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Volumn 24, Issue 7, 2014, Pages 1138-1146

Extreme HOT regions are CpG-dense promoters in C. elegans and humans

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; HISTONE H3; TRANSCRIPTION FACTOR; HISTONE; NUCLEOSOME; PROTEIN BINDING;

EID: 84904262426     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.161992.113     Document Type: Article
Times cited : (45)

References (63)
  • 2
    • 39449088247 scopus 로고    scopus 로고
    • Human CpG binding protein interacts with MLL1, MLL2 and hSet1 and regulates Hox gene expression
    • Ansari KI, Mishra BP, Mandal SS. 2008. Human CpG binding protein interacts with MLL1, MLL2 and hSet1 and regulates Hox gene expression. Biochim Biophys Acta 1779: 66-73.
    • (2008) Biochim Biophys Acta , vol.1779 , pp. 66-73
    • Ansari, K.I.1    Mishra, B.P.2    Mandal, S.S.3
  • 3
    • 0033539168 scopus 로고    scopus 로고
    • CpG islands as genomic footprints of promoters that are associated with replication origins
    • DOI 10.1016/S0960-9822(99)80418-7
    • Antequera F, Bird A. 1999. CpG islands as genomic footprints of promoters that are associated with replication origins. Curr Biol 9: R661-R667. (Pubitemid 29442475)
    • (1999) Current Biology , vol.9 , Issue.17
    • Antequera, F.1    Bird, A.2
  • 4
    • 0024295763 scopus 로고
    • C. elegans mRNAs acquire a spliced leader through a trans-splicing mechanism
    • Bektesh SL, Hirsh DI. 1988. C. elegans mRNAs acquire a spliced leader through a trans-splicing mechanism. Nucleic Acids Res 16: 5692.
    • (1988) Nucleic Acids Res , vol.16 , pp. 5692
    • Bektesh, S.L.1    Hirsh, D.I.2
  • 5
    • 0022540321 scopus 로고
    • CpG-rich islands and the function of DNA methylation
    • Bird AP. 1986. CpG-rich islands and the function of DNA methylation. Nature 321: 209-213. (Pubitemid 16016411)
    • (1986) Nature , vol.321 , Issue.6067 , pp. 209-213
    • Bird, A.P.1
  • 6
    • 0022000776 scopus 로고
    • A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA
    • Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. 1985. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40: 91-99. (Pubitemid 15169310)
    • (1985) Cell , vol.40 , Issue.1 , pp. 91-99
    • Bird, A.1    Taggart, M.2    Frommer, M.3
  • 7
    • 0028965514 scopus 로고
    • Trans-splicing and polycistronic transcription in Caenorhabditis elegans
    • Blumenthal T. 1995. Trans-splicing and polycistronic transcription in Caenorhabditis elegans. Trends Genet 11: 132-136.
    • (1995) Trends Genet , vol.11 , pp. 132-136
    • Blumenthal, T.1
  • 9
    • 0016063911 scopus 로고
    • The genetics of Caenorhabditis elegans
    • Brenner S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71-94.
    • (1974) Genetics , vol.77 , pp. 71-94
    • Brenner, S.1
  • 10
    • 52749095587 scopus 로고    scopus 로고
    • CFP1 interacts with DNMT1 independently of association with the Setd1 Histone H3K4 methyltransferase complexes
    • Butler JS, Lee JH, Skalnik DG. 2008. CFP1 interacts with DNMT1 independently of association with the Setd1 Histone H3K4 methyltransferase complexes. DNA Cell Biol 27: 533-543.
    • (2008) DNA Cell Biol , vol.27 , pp. 533-543
    • Butler, J.S.1    Lee, J.H.2    Skalnik, D.G.3
  • 11
    • 18444361838 scopus 로고    scopus 로고
    • DNA methylation and chromatin structure: The puzzling CpG islands
    • DOI 10.1002/jcb.20325
    • Caiafa P, Zampieri M. 2005. DNA methylation and chromatin structure: the puzzling CpG islands. J Cell Biochem 94: 257-265. (Pubitemid 41420304)
    • (2005) Journal of Cellular Biochemistry , vol.94 , Issue.2 , pp. 257-265
    • Caiafa, P.1    Zampieri, M.2
  • 12
    • 0032948005 scopus 로고    scopus 로고
    • Synergy of demethylation and histone deacetylase inhibition in the re- expression of genes silenced in cancer
    • DOI 10.1038/5047
    • Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB. 1999. Synergy of demethylation and histone deacetylase inhibition in the reexpression of genes silenced in cancer. Nat Genet 21: 103-107. (Pubitemid 29036293)
    • (1999) Nature Genetics , vol.21 , Issue.1 , pp. 103-107
    • Cameron, E.E.1    Bachman, K.E.2    Myohanen, S.3    Herman, J.G.4    Baylin, S.B.5
  • 14
    • 80052990473 scopus 로고    scopus 로고
    • Systematic bias in high-throughput sequencing data and its correction by BEADS
    • Cheung MS, Down TA, Latorre I, Ahringer J. 2011. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res 39: e103.
    • (2011) Nucleic Acids Res , vol.39
    • Cheung, M.S.1    Down, T.A.2    Latorre, I.3    Ahringer, J.4
  • 15
    • 0024342297 scopus 로고
    • Cytosine methylation and the fate of CpG dinucleotides in vertebrates genomes
    • Cooper DN, Krawczak M. 1989. Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum Genet 83: 181-188. (Pubitemid 19234570)
    • (1989) Human Genetics , vol.83 , Issue.2 , pp. 181-188
    • Cooper, D.N.1    Krawczak, M.2
  • 16
    • 79956330964 scopus 로고    scopus 로고
    • CpG islands and the regulation of transcription
    • Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes Dev 25: 1010-1022.
    • (2011) Genes Dev , vol.25 , pp. 1010-1022
    • Deaton, A.M.1    Bird, A.2
  • 17
    • 0019198357 scopus 로고
    • Mutagenic deamination of cytosine residues in DNA
    • DOI 10.1038/287560a0
    • Duncan BK, Miller JH. 1980. Mutagenic deamination of cytosine residues in DNA. Nature 287: 560-561. (Pubitemid 11232861)
    • (1980) Nature , vol.287 , Issue.5782 , pp. 560-561
    • Duncan, B.K.1    Miller, J.H.2
  • 18
    • 0025268279 scopus 로고
    • Spontaneous deamination of cytosine and 5-methylcytosine residues in DNA and replacement of 5-methylcytosine residues with cytosine residues
    • Ehrlich M, Zhang XY, Inamdar NM. 1990. Spontaneous deamination of cytosine and 5-methylcytosine residues in DNA and replacement of 5-methylcytosine residues with cytosine residues. Mutat Res 238: 277-286.
    • (1990) Mutat Res , vol.238 , pp. 277-286
    • Ehrlich, M.1    Zhang, X.Y.2    Inamdar, N.M.3
  • 19
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 20
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of DNA elements (ENCODE)
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
    • (2011) PLoS Biol , vol.9
  • 21
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 22
    • 80051992044 scopus 로고    scopus 로고
    • Using MACS to identify peaks from ChIP-Seq data
    • Feng J, Liu T, Zhang Y. 2011. Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinformatics 34: 2.14.1-2.14.14.
    • (2011) Curr Protoc Bioinformatics , vol.34
    • Feng, J.1    Liu, T.2    Zhang, Y.3
  • 28
    • 67349255210 scopus 로고    scopus 로고
    • CpG islands-'a rough guide'
    • Illingworth RS, Bird AP. 2009. CpG islands-'a rough guide'. FEBS Lett 583: 1713-1720.
    • (2009) FEBS Lett , vol.583 , pp. 1713-1720
    • Illingworth, R.S.1    Bird, A.P.2
  • 30
    • 78649513916 scopus 로고    scopus 로고
    • Mammalian methyl-binding proteins: What might they do?
    • Joulie M, Miotto B, Defossez PA. 2010. Mammalian methyl-binding proteins: what might they do? Bioessays 32: 1025-1032.
    • (2010) Bioessays , vol.32 , pp. 1025-1032
    • Joulie, M.1    Miotto, B.2    Defossez, P.A.3
  • 31
    • 32344450824 scopus 로고    scopus 로고
    • Genomic DNA methylation: The mark and its mediators
    • DOI 10.1016/j.tibs.2005.12.008, PII S096800040500352X
    • Klose RJ, Bird AP. 2006. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: 89-97. (Pubitemid 43221841)
    • (2006) Trends in Biochemical Sciences , vol.31 , Issue.2 , pp. 89-97
    • Klose, R.J.1    Bird, A.P.2
  • 33
    • 84879288762 scopus 로고    scopus 로고
    • Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation
    • Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ. 2013. Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Elife 2: e00808.
    • (2013) Elife , vol.2
    • Kruesi, W.S.1    Core, L.J.2    Waters, C.T.3    Lis, J.T.4    Meyer, B.J.5
  • 34
    • 84860503075 scopus 로고    scopus 로고
    • HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
    • Kvon EZ, Stampfel G, Yáñez-Cuna JO, Dickson BJ, Stark A. 2012. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev 26: 908-913.
    • (2012) Genes Dev , vol.26 , pp. 908-913
    • Kvon, E.Z.1    Stampfel, G.2    Yáñez-Cuna, J.O.3    Dickson, B.J.4    Stark, A.5
  • 35
    • 29244438472 scopus 로고    scopus 로고
    • 4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex
    • 4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 280: 41725-41731.
    • (2005) J Biol Chem , vol.280 , pp. 41725-41731
    • Lee, J.H.1    Skalnik, D.G.2
  • 36
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 37
    • 79953741829 scopus 로고    scopus 로고
    • A role for Set1/MLL-related components in epigenetic regulation of the Caenorhabditis elegans germ line
    • Li T, Kelly WG. 2011. A role for Set1/MLL-related components in epigenetic regulation of the Caenorhabditis elegans germ line. PLoS Genet 7:e1001349.
    • (2011) PLoS Genet , vol.7
    • Li, T.1    Kelly, W.G.2
  • 41
    • 78650331647 scopus 로고    scopus 로고
    • Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • The modENCODE Project Consortium
    • The modENCODE Project Consortium. 2010. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
    • (2010) Science , vol.330 , pp. 1787-1797
  • 42
    • 0032574977 scopus 로고    scopus 로고
    • Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
    • DOI 10.1038/30764
    • Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386-389. (Pubitemid 28269714)
    • (1998) Nature , vol.393 , Issue.6683 , pp. 386-389
    • Nan, X.1    Ng, H.-H.2    Johnson, C.A.3    Laherty, C.D.4    Turner, B.M.5    Eisenman, R.N.6    Bird, A.7
  • 45
    • 77951160864 scopus 로고    scopus 로고
    • A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans
    • Ooi SL, Henikoff JG, Henikoff S. 2010. A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res 38: e26.
    • (2010) Nucleic Acids Res , vol.38
    • Ooi, S.L.1    Henikoff, J.G.2    Henikoff, S.3
  • 47
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • Ramskold D, Wang ET, Burge CB, Sandberg R. 2009. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5: e1000598.
    • (2009) PLoS Comput Biol , vol.5
    • Ramskold, D.1    Wang, E.T.2    Burge, C.B.3    Sandberg, R.4
  • 50
    • 36549031782 scopus 로고    scopus 로고
    • Antagonistic functions of SET-2/SET1 and HPL/HP1 proteins in C. elegans development
    • DOI 10.1016/j.ydbio.2007.09.035, PII S0012160607013899
    • Simonet T, Dulermo R, Schott S, Palladino F. 2007. Antagonistic functions of SET-2/SET1 and HPL/HP1 proteins in C. elegans development. Dev Biol 312: 367-383. (Pubitemid 350180764)
    • (2007) Developmental Biology , vol.312 , Issue.1 , pp. 367-383
    • Simonet, T.1    Dulermo, R.2    Schott, S.3    Palladino, F.4
  • 51
    • 0023057540 scopus 로고
    • Caenorhabditis elegans DNA does not contain 5-methylcytosine at any time during development or aging
    • Simpson VJ, Johnson TE, Hammen RF. 1986. Caenorhabditis elegans DNA does not contain 5-methylcytosine at any time during development or aging. Nucleic Acids Res 14: 6711-6719.
    • (1986) Nucleic Acids Res , vol.14 , pp. 6711-6719
    • Simpson, V.J.1    Johnson, T.E.2    Hammen, R.F.3
  • 53
    • 73649129275 scopus 로고    scopus 로고
    • CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin
    • Tate CM, Lee JH, Skalnik DG. 2010. CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin. FEBS J 277: 210-223.
    • (2010) FEBS J , vol.277 , pp. 210-223
    • Tate, C.M.1    Lee, J.H.2    Skalnik, D.G.3
  • 57
    • 84869880642 scopus 로고    scopus 로고
    • Human genes with CpG island promoters have a distinct transcription-associated chromatin organization
    • Vavouri T, Lehner B. 2012. Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol 13: R110.
    • (2012) Genome Biol , vol.13
    • Vavouri, T.1    Lehner, B.2
  • 60
    • 79952473660 scopus 로고    scopus 로고
    • The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain
    • Xu C, Bian C, Lam R, Dong A, Min J. 2011. The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain. Nat Commun 2: 227.
    • (2011) Nat Commun , vol.2 , pp. 227
    • Xu, C.1    Bian, C.2    Lam, R.3    Dong, A.4    Min, J.5
  • 62
    • 79957554781 scopus 로고    scopus 로고
    • MosSCI and gateway compatible plasmid toolkit for constitutive and inducible expression of transgenes in the C. elegans germline
    • Zeiser E, Frøkjær-Jensen C, Jorgensen E, Ahringer J. 2011. MosSCI and gateway compatible plasmid toolkit for constitutive and inducible expression of transgenes in the C. elegans germline. PLoS ONE 6: e20082.
    • (2011) PLoS ONE , vol.6
    • Zeiser, E.1    Frøkjær-Jensen, C.2    Jorgensen, E.3    Ahringer, J.4
  • 63
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang A, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332: 977-980.
    • (2011) Science , vol.332 , pp. 977-980
    • Zhang, A.1    Wippo, C.J.2    Wal, M.3    Ward, E.4    Korber, P.5    Pugh, B.F.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.