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Volumn 21, Issue 8, 2014, Pages 569-577

Chromatin properties of regulatory DNA probed by manipulation of transcription factors

Author keywords

chromatin modification; cis regulatory module; embryonic stem cells; enhancer; target genes; transcription factor binding site

Indexed keywords

CHROMATIN; DNA; HISTONE; TRANSCRIPTION FACTOR;

EID: 84905259973     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2013.0126     Document Type: Article
Times cited : (5)

References (41)
  • 1
    • 77957256578 scopus 로고    scopus 로고
    • OCT3/4 regulates transcription of histone deacetylase 4 (Hdac4) in mouse embryonic stem cells
    • Addis, R.C., Prasad, M.K., Yochem, R.L., et al. 2010. OCT3/4 regulates transcription of histone deacetylase 4 (Hdac4) in mouse embryonic stem cells. J. Cell Biochem. 111, 391-401.
    • (2010) J. Cell Biochem , vol.111 , pp. 391-401
    • Addis, R.C.1    Prasad, M.K.2    Yochem, R.L.3
  • 2
    • 65249110433 scopus 로고    scopus 로고
    • Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells
    • Aiba, K., Nedorezov, T., Piao, Y., et al. 2009. Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells. DNA Res. 16, 73-80.
    • (2009) DNA Res , vol.16 , pp. 73-80
    • Aiba, K.1    Nedorezov, T.2    Piao, Y.3
  • 3
    • 84874381107 scopus 로고    scopus 로고
    • Genome-wide quantitative enhancer activity maps identified by STARR-seq
    • Arnold, C.D., Gerlach, D., Stelzer, C., et al. 2013. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074-1077.
    • (2013) Science , vol.339 , pp. 1074-1077
    • Arnold, C.D.1    Gerlach, D.2    Stelzer, C.3
  • 4
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • Barski, A., Cuddapah, S., Cui, K., et al. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3
  • 5
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck, M.J., and Lieb, J.D. 2004. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349-360.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 6
    • 77951935861 scopus 로고    scopus 로고
    • Genome-wide MyoD binding in skeletal muscle cells: A potential for broad cellular reprogramming
    • Cao, Y., Yao, Z., Sarkar, D., et al. 2010. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev. Cell 18, 662-674.
    • (2010) Dev. Cell , vol.18 , pp. 662-674
    • Cao, Y.1    Yao, Z.2    Sarkar, D.3
  • 7
    • 48649091905 scopus 로고    scopus 로고
    • Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency
    • Chamberlain, S.J., Yee, D., and Magnuson, T. 2008. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells 26, 1496-1505.
    • (2008) Stem Cells , vol.26 , pp. 1496-1505
    • Chamberlain, S.J.1    Yee, D.2    Magnuson, T.3
  • 8
    • 84862163181 scopus 로고    scopus 로고
    • Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features
    • Chen, C.Y., Morris, Q., and Mitchell, J.A. 2012. Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics 13, 152.
    • (2012) BMC Genomics , vol.13 , pp. 152
    • Chen, C.Y.1    Morris, Q.2    Mitchell, J.A.3
  • 9
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen, X., Xu, H., Yuan, P., et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117.
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1    Xu, H.2    Yuan, P.3
  • 10
    • 41149174852 scopus 로고    scopus 로고
    • Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells
    • Cole, M.F., Johnstone, S.E., Newman, J.J., et al. 2008. Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev. 22, 746-755.
    • (2008) Genes Dev , vol.22 , pp. 746-755
    • Cole, M.F.1    Johnstone, S.E.2    Newman, J.J.3
  • 11
    • 84859736980 scopus 로고    scopus 로고
    • Generation of mouse ES cell lines engineered for the forced induction of transcription factors
    • Correa-Cerro, L.S., Piao, Y., Sharov, A.A., et al. 2011. Generation of mouse ES cell lines engineered for the forced induction of transcription factors. Sci. Rep. 1, 176.
    • (2011) Sci. Rep , vol.1 , pp. 176
    • Correa-Cerro, L.S.1    Piao, Y.2    Sharov, A.A.3
  • 12
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton, M.P., Cheng, A.W., Welstead, G.G., et al. 2010. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931-21936.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1    Cheng, A.W.2    Welstead, G.G.3
  • 13
    • 84855278198 scopus 로고    scopus 로고
    • Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development
    • Goke, J., Jung, M., Behrens, S., et al. 2012. Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Comput. Biol. 7, e1002304.
    • (2012) PLoS Comput. Biol , vol.7
    • Goke, J.1    Jung, M.2    Behrens, S.3
  • 14
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • Heintzman, N.D., Stuart, R.K., Hon, G., et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318.
    • (2007) Nat. Genet , vol.39 , pp. 311-318
    • Heintzman, N.D.1    Stuart, R.K.2    Hon, G.3
  • 15
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz, S., Benner, C., Spann, N., et al. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589.
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3
  • 16
    • 79961002967 scopus 로고    scopus 로고
    • EsBAF facilitates pluripotency by conditioning the genome for LIF/ STAT3 signalling and by regulating polycomb function
    • Ho, L., Miller, E.L., Ronan, J.L., et al. 2011. esBAF facilitates pluripotency by conditioning the genome for LIF/ STAT3 signalling and by regulating polycomb function. Nat. Cell Biol. 13, 903-913.
    • (2011) Nat. Cell Biol , vol.13 , pp. 903-913
    • Ho, L.1    Miller, E.L.2    Ronan, J.L.3
  • 17
    • 54949103985 scopus 로고    scopus 로고
    • REST regulates distinct transcriptional networks in embryonic and neural stem cells
    • Johnson, R., Teh, C.H., Kunarso, G., et al. 2008. REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biol. 6, e256.
    • (2008) PLoS Biol , vol.6
    • Johnson, R.1    Teh, C.H.2    Kunarso, G.3
  • 18
    • 77957139539 scopus 로고    scopus 로고
    • Mediator and cohesin connect gene expression and chromatin architecture
    • Kagey, M.H., Newman, J.J., Bilodeau, S., et al. 2010. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435.
    • (2010) Nature , vol.467 , pp. 430-435
    • Kagey, M.H.1    Newman, J.J.2    Bilodeau, S.3
  • 19
    • 84455208122 scopus 로고    scopus 로고
    • Mouse B-type lamins are required for proper organogenesis but not by embryonic stem cells
    • Kim, Y., Sharov, A.A., McDole, K., et al. 2011. Mouse B-type lamins are required for proper organogenesis but not by embryonic stem cells. Science 334, 1706-1710.
    • (2011) Science , vol.334 , pp. 1706-1710
    • Kim, Y.1    Sharov, A.A.2    McDole, K.3
  • 20
    • 76249102530 scopus 로고    scopus 로고
    • A genomewide study identifies the Wnt signaling pathway as a major target of p53 in murine embryonic stem cells
    • Lee, K.H., Li, M., Michalowski, A.M., et al. 2010. A genomewide study identifies the Wnt signaling pathway as a major target of p53 in murine embryonic stem cells. Proc. Natl. Acad. Sci. USA 107, 69-74.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 69-74
    • Lee, K.H.1    Li, M.2    Michalowski, A.M.3
  • 21
    • 44649086468 scopus 로고    scopus 로고
    • Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells
    • Liang, J., Wan, M., Zhang, Y., et al. 2008. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat. Cell Biol. 10, 731-739.
    • (2008) Nat. Cell Biol , vol.10 , pp. 731-739
    • Liang, J.1    Wan, M.2    Zhang, Y.3
  • 22
    • 15744367559 scopus 로고    scopus 로고
    • Kruppel-like factor 4 abrogates myocardin-induced activation of smooth muscle gene expression
    • Liu, Y., Sinha, S., McDonald, O.G., et al. 2005. Kruppel-like factor 4 abrogates myocardin-induced activation of smooth muscle gene expression. J. Biol. Chem. 280, 9719-9727.
    • (2005) J. Biol. Chem , vol.280 , pp. 9719-9727
    • Liu, Y.1    Sinha, S.2    McDonald, O.G.3
  • 23
    • 33645381936 scopus 로고    scopus 로고
    • The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    • Loh, Y.H., Wu, Q., Chew, J.L., et al. 2006. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38, 431-440.
    • (2006) Nat. Genet , vol.38 , pp. 431-440
    • Loh, Y.H.1    Wu, Q.2    Chew, J.L.3
  • 24
    • 48449084118 scopus 로고    scopus 로고
    • Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
    • Marson, A., Levine, S.S., Cole, M.F., et al. 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-533.
    • (2008) Cell , vol.134 , pp. 521-533
    • Marson, A.1    Levine, S.S.2    Cole, M.F.3
  • 25
    • 55149099432 scopus 로고    scopus 로고
    • Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling
    • Matoba, R., Niwa, H., Masui, S., et al. 2006. Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling. PLoS One 1, e26.
    • (2006) PLoS One , vol.1
    • Matoba, R.1    Niwa, H.2    Masui, S.3
  • 26
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineagecommitted cells
    • Mikkelsen, T.S., Ku, M., Jaffe, D.B., et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineagecommitted cells. Nature 448, 553-560.
    • (2007) Nature , vol.448 , pp. 553-560
    • Mikkelsen, T.S.1    Ku, M.2    Jaffe, D.B.3
  • 27
    • 84875126962 scopus 로고    scopus 로고
    • Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells
    • Nishiyama, A., Sharov, A.A., Piao, Y., et al. 2013. Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci. Rep. 3, 1390.
    • (2013) Sci. Rep , vol.3 , pp. 1390
    • Nishiyama, A.1    Sharov, A.A.2    Piao, Y.3
  • 28
    • 70349325798 scopus 로고    scopus 로고
    • Uncovering early response of gene regulatory networks in ES cells by systematic induction of transcription factors
    • Nishiyama, A., Xin, L., Sharov, A.A., et al. 2009. Uncovering early response of gene regulatory networks in ES cells by systematic induction of transcription factors. Cell Stem Cells 5, 420-433.
    • (2009) Cell Stem Cells , vol.5 , pp. 420-433
    • Nishiyama, A.1    Xin, L.2    Sharov, A.A.3
  • 29
    • 0034028901 scopus 로고    scopus 로고
    • Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
    • Niwa, H., Miyazaki, J., and Smith, A.G. 2000. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 24, 372-376.
    • (2000) Nat. Genet , vol.24 , pp. 372-376
    • Niwa, H.1    Miyazaki, J.2    Smith, A.G.3
  • 30
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • Rada-Iglesias, A., Bajpai, R., Swigut, T., et al. 2011. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283.
    • (2011) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1    Bajpai, R.2    Swigut, T.3
  • 31
    • 82055181847 scopus 로고    scopus 로고
    • Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
    • Rye, M., Saetrom, P., Handstad, T., and Drablos, F. 2011. Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. BMC Biol. 9, 80.
    • (2011) BMC Biol , vol.9 , pp. 80
    • Rye, M.1    Saetrom, P.2    Handstad, T.3    Drablos, F.4
  • 32
    • 77957344798 scopus 로고    scopus 로고
    • CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression
    • Schnetz, M.P., Handoko, L., Akhtar-Zaidi, B., et al. 2010. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 6, e1001023.
    • (2010) PLoS Genet , vol.6
    • Schnetz, M.P.1    Handoko, L.2    Akhtar-Zaidi, B.3
  • 33
    • 33750048444 scopus 로고    scopus 로고
    • CisView: A browser and database of cis-regulatory modules predicted in the mouse genome
    • Sharov, A.A., Dudekula, D.B., and Ko, M.S. 2006. CisView: a browser and database of cis-regulatory modules predicted in the mouse genome. DNA Res. 13, 123-134.
    • (2006) DNA Res , vol.13 , pp. 123-134
    • Sharov, A.A.1    Dudekula, D.B.2    Ko, M.S.3
  • 34
    • 45249117247 scopus 로고    scopus 로고
    • Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data
    • Sharov, A.A., Masui, S., Sharova, L.V., et al. 2008. Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics 9, 269.
    • (2008) BMC Genomics , vol.9 , pp. 269
    • Sharov, A.A.1    Masui, S.2    Sharova, L.V.3
  • 35
    • 77949900026 scopus 로고    scopus 로고
    • An Oct4-centered protein interaction network in embryonic stem cells
    • van den Berg, D.L., Snoek, T., Mullin, N.P., et al. 2010. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6, 369-381.
    • (2010) Cell Stem Cell , vol.6 , pp. 369-381
    • Van Den Berg, D.L.1    Snoek, T.2    Mullin, N.P.3
  • 36
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specific activity of enhancers
    • Visel, A., Blow, M.J., Li, Z., et al. 2009. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858.
    • (2009) Nature , vol.457 , pp. 854-858
    • Visel, A.1    Blow, M.J.2    Li, Z.3
  • 37
    • 75349104610 scopus 로고    scopus 로고
    • Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation
    • Walker, E., Chang, W.Y., Hunkapiller, J., et al. 2010. Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. Cell Stem Cell 6, 153-166.
    • (2010) Cell Stem Cell , vol.6 , pp. 153-166
    • Walker, E.1    Chang, W.Y.2    Hunkapiller, J.3
  • 38
    • 84861977900 scopus 로고    scopus 로고
    • Comparative epigenomic annotation of regulatory DNA
    • Xiao, S., Xie, D., Cao, X., et al. 2012. Comparative epigenomic annotation of regulatory DNA. Cell 149, 1381-1392.
    • (2012) Cell , vol.149 , pp. 1381-1392
    • Xiao, S.1    Xie, D.2    Cao, X.3
  • 39
    • 80051571400 scopus 로고    scopus 로고
    • Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
    • Yu, H.B., Johnson, R., Kunarso, G., and Stanton, L.W. 2011. Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells. Genome Res. 21, 1284-1293.
    • (2011) Genome Res , vol.21 , pp. 1284-1293
    • Yu, H.B.1    Johnson, R.2    Kunarso, G.3    Stanton, L.W.4
  • 40
    • 80051564877 scopus 로고    scopus 로고
    • Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
    • Zentner, G.E., Tesar, P.J., and Scacheri, P.C. 2011. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 21, 1273-1283.
    • (2011) Genome Res , vol.21 , pp. 1273-1283
    • Zentner, G.E.1    Tesar, P.J.2    Scacheri, P.C.3
  • 41
    • 66149140599 scopus 로고    scopus 로고
    • Critical roles of coactivator p300 in mouse embryonic stem cell differentiation and Nanog expression
    • Zhong, X., and Jin, Y. 2009. Critical roles of coactivator p300 in mouse embryonic stem cell differentiation and Nanog expression. J. Biol. Chem. 284, 9168-9175.
    • (2009) J. Biol. Chem , vol.284 , pp. 9168-9175
    • Zhong, X.1    Jin, Y.2


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