent LC, Young RA, Murry CE.

PLoS One. 2011;6(8):e22416. doi: 10.1371/journal.pone.0022416. Epub 2011 Aug 19.


Dual roles of histone H3 lysine 9 acetylation in human embryonic stem cell pluripotency and neural differentiation.

Qiao Y, Wang R, Yang X, Tang K, Jing N.

J Biol Chem. 2015 Jan 23;290(4):2508-20. doi: 10.1074/jbc.M114.603761. Epub 2014 Dec 17. Erratum in: J Biol Chem. 2015 Apr 17;290(16):9949.


Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.

Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B.

Cell Res. 2011 Oct;21(10):1393-409. doi: 10.1038/cr.2011.146. Epub 2011 Aug 30.


Global transcription in pluripotent embryonic stem cells.

Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, Dash C, Bazett-Jones DP, Le Grice S, McKay RD, Buetow KH, Gingeras TR, Misteli T, Meshorer E.

Cell Stem Cell. 2008 May 8;2(5):437-47. doi: 10.1016/j.stem.2008.03.021.


Developmental pluripotency-associated 4 (DPPA4) localized in active chromatin inhibits mouse embryonic stem cell differentiation into a primitive ectoderm lineage.

Masaki H, Nishida T, Kitajima S, Asahina K, Teraoka H.

J Biol Chem. 2007 Nov 9;282(45):33034-42. Epub 2007 Sep 13.


Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation.

Binder H, Steiner L, Przybilla J, Rohlf T, Prohaska S, Galle J.

Phys Biol. 2013 Apr;10(2):026006. doi: 10.1088/1478-3975/10/2/026006. Epub 2013 Mar 12.


Generation of platform human embryonic stem cell lines that allow efficient targeting at a predetermined genomic location.

Liu Y, Thyagarajan B, Lakshmipathy U, Xue H, Lieu P, Fontes A, MacArthur CC, Scheyhing K, Rao MS, Chesnut JD.

Stem Cells Dev. 2009 Dec;18(10):1459-72. doi: 10.1089/scd.2009.0047.


Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.

Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT.

Genes Dev. 2011 Apr 1;25(7):742-54. doi: 10.1101/gad.2005511.


Corepressor for element-1-silencing transcription factor preferentially mediates gene networks underlying neural stem cell fate decisions.

Abrajano JJ, Qureshi IA, Gokhan S, Molero AE, Zheng D, Bergman A, Mehler MF.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16685-90. doi: 10.1073/pnas.0906917107. Epub 2010 Sep 7.


Developmentally programmed 3' CpG island methylation confers tissue- and cell-type-specific transcriptional activation.

Yu DH, Ware C, Waterland RA, Zhang J, Chen MH, Gadkari M, Kunde-Ramamoorthy G, Nosavanh LM, Shen L.

Mol Cell Biol. 2013 May;33(9):1845-58. doi: 10.1128/MCB.01124-12. Epub 2013 Mar 4.


A novel SALL4/OCT4 transcriptional feedback network for pluripotency of embryonic stem cells.

Yang J, Gao C, Chai L, Ma Y.

PLoS One. 2010 May 21;5(5):e10766. doi: 10.1371/journal.pone.0010766.


Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.

Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL.

Cell Stem Cell. 2007 Sep 13;1(3):286-98. doi: 10.1016/j.stem.2007.08.004.


Transcriptional and post-transcriptional regulation of retrotransposons IAP and MuERV-L affect pluripotency of mice ES cells.

Ramírez MA, Pericuesta E, Fernandez-Gonzalez R, Moreira P, Pintado B, Gutierrez-Adan A.

Reprod Biol Endocrinol. 2006 Nov 8;4:55.


Induction of intermediate mesoderm by retinoic acid receptor signaling from differentiating mouse embryonic stem cells.

Oeda S, Hayashi Y, Chan T, Takasato M, Aihara Y, Okabayashi K, Ohnuma K, Asashima M.

Int J Dev Biol. 2013;57(5):383-9. doi: 10.1387/ijdb.130058ma.


The "occlusis" model of cell fate restriction.

Lahn BT.

Bioessays. 2011 Jan;33(1):13-20. doi: 10.1002/bies.201000090. Epub 2010 Oct 15.


Rapid activation of the bivalent gene Sox21 requires displacement of multiple layers of gene-silencing machinery.

Chakravarthy H, Ormsbee BD, Mallanna SK, Rizzino A.

FASEB J. 2011 Jan;25(1):206-18. doi: 10.1096/fj.10-166926. Epub 2010 Sep 27.


The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin.

Bertani S, Sauer S, Bolotin E, Sauer F.

Mol Cell. 2011 Sep 16;43(6):1040-6. doi: 10.1016/j.molcel.2011.08.019. Retraction in: Mol Cell. 2015 Feb 5;57(3):572.


Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells.

Gan Q, Yoshida T, McDonald OG, Owens GK.

Stem Cells. 2007 Jan;25(1):2-9. Epub 2006 Oct 5. Review.


Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).

Lin C, Garrett AS, De Kumar B, Smith ER, Gogol M, Seidel C, Krumlauf R, Shilatifard A.

Genes Dev. 2011 Jul 15;25(14):1486-98. doi: 10.1101/gad.2059211.

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