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Volumn 528, Issue 7583, 2015, Pages 575-579

Competition between DNA methylation and transcription factors determines binding of NRF1

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CRE RECOMBINASE; CYTOSINE; DEOXYRIBONUCLEASE I; DINUCLEOTIDE; DNA METHYLTRANSFERASE; HISTONE H3; METHYLTRANSFERASE; TRANSCRIPTION FACTOR NRF1; CHROMATIN; NRF1 PROTEIN, MOUSE; NUCLEAR RESPIRATORY FACTOR 1; PROTEIN BINDING; TRANSCRIPTION FACTOR;

EID: 84951325892     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature16462     Document Type: Article
Times cited : (358)

References (54)
  • 1
    • 84906935775 scopus 로고    scopus 로고
    • Absence of a simple code: How transcription factors read the genome
    • Slattery, M. et al. Absence of a simple code: how transcription factors read the genome. Trends Biochem. Sci. 39, 381-399 (2014).
    • (2014) Trends Biochem. Sci. , vol.39 , pp. 381-399
    • Slattery, M.1
  • 2
    • 84918527386 scopus 로고    scopus 로고
    • Pioneer transcription factors in cell reprogramming
    • Iwafuchi-Doi, M. & Zaret, K. S. Pioneer transcription factors in cell reprogramming. Genes Dev. 28, 2679-2692 (2014).
    • (2014) Genes Dev. , vol.28 , pp. 2679-2692
    • Iwafuchi-Doi, M.1    Zaret, K.S.2
  • 3
    • 0027535235 scopus 로고
    • Effects of DNA methylation on DNA-binding proteins and gene expression
    • Tate, P. H. & Bird, A. P. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev. 3, 226-231 (1993).
    • (1993) Curr. Opin. Genet. Dev. , vol.3 , pp. 226-231
    • Tate, P.H.1    Bird, A.P.2
  • 4
    • 0023646729 scopus 로고
    • Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors
    • Becker, P. B., Ruppert, S. & Schütz, G. Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors. Cell 51, 435-443 (1987).
    • (1987) Cell , vol.51 , pp. 435-443
    • Becker, P.B.1    Ruppert, S.2    Schütz, G.3
  • 5
    • 0025816339 scopus 로고
    • Analysis of CpG methylation and genomic footprinting at the tyrosine aminotransferase gene: DNA methylation alone is not sufficient to prevent protein binding in vivo
    • Weih, F., Nitsch, D., Reik, A., Schütz, G. & Becker, P. B. Analysis of CpG methylation and genomic footprinting at the tyrosine aminotransferase gene: DNA methylation alone is not sufficient to prevent protein binding in vivo. EMBO J. 10, 2559-2567 (1991).
    • (1991) EMBO J. , vol.10 , pp. 2559-2567
    • Weih, F.1    Nitsch, D.2    Reik, A.3    Schütz, G.4    Becker, P.B.5
  • 6
    • 0034713375 scopus 로고    scopus 로고
    • Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
    • Bell, A. C. & Felsenfeld, G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482-485 (2000).
    • (2000) Nature , vol.405 , pp. 482-485
    • Bell, A.C.1    Felsenfeld, G.2
  • 7
    • 0034713275 scopus 로고    scopus 로고
    • CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
    • Hark, A. T. et al. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405, 486-489 (2000).
    • (2000) Nature , vol.405 , pp. 486-489
    • Hark, A.T.1
  • 8
    • 84355163093 scopus 로고    scopus 로고
    • DNA-binding factors shape the mouse methylome at distal regulatory regions
    • Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490-495 (2011).
    • (2011) Nature , vol.480 , pp. 490-495
    • Stadler, M.B.1
  • 9
    • 84941021874 scopus 로고    scopus 로고
    • Role of DNA methylation in modulating transcription factor occupancy
    • Maurano, M. T. et al. Role of DNA methylation in modulating transcription factor occupancy. Cell Rep. 12, 1184-1195 (2015).
    • (2015) Cell Rep. , vol.12 , pp. 1184-1195
    • Maurano, M.T.1
  • 10
    • 84892690160 scopus 로고    scopus 로고
    • Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions
    • Feldmann, A. et al. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet. 9, e1003994 (2013).
    • (2013) PLoS Genet. , vol.9
    • Feldmann, A.1
  • 11
    • 84892763878 scopus 로고    scopus 로고
    • Reversing DNA methylation: Mechanisms, genomics, and biological functions
    • Wu, H. & Zhang, Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156, 45-68 (2014).
    • (2014) Cell , vol.156 , pp. 45-68
    • Wu, H.1    Zhang, Y.2
  • 12
    • 84882884517 scopus 로고    scopus 로고
    • Charting a dynamic DNA methylation landscape of the human genome
    • Ziller, M. J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481 (2013).
    • (2013) Nature , vol.500 , pp. 477-481
    • Ziller, M.J.1
  • 13
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature Rev. Genet. 13, 484-492 (2012).
    • (2012) Nature Rev. Genet. , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 14
    • 84922621952 scopus 로고    scopus 로고
    • Function and information content of DNA methylation
    • Schübeler, D. Function and information content of DNA methylation. Nature 517, 321-326 (2015).
    • (2015) Nature , vol.517 , pp. 321-326
    • Schübeler, D.1
  • 15
    • 33745270104 scopus 로고    scopus 로고
    • Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b
    • Tsumura, A. et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805-814 (2006).
    • (2006) Genes Cells , vol.11 , pp. 805-814
    • Tsumura, A.1
  • 16
    • 79957844585 scopus 로고    scopus 로고
    • DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs
    • Karimi, M. M. et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8, 676-687 (2011).
    • (2011) Cell Stem Cell , vol.8 , pp. 676-687
    • Karimi, M.M.1
  • 17
    • 84865708757 scopus 로고    scopus 로고
    • An expansive human regulatory lexicon encoded in transcription factor footprints
    • Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012).
    • (2012) Nature , vol.489 , pp. 83-90
    • Neph, S.1
  • 18
    • 0027135555 scopus 로고
    • NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA-binding domain conserved in a family of developmental regulators
    • Virbasius, C. A., Virbasius, J. V. & Scarpulla, R. C. NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA-binding domain conserved in a family of developmental regulators. Genes Dev. 7, 2431-2445 (1993).
    • (1993) Genes Dev. , vol.7 , pp. 2431-2445
    • Virbasius, C.A.1    Virbasius, J.V.2    Scarpulla, R.C.3
  • 19
    • 0035830879 scopus 로고    scopus 로고
    • Interaction of the transcription factors USF1, USF2, and α-Pal/Nrf-1 with the FMR1 promoter. Implications for Fragile X mental retardation syndrome
    • Kumari, D. & Usdin, K. Interaction of the transcription factors USF1, USF2, and α-Pal/Nrf-1 with the FMR1 promoter. Implications for Fragile X mental retardation syndrome. J. Biol. Chem. 276, 4357-4364 (2001).
    • (2001) J. Biol. Chem. , vol.276 , pp. 4357-4364
    • Kumari, D.1    Usdin, K.2
  • 20
    • 84874771985 scopus 로고    scopus 로고
    • Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives
    • Spruijt, C. G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146-1159 (2013).
    • (2013) Cell , vol.152 , pp. 1146-1159
    • Spruijt, C.G.1
  • 21
    • 84884692057 scopus 로고    scopus 로고
    • DNA methylation presents distinct binding sites for human transcription factors
    • Hu, S.et al. DNA methylation presents distinct binding sites for human transcription factors. eLife 2, e00726 (2013).
    • (2013) eLife , vol.2
    • Hu, S.1
  • 22
    • 84876278080 scopus 로고    scopus 로고
    • Methylation-dependent and -independent genomic targeting principles of the MBD protein Family
    • Baubec, T., Ivanek, R., Lienert, F. & Schübeler, D. Methylation-dependent and -independent genomic targeting principles of the MBD protein Family. Cell 153, 480-492 (2013).
    • (2013) Cell , vol.153 , pp. 480-492
    • Baubec, T.1    Ivanek, R.2    Lienert, F.3    Schübeler, D.4
  • 23
    • 78649459828 scopus 로고    scopus 로고
    • Targets and dynamics of promoter DNA methylation during early mouse development
    • Borgel, J. et al. Targets and dynamics of promoter DNA methylation during early mouse development. Nature Genet. 42, 1093-1100 (2010).
    • (2010) Nature Genet. , vol.42 , pp. 1093-1100
    • Borgel, J.1
  • 24
    • 84884164554 scopus 로고    scopus 로고
    • FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency
    • Ficz, G. et al. FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 13, 351-359 (2013).
    • (2013) Cell Stem Cell , vol.13 , pp. 351-359
    • Ficz, G.1
  • 25
    • 84884133672 scopus 로고    scopus 로고
    • Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells
    • Habibi, E. et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 13, 360-369 (2013).
    • (2013) Cell Stem Cell , vol.13 , pp. 360-369
    • Habibi, E.1
  • 26
    • 84856528270 scopus 로고    scopus 로고
    • Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
    • Hon, G. C. et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 22, 246-258 (2012).
    • (2012) Genome Res. , vol.22 , pp. 246-258
    • Hon, G.C.1
  • 27
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
  • 28
    • 80054994283 scopus 로고    scopus 로고
    • Identification of genetic elements that autonomously determine DNA methylation states
    • Lienert, F. et al. Identification of genetic elements that autonomously determine DNA methylation states. Nature Genet. 43, 1091-1097 (2011).
    • (2011) Nature Genet. , vol.43 , pp. 1091-1097
    • Lienert, F.1
  • 29
    • 84923119852 scopus 로고    scopus 로고
    • High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
    • Krebs, A. R., Dessus-Babus, S., Burger, L. & Schübeler, D. High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. eLife 3, e04094 (2014).
    • (2014) eLife , vol.3
    • Krebs, A.R.1    Dessus-Babus, S.2    Burger, L.3    Schübeler, D.4
  • 30
    • 84893863046 scopus 로고    scopus 로고
    • Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
    • Sherwood, R. I. et al. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nature Biotechnol. 32, 171-178 (2014).
    • (2014) Nature Biotechnol. , vol.32 , pp. 171-178
    • Sherwood, R.I.1
  • 32
    • 0031694917 scopus 로고    scopus 로고
    • NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis
    • Chen, Z. F., Paquette, A. J. & Anderson, D. J. NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis. Nature Genet. 20, 136-142 (1998).
    • (1998) Nature Genet. , vol.20 , pp. 136-142
    • Chen, Z.F.1    Paquette, A.J.2    Anderson, D.J.3
  • 33
    • 34250192881 scopus 로고    scopus 로고
    • Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells
    • Bibel, M., Richter, J., Lacroix, E. & Barde, Y.-A. Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells. Nature Protocols 2, 1034-1043 (2007).
    • (2007) Nature Protocols , vol.2 , pp. 1034-1043
    • Bibel, M.1    Richter, J.2    Lacroix, E.3    Barde, Y.-A.4
  • 34
    • 84880845871 scopus 로고    scopus 로고
    • Genome-scale mapping of DNase I hypersensitivity
    • Chapter 27, Unit 21.27-21.27.20
    • John, S.et al. Genome-scale mapping of DNase I hypersensitivity. Curr. Protoc. Mol. Biol. Chapter 27, Unit 21.27-21.27.20 (2013).
    • (2013) Curr. Protoc. Mol. Biol.
    • John, S.1
  • 35
    • 84906302982 scopus 로고    scopus 로고
    • Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation
    • Jermann, P., Hoerner, L., Burger, L. & Schübeler, D. Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation. Proc. Natl Acad. Sci. USA 111, E3415-E3421 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. E3415-E3421
    • Jermann, P.1    Hoerner, L.2    Burger, L.3    Schübeler, D.4
  • 36
    • 0034458963 scopus 로고    scopus 로고
    • Genomic targeting of methylated DNA: Influence of methylation on transcription, replication, chromatin structure, and histone acetylation
    • Schübeler, D. et al. Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol. Cell. Biol. 20, 9103-9112 (2000).
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 9103-9112
    • Schübeler, D.1
  • 37
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-seq
    • Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 38
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 39
    • 84929144040 scopus 로고    scopus 로고
    • QuasR: Quantification and annotation of short reads in R
    • Gaidatzis, D., Lerch, A., Hahne, F. & Stadler, M. B. QuasR: quantification and annotation of short reads in R. Bioinformatics 31, 1130-1132 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 1130-1132
    • Gaidatzis, D.1    Lerch, A.2    Hahne, F.3    Stadler, M.B.4
  • 40
    • 0036079158 scopus 로고    scopus 로고
    • The Human Genome Browser at UCSC
    • Kent, W. J. et al. The Human Genome Browser at UCSC. Genome Res. 12, 996-1006 (2002).
    • (2002) Genome Res. , vol.12 , pp. 996-1006
    • Kent, W.J.1
  • 41
    • 84886038381 scopus 로고    scopus 로고
    • Identification of transcription factor binding sites from ChIP-seq data at high resolution
    • Bardet, A. F. et al. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics 29, 2705-2713 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2705-2713
    • Bardet, A.F.1
  • 42
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 43
    • 84857331867 scopus 로고    scopus 로고
    • Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
    • Xie, W. et al. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148, 816-831 (2012).
    • (2012) Cell , vol.148 , pp. 816-831
    • Xie, W.1
  • 44
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
    • (2005) Genome Res. , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 45
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin, A. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. D91-D94
    • Sandelin, A.1
  • 46
    • 84872540994 scopus 로고    scopus 로고
    • DNA-binding specificities of human transcription factors
    • Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013).
    • (2013) Cell , vol.152 , pp. 327-339
    • Jolma, A.1
  • 47
    • 58149200952 scopus 로고    scopus 로고
    • UniPROBE: An online database of protein binding microarray data on protein-DNA interactions
    • Newburger, D. E. & Bulyk, M. L. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 37, D77-D82 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. D77-D82
    • Newburger, D.E.1    Bulyk, M.L.2
  • 48
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: Application to sequence homology searches
    • Bailey, T. L. & Gribskov, M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54 (1998).
    • (1998) Bioinformatics , vol.14 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 49
    • 84860351082 scopus 로고    scopus 로고
    • The transcriptional and epigenomic foundations of ground state pluripotency
    • Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590-604 (2012).
    • (2012) Cell , vol.149 , pp. 590-604
    • Marks, H.1
  • 50
    • 84864216831 scopus 로고    scopus 로고
    • Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels
    • Tippmann, S. C. et al. Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol. Syst. Biol. 8, 593 (2012).
    • (2012) Mol. Syst. Biol. , vol.8 , pp. 593
    • Tippmann, S.C.1
  • 51
    • 84911462077 scopus 로고    scopus 로고
    • A comparative encyclopedia of DNA elements in the mouse genome
    • Yue, F. et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515, 355-364 (2014).
    • (2014) Nature , vol.515 , pp. 355-364
    • Yue, F.1
  • 52
    • 84871984418 scopus 로고    scopus 로고
    • Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
    • Arnold, P. et al. Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res. 23, 60-73 (2013).
    • (2013) Genome Res. , vol.23 , pp. 60-73
    • Arnold, P.1
  • 53
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1
  • 54
    • 48449084118 scopus 로고    scopus 로고
    • Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
    • Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-533 (2008).
    • (2008) Cell , vol.134 , pp. 521-533
    • Marson, A.1


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