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Volumn 24, Issue 8, 2014, Pages 1285-1295

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; ENZYME; TET1 ENZYME; TRANSCRIPTION FACTOR CTCF; UNCLASSIFIED DRUG; CCCTC-BINDING FACTOR; DNA BINDING PROTEIN; NUCLEOSOME; ONCOPROTEIN; PROTEIN BINDING; REPRESSOR PROTEIN; TET1 PROTEIN, MOUSE;

EID: 84905452505     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.164418.113     Document Type: Article
Times cited : (119)

References (69)
  • 1
    • 84876278080 scopus 로고    scopus 로고
    • Methylation-dependent and -independent genomic targeting principles of the MBD protein family
    • Baubec T, Ivanek R, Lienert F, Schubeler D. 2013. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 153: 480-492.
    • (2013) Cell , vol.153 , pp. 480-492
    • Baubec, T.1    Ivanek, R.2    Lienert, F.3    Schubeler, D.4
  • 2
    • 84865320061 scopus 로고    scopus 로고
    • Concise review: Chromatin and genome organization in reprogramming
    • Biran A, Meshorer E. 2012. Concise review: chromatin and genome organization in reprogramming. Stem Cells 30: 1793-1799.
    • (2012) Stem Cells , vol.30 , pp. 1793-1799
    • Biran, A.1    Meshorer, E.2
  • 6
    • 77957174102 scopus 로고    scopus 로고
    • Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
    • Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS. 2010. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated. BMC Genomics 11: 519.
    • (2010) BMC Genomics , vol.11 , pp. 519
    • Choy, M.K.1    Movassagh, M.2    Goh, H.G.3    Bennett, M.R.4    Down, T.A.5    Foo, R.S.6
  • 9
    • 84892690160 scopus 로고    scopus 로고
    • Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions
    • Feldmann A, Ivanek R, Murr R, Gaidatzis D, Burger L, Schubeler D. 2013. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet 9: e1003994.
    • (2013) PLoS Genet , vol.9
    • Feldmann, A.1    Ivanek, R.2    Murr, R.3    Gaidatzis, D.4    Burger, L.5    Schubeler, D.6
  • 12
    • 84877108379 scopus 로고    scopus 로고
    • DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exonintron structure
    • Gelfman S, Cohen N, Yearim A, Ast G. 2013. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exonintron structure. Genome Res 23: 789-799.
    • (2013) Genome Res , vol.23 , pp. 789-799
    • Gelfman, S.1    Cohen, N.2    Yearim, A.3    Ast, G.4
  • 13
    • 76749107562 scopus 로고    scopus 로고
    • Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local
    • Goh WS, Orlov Y, Li J, Clarke ND. 2010. Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6: e1000649.
    • (2010) PLoS Comput Biol , vol.6
    • Goh, W.S.1    Orlov, Y.2    Li, J.3    Clarke, N.D.4
  • 14
    • 70350731108 scopus 로고    scopus 로고
    • Distinguishing direct versus indirect transcription factor-DNA interactions
    • Gordan R, Hartemink AJ, Bulyk ML. 2009.Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 19: 2090-2100.
    • (2009) Genome Res , vol.19 , pp. 2090-2100
    • Gordan, R.1    Hartemink, A.J.2    Bulyk, M.L.3
  • 18
    • 84873581550 scopus 로고    scopus 로고
    • H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
    • Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K. 2013a. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 12: 180-192.
    • (2013) Cell Stem Cell , vol.12 , pp. 180-192
    • Hu, G.1    Cui, K.2    Northrup, D.3    Liu, C.4    Wang, C.5    Tang, Q.6    Ge, K.7    Levens, D.8    Crane-Robinson, C.9    Zhao, K.10
  • 20
    • 84896324622 scopus 로고    scopus 로고
    • Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes
    • Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 156: 1286-1297.
    • (2014) Cell , vol.156 , pp. 1286-1297
    • Huff, J.T.1    Zilberman, D.2
  • 23
    • 79952273012 scopus 로고    scopus 로고
    • Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
    • Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. 2011. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet 7: e1001290.
    • (2011) PLoS Genet , vol.7
    • Kaplan, T.1    Li, X.Y.2    Sabo, P.J.3    Thomas, S.4    Stamatoyannopoulos, J.A.5    Biggin, M.D.6    Eisen, M.B.7
  • 25
    • 84870552401 scopus 로고    scopus 로고
    • Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
    • Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. 2012. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22: 2497-2506.
    • (2012) Genome Res , vol.22 , pp. 2497-2506
    • Kelly, T.K.1    Liu, Y.2    Lay, F.D.3    Liang, G.4    Berman, B.P.5    Jones, P.A.6
  • 26
    • 79953709415 scopus 로고    scopus 로고
    • The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
    • Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. 2011. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol 12: R34.
    • (2011) Genome Biol , vol.12
    • Li, X.Y.1    Thomas, S.2    Sabo, P.J.3    Eisen, M.B.4    Stamatoyannopoulos, J.A.5    Biggin, M.D.6
  • 27
    • 84871539869 scopus 로고    scopus 로고
    • Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation
    • Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH. 2012. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell 151: 1608-1616.
    • (2012) Cell , vol.151 , pp. 1608-1616
    • Li, Z.1    Gadue, P.2    Chen, K.3    Jiao, Y.4    Tuteja, G.5    Schug, J.6    Li, W.7    Kaestner, K.H.8
  • 28
    • 84859582058 scopus 로고    scopus 로고
    • Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
    • Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD. 2012. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484: 251-255.
    • (2012) Nature , vol.484 , pp. 251-255
    • Lickwar, C.R.1    Mueller, F.2    Hanlon, S.E.3    McNally, J.G.4    Lieb, J.D.5
  • 29
    • 78650445679 scopus 로고    scopus 로고
    • High-throughput sequencing reveals a simple model of nucleosome energetics
    • Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV. 2010. High-throughput sequencing reveals a simple model of nucleosome energetics. Proc Natl Acad Sci 107: 20998-21003.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 20998-21003
    • Locke, G.1    Tolkunov, D.2    Moqtaderi, Z.3    Struhl, K.4    Morozov, A.V.5
  • 30
    • 84890504504 scopus 로고    scopus 로고
    • Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
    • Luu PL, Scholer HR, Arauzo-BravoMJ. 2013. Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs. Genome Res 23: 2013-2029.
    • (2013) Genome Res , vol.23 , pp. 2013-2029
    • Luu, P.L.1    Scholer, H.R.2    Arauzo-Bravo, M.J.3
  • 32
    • 84875127327 scopus 로고    scopus 로고
    • CTCF and cohesin: Linking gene regulatory elements with their targets
    • Merkenschlager M, Odom DT. 2013. CTCF and cohesin: linking gene regulatory elements with their targets. Cell 152: 1285-1297.
    • (2013) Cell , vol.152 , pp. 1285-1297
    • Merkenschlager, M.1    Odom, D.T.2
  • 33
    • 36949023082 scopus 로고    scopus 로고
    • A nucleosome-guided map of transcription factor binding sites in yeast
    • Narlikar L, Gordan R, Hartemink AJ. 2007. A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol 3: e215.
    • (2007) PLoS Comput Biol , vol.3
    • Narlikar, L.1    Gordan, R.2    Hartemink, A.J.3
  • 34
    • 84878260646 scopus 로고    scopus 로고
    • TETonic shift: Biological roles of TET proteins in DNA demethylation and transcription
    • Pastor WA, Aravind L, Rao A. 2013. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol 14: 341-356.
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 341-356
    • Pastor, W.A.1    Aravind, L.2    Rao, A.3
  • 37
    • 84888373028 scopus 로고    scopus 로고
    • DNA methylation determines nucleosome occupancy in the 5′-CpG islands of tumor suppressor genes
    • Portela A, Liz J, Nogales V, Setien F, Villanueva A, Esteller M. 2013. DNA methylation determines nucleosome occupancy in the 5′-CpG islands of tumor suppressor genes. Oncogene 32: 5421-5428.
    • (2013) Oncogene , vol.32 , pp. 5421-5428
    • Portela, A.1    Liz, J.2    Nogales, V.3    Setien, F.4    Villanueva, A.5    Esteller, M.6
  • 38
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 40
    • 68049083831 scopus 로고    scopus 로고
    • Incorporating nucleosomes into thermodynamic models of transcription regulation
    • Raveh-Sadka T, Levo M, Segal E. 2009. Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19: 1480-1496.
    • (2009) Genome Res , vol.19 , pp. 1480-1496
    • Raveh-Sadka, T.1    Levo, M.2    Segal, E.3
  • 42
    • 84875167169 scopus 로고    scopus 로고
    • Non-canonical functions of the DNA methylome in gene regulation
    • Reddington JP, Pennings S, Meehan RR. 2013. Non-canonical functions of the DNA methylome in gene regulation. Biochem J 451: 13-23.
    • (2013) Biochem J , vol.451 , pp. 13-23
    • Reddington, J.P.1    Pennings, S.2    Meehan, R.R.3
  • 43
    • 33846700587 scopus 로고    scopus 로고
    • Predicting transcription factor affinities to DNA from a biophysical model
    • DOI 10.1093/bioinformatics/btl565
    • Roider HG, Kanhere A, Manke T, Vingron M. 2007. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23: 134-141. (Pubitemid 46189601)
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 134-141
    • Roider, H.G.1    Kanhere, A.2    Manke, T.3    Vingron, M.4
  • 45
    • 84876946045 scopus 로고    scopus 로고
    • Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics
    • Shen L, Wu H, Diep D, Yamaguchi S, D'Alessio AC, Fung HL, Zhang K, Zhang Y. 2013. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153: 692-706.
    • (2013) Cell , vol.153 , pp. 692-706
    • Shen, L.1    Wu, H.2    Diep, D.3    Yamaguchi, S.4    D'Alessio, A.C.5    Fung, H.L.6    Zhang, K.7    Zhang, Y.8
  • 46
    • 84874194072 scopus 로고    scopus 로고
    • DNA methylation: Roles in mammalian development
    • Smith ZD, Meissner A. 2013. DNA methylation: roles in mammalian development. Nat Rev Genet 14: 204-220.
    • (2013) Nat Rev Genet , vol.14 , pp. 204-220
    • Smith, Z.D.1    Meissner, A.2
  • 51
    • 84876580885 scopus 로고    scopus 로고
    • Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method
    • Tan L, Xiong L, Xu W, Wu F, Huang N, Xu Y, Kong L, Zheng L, Schwartz L, Shi Y, et al. 2013. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res 41: e84.
    • (2013) Nucleic Acids Res , vol.41
    • Tan, L.1    Xiong, L.2    Xu, W.3    Wu, F.4    Huang, N.5    Xu, Y.6    Kong, L.7    Zheng, L.8    Schwartz, L.9    Shi, Y.10
  • 52
    • 34547128905 scopus 로고    scopus 로고
    • General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: Application to OR operator of phage l
    • Teif VB. 2007. General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage l. Nucleic Acids Res 35: e80.
    • (2007) Nucleic Acids Res , vol.35
    • Teif, V.B.1
  • 53
    • 77950669526 scopus 로고    scopus 로고
    • Predicting gene-regulation functions: Lessons from temperate bacteriophages
    • Teif VB. 2010. Predicting gene-regulation functions: lessons from temperate bacteriophages. Biophys J 98: 1247-1256.
    • (2010) Biophys J , vol.98 , pp. 1247-1256
    • Teif, V.B.1
  • 54
    • 84858266682 scopus 로고    scopus 로고
    • Calculating transcription factor binding maps for chromatin
    • Teif VB, Rippe K. 2012. Calculating transcription factor binding maps for chromatin. Brief Bioinform 13: 187-201.
    • (2012) Brief Bioinform , vol.13 , pp. 187-201
    • Teif, V.B.1    Rippe, K.2
  • 58
    • 84877795975 scopus 로고    scopus 로고
    • The role of chromatin insulators in nuclear architecture and genome function
    • Van Bortle K, Corces VG. 2013. The role of chromatin insulators in nuclear architecture and genome function. Curr Opin Genet Dev 23: 212-218.
    • (2013) Curr Opin Genet Dev , vol.23 , pp. 212-218
    • Van Bortle, K.1    Corces, V.G.2
  • 59
    • 84860370054 scopus 로고    scopus 로고
    • Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells
    • Vella P, Barozzi I, Cuomo A, Bonaldi T, Pasini D. 2012. Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic Acids Res 40: 3403-3418.
    • (2012) Nucleic Acids Res , vol.40 , pp. 3403-3418
    • Vella, P.1    Barozzi, I.2    Cuomo, A.3    Bonaldi, T.4    Pasini, D.5
  • 61
    • 70350741354 scopus 로고    scopus 로고
    • An ensemble model of competitive multifactor binding of the genome
    • Wasson T, Hartemink AJ. 2009. An ensemble model of competitive multifactor binding of the genome. Genome Res 19: 2101-2112.
    • (2009) Genome Res , vol.19 , pp. 2101-2112
    • Wasson, T.1    Hartemink, A.J.2
  • 66
    • 79955948324 scopus 로고    scopus 로고
    • Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells
    • Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, et al. 2011. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell 42: 451-464.
    • (2011) Mol Cell , vol.42 , pp. 451-464
    • Xu, Y.1    Wu, F.2    Tan, L.3    Kong, L.4    Xiong, L.5    Deng, J.6    Barbera, A.J.7    Zheng, L.8    Zhang, H.9    Huang, S.10
  • 69
    • 79959359483 scopus 로고    scopus 로고
    • Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
    • Zhou X, O'Shea EK. 2011. Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol Cell 42: 826-836.
    • (2011) Mol Cell , vol.42 , pp. 826-836
    • Zhou, X.1    O'Shea, E.K.2


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