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Volumn 3, Issue 4, 2012, Pages 651-670

Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays

Author keywords

DNaseI; ENCODE; Open chromatin; Transcriptional regulation

Indexed keywords

DEOXYRIBONUCLEASE I; FORMALDEHYDE; MICROCOCCAL NUCLEASE; SPACER DNA; TRANSCRIPTION FACTOR;

EID: 84871592810     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes3040651     Document Type: Review
Times cited : (32)

References (77)
  • 1
    • 79951472909 scopus 로고    scopus 로고
    • Charting a course for genomic medicine from base pairs to bedside
    • Green, E.D.; Guyer, M.S. Charting a course for genomic medicine from base pairs to bedside. Nature 2011, 470, 204-213.
    • (2011) Nature , vol.470 , pp. 204-213
    • Green, E.D.1    Guyer, M.S.2
  • 2
    • 0015271630 scopus 로고
    • So much junk DNA in our genome
    • Ohno, S. So much junk DNA in our genome. Brookhaven Symp Biol. 1972, 23, 366-370.
    • (1972) Brookhaven Symp Biol , vol.23 , pp. 366-370
    • Ohno, S.1
  • 5
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • Schones, D.E.; Zhao, K. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet. 2008, 9, 179-191.
    • (2008) Nat. Rev. Genet , vol.9 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 7
    • 77956276383 scopus 로고    scopus 로고
    • DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    • 2010, pdb.prot5384
    • Song, L.; Crawford, G.E. DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. CSH Protoc. 2010, 2010, pdb.prot5384.
    • (2010) CSH Protoc
    • Song, L.1    Crawford, G.E.2
  • 8
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    • Giresi, P.G.; Kim, J.; McDaniell, R.M.; Iyer, V.R.; Lieb, J.D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007, 17, 877-885.
    • (2007) Genome Res , vol.17 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3    Iyer, V.R.4    Lieb, J.D.5
  • 9
    • 34250159524 scopus 로고    scopus 로고
    • Genome-Wide Mapping of in Vivo Protein- DNA Interactions
    • Johnson, D.S.; Mortazavi, A.; Myers, R.M.; Wold, B. Genome-Wide Mapping of in Vivo Protein- DNA Interactions. Science 2007, 316, 1497-1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 11
    • 0029921392 scopus 로고    scopus 로고
    • Heterochromatin and gene regulation in Drosophila
    • Elgin, S.C. Heterochromatin and gene regulation in Drosophila. Curr. Opin. Genet. Dev. 1996, 6, 193-202.
    • (1996) Curr. Opin. Genet. Dev , vol.6 , pp. 193-202
    • Elgin, S.C.1
  • 12
    • 0019542744 scopus 로고
    • Tissue-specific exposure of chromatin structure at the 5' terminus of the rat preproinsulin II gene
    • Wu, C.; Gilbert, W. Tissue-specific exposure of chromatin structure at the 5' terminus of the rat preproinsulin II gene. Proc. Natl. Acad. Sci. USA 1981, 78, 1577.
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 1577
    • Wu, C.1    Gilbert, W.2
  • 13
    • 0345938187 scopus 로고
    • Isolation of a subclass of nuclear proteins responsible for conferring a DNase I-sensitive structure on globin chromatin
    • Weisbrod, S.; Weintraub, H. Isolation of a subclass of nuclear proteins responsible for conferring a DNase I-sensitive structure on globin chromatin. Proc. Natl. Acad. Sci. USA 1979, 76, 630-634.
    • (1979) Proc. Natl. Acad. Sci. USA , vol.76 , pp. 630-634
    • Weisbrod, S.1    Weintraub, H.2
  • 14
    • 24644505259 scopus 로고    scopus 로고
    • Fewer genes, more noncoding RNA
    • Claverie, J.-M. Fewer genes, more noncoding RNA. Science 2005, 309, 1529-1530.
    • (2005) Science , vol.309 , pp. 1529-1530
    • Claverie, J.-M.1
  • 17
    • 3242891274 scopus 로고    scopus 로고
    • ConSite: Web-based prediction of regulatory elements using cross-species comparison
    • Sandelin, A.; Wasserman, W.W.; Lenhard, B. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 2004, 32, W249-W252.
    • (2004) Nucleic Acids Res , vol.32
    • Sandelin, A.1    Wasserman, W.W.2    Lenhard, B.3
  • 19
    • 39049147650 scopus 로고    scopus 로고
    • Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
    • McGaughey, D.M.; Vinton, R.M.; Huynh, J.; Al-Saif, A.; Beer, M.A.; McCallion, A.S. Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res. 2008, 18, 252-260.
    • (2008) Genome Res , vol.18 , pp. 252-260
    • McGaughey, D.M.1    Vinton, R.M.2    Huynh, J.3    Al-Saif, A.4    Beer, M.A.5    McCallion, A.S.6
  • 20
    • 71749120382 scopus 로고    scopus 로고
    • Finding distal regulatory elements in the human genome
    • Heintzman, N.D.; Ren, B. Finding distal regulatory elements in the human genome. Curr. Opin. Genet. Dev. 2009, 19, 541-549.
    • (2009) Curr. Opin. Genet. Dev , vol.19 , pp. 541-549
    • Heintzman, N.D.1    Ren, B.2
  • 21
    • 58149463874 scopus 로고    scopus 로고
    • Chromosomal dynamics at the Shh locus: Limb bud-specific differential regulation of competence and active transcription
    • Amano, T.; Sagai, T.; Tanabe, H.; Mizushina, Y.; Nakazawa, H.; Shiroishi, T. Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription. Dev. Cell 2009, 16, 47-57.
    • (2009) Dev. Cell , vol.16 , pp. 47-57
    • Amano, T.1    Sagai, T.2    Tanabe, H.3    Mizushina, Y.4    Nakazawa, H.5    Shiroishi, T.6
  • 22
    • 84857192750 scopus 로고    scopus 로고
    • HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter
    • Visser, M.; Kayser, M.; Palstra, R.J. HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res. 2012, 22, 446-455.
    • (2012) Genome Res , vol.22 , pp. 446-455
    • Visser, M.1    Kayser, M.2    Palstra, R.J.3
  • 23
    • 20444494936 scopus 로고    scopus 로고
    • Interchromosomal associations between alternatively expressed loci
    • Spilianakis, C.G.; Lalioti, M.D.; Town, T.; Lee, G.R.; Flavell, R.A. Interchromosomal associations between alternatively expressed loci. Nature 2005, 435, 637-645.
    • (2005) Nature , vol.435 , pp. 637-645
    • Spilianakis, C.G.1    Lalioti, M.D.2    Town, T.3    Lee, G.R.4    Flavell, R.A.5
  • 25
    • 79551655285 scopus 로고    scopus 로고
    • Functional and mechanistic diversity of distal transcription enhancers
    • Bulger, M.; Groudine, M. Functional and mechanistic diversity of distal transcription enhancers. Cell 2011, 144, 327-339.
    • (2011) Cell , vol.144 , pp. 327-339
    • Bulger, M.1    Groudine, M.2
  • 26
    • 58149498240 scopus 로고    scopus 로고
    • CTCF-dependent enhancer-blocking by alternative chromatin loop formation
    • Hou, C.; Zhao, H.; Tanimoto, K.; Dean, A. CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc. Natl. Acad. Sci. USA 2008, 105, 20398-20403.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 20398-20403
    • Hou, C.1    Zhao, H.2    Tanimoto, K.3    Dean, A.4
  • 27
    • 0036467996 scopus 로고    scopus 로고
    • Insulators: Many functions, many mechanisms
    • West, A.G.; Gaszner, M.; Felsenfeld, G. Insulators: many functions, many mechanisms. Gene. Dev. 2002, 16, 271-288.
    • (2002) Gene. Dev , vol.16 , pp. 271-288
    • West, A.G.1    Gaszner, M.2    Felsenfeld, G.3
  • 28
    • 29444448047 scopus 로고    scopus 로고
    • On a chromosome far, far away: LCRs and gene expression
    • Dean, A. On a chromosome far, far away: LCRs and gene expression. TRENDS Genet. 2006, 22, 38-45.
    • (2006) TRENDS Genet , vol.22 , pp. 38-45
    • Dean, A.1
  • 29
    • 70349469565 scopus 로고    scopus 로고
    • Mechanisms of polycomb gene silencing: Knowns and unknowns
    • Simon, J.A.; Kingston, R.E. Mechanisms of polycomb gene silencing: Knowns and unknowns. Nat. Rev. Mol. Cell Biol. 2009, 10, 697-708.
    • (2009) Nat. Rev. Mol. Cell Biol , vol.10 , pp. 697-708
    • Simon, J.A.1    Kingston, R.E.2
  • 31
    • 83055181959 scopus 로고    scopus 로고
    • Discriminative prediction of mammalian enhancers from DNA sequence
    • Lee, D.; Karchin, R.; Beer, M.A. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011, 21, 2167-2180.
    • (2011) Genome Res , vol.21 , pp. 2167-2180
    • Lee, D.1    Karchin, R.2    Beer, M.A.3
  • 32
    • 0019303186 scopus 로고
    • The 5[prime] ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I
    • Wu, C. The 5[prime] ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 1980, 286, 854-860.
    • (1980) Nature , vol.286 , pp. 854-860
    • Wu, C.1
  • 33
    • 85015069067 scopus 로고    scopus 로고
    • Controlling the double helix
    • Felsenfeld, G.; Groudine, M. Controlling the double helix. Nature 2003, 421, 448-453.
    • (2003) Nature , vol.421 , pp. 448-453
    • Felsenfeld, G.1    Groudine, M.2
  • 34
    • 0023899769 scopus 로고
    • Nuclease Hypersensitive Sites in Chromatin
    • Gross, D.S.; Garrard, W.T. Nuclease Hypersensitive Sites in Chromatin. Annu. Rev. Biochem. 1988, 57, 159-197.
    • (1988) Annu. Rev. Biochem , vol.57 , pp. 159-197
    • Gross, D.S.1    Garrard, W.T.2
  • 37
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi, R.; Degner, J.F.; Pai, A.A.; Gaffney, D.J.; Gilad, Y.; Pritchard, J.K. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011, 21, 447-455.
    • (2011) Genome Res , vol.21 , pp. 447-455
    • Pique-Regi, R.1    Degner, J.F.2    Pai, A.A.3    Gaffney, D.J.4    Gilad, Y.5    Pritchard, J.K.6
  • 38
    • 0023948705 scopus 로고
    • Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
    • Solomon, M.J.; Larsen, P.L.; Varshavsky, A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 1988, 53, 937-947.
    • (1988) Cell , vol.53 , pp. 937-947
    • Solomon, M.J.1    Larsen, P.L.2    Varshavsky, A.3
  • 40
    • 44949138461 scopus 로고    scopus 로고
    • A rapid micro chromatin immunoprecipitation assay (microChIP)
    • Dahl, J.A.; Collas, P. A rapid micro chromatin immunoprecipitation assay (microChIP). Nature Protoc. 2008, 3, 1032-1045.
    • (2008) Nature Protoc , vol.3 , pp. 1032-1045
    • Dahl, J.A.1    Collas, P.2
  • 41
    • 84861916932 scopus 로고    scopus 로고
    • Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
    • Statham, A.L.; Robinson, M.D.; Song, J.Z.; Coolen, M.W.; Stirzaker, C.; Clark, S.J. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 2012, 22, 1120-1127.
    • (2012) Genome Res , vol.22 , pp. 1120-1127
    • Statham, A.L.1    Robinson, M.D.2    Song, J.Z.3    Coolen, M.W.4    Stirzaker, C.5    Clark, S.J.6
  • 42
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single- nucleotide resolution
    • Rhee, H.S.; Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single- nucleotide resolution. Cell 2011, 147, 1408-1419.
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 46
    • 80052284848 scopus 로고    scopus 로고
    • OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes
    • You, J.S.; Kelly, T.K.; De Carvalho, D.D.; Taberlay, P.C.; Liang, G.; Jones, P.A. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc. Natl. Acad. Sci USA 2011, 108, 14497-14502.
    • (2011) Proc. Natl. Acad. Sci USA , vol.108 , pp. 14497-14502
    • You, J.S.1    Kelly, T.K.2    de Carvalho, D.D.3    Taberlay, P.C.4    Liang, G.5    Jones, P.A.6
  • 48
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park, P.J. ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet. 2009, 10, 669-680.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 669-680
    • Park, P.J.1
  • 49
    • 77954834510 scopus 로고    scopus 로고
    • The current state of chromatin immunoprecipitation
    • Collas, P. The current state of chromatin immunoprecipitation. Mol. Biotechnol. 2010, 45, 87-100.
    • (2010) Mol. Biotechnol , vol.45 , pp. 87-100
    • Collas, P.1
  • 50
    • 0036911605 scopus 로고    scopus 로고
    • Distribution and characterization of regulatory elements in the human genome
    • Majewski, J.; Ott, J. Distribution and characterization of regulatory elements in the human genome. Genome Res. 2002, 12, 1827-1836.
    • (2002) Genome Res , vol.12 , pp. 1827-1836
    • Majewski, J.1    Ott, J.2
  • 52
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master Weaver of the Genome
    • Phillips, J.E.; Corces, V.G. CTCF: Master Weaver of the Genome. Cell 2009, 137, 1194-1211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 53
    • 77649261872 scopus 로고    scopus 로고
    • Cell type specificity of chromatin organization mediated by CTCF and cohesin
    • Hou, C.; Dale, R.; Dean, A. Cell type specificity of chromatin organization mediated by CTCF and cohesin. Proc. Natl. Acad. Sci. USA 2010, 107, 3651-3656.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 3651-3656
    • Hou, C.1    Dale, R.2    Dean, A.3
  • 58
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer, M.A.; Tavazoie, S. Predicting gene expression from sequence. Cell 2004, 117, 185-198.
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 59
    • 36949030484 scopus 로고    scopus 로고
    • Predicting gene expression from sequence: A reexamination
    • Yuan, Y.; Guo, L.; Shen, L.; Liu, J.S. Predicting gene expression from sequence: a reexamination. PLoS Comput. Biol. 2007, 3, e243.
    • (2007) PLoS Comput. Biol , vol.3
    • Yuan, Y.1    Guo, L.2    Shen, L.3    Liu, J.S.4
  • 60
    • 38749127589 scopus 로고    scopus 로고
    • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    • Segal, E.; Raveh-Sadka, T.; Schroeder, M.; Unnerstall, U.; Gaul, U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 2008, 451, 535-540.
    • (2008) Nature , vol.451 , pp. 535-540
    • Segal, E.1    Raveh-Sadka, T.2    Schroeder, M.3    Unnerstall, U.4    Gaul, U.5
  • 61
    • 84865840434 scopus 로고    scopus 로고
    • Predicting Cell-Type Specific Gene Expression from Regions of Open Chromatin
    • Natarajan, A.; Yardimci, G.G.; Sheffield, N.C.; Crawford, G.E.; Ohler, U. Predicting Cell-Type Specific Gene Expression from Regions of Open Chromatin. Genome Res. 2012, 22, 1711-1722.
    • (2012) Genome Res , vol.22 , pp. 1711-1722
    • Natarajan, A.1    Yardimci, G.G.2    Sheffield, N.C.3    Crawford, G.E.4    Ohler, U.5
  • 63
    • 73249130316 scopus 로고    scopus 로고
    • Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
    • Reddy, T.E.; Pauli, F.; Sprouse, R.O.; Neff, N.F.; Newberry, K.M.; Garabedian, M.J.; Myers, R.M. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 2009, 19, 2163-2171.
    • (2009) Genome Res , vol.19 , pp. 2163-2171
    • Reddy, T.E.1    Pauli, F.2    Sprouse, R.O.3    Neff, N.F.4    Newberry, K.M.5    Garabedian, M.J.6    Myers, R.M.7
  • 67
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin Modifications and Their Function
    • Kouzarides, T. Chromatin Modifications and Their Function. Cell 2007, 128, 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 68
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst, J.; Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 2010, 28, 817-825.
    • (2010) Nat. Biotechnol , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 71
    • 79251607477 scopus 로고    scopus 로고
    • 3C-based methods to detect long-range chromatin interactions
    • Wei, G.; Zhao, K. 3C-based methods to detect long-range chromatin interactions. Front. Biol. 2011, 6, 76-81.
    • (2011) Front. Biol , vol.6 , pp. 76-81
    • Wei, G.1    Zhao, K.2
  • 72
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker, J.; Rippe, K.; Dekker, M.; Kleckner, N. Capturing chromosome conformation. Science 2002, 295, 1306-1311.
    • (2002) Science , vol.295 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 74
    • 70349326007 scopus 로고    scopus 로고
    • Genomic interactions: Chromatin loops and gene meeting points in transcriptional regulation
    • Sexton, T.; Bantignies, F.; Cavalli, G. Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation. Semin. Cell Dev. Biol. 2009, 20, 849-855.
    • (2009) Semin. Cell Dev. Biol , vol.20 , pp. 849-855
    • Sexton, T.1    Bantignies, F.2    Cavalli, G.3
  • 75
    • 34249307315 scopus 로고    scopus 로고
    • Nuclear organization of the genome and the potential for gene regulation
    • Fraser, P.; Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 2007, 447, 413-417.
    • (2007) Nature , vol.447 , pp. 413-417
    • Fraser, P.1    Bickmore, W.2
  • 76
    • 31344477982 scopus 로고    scopus 로고
    • The three 'C' s of chromosome conformation capture: Controls, controls, controls
    • Dekker, J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat. Methods 2006, 3, 17-21.
    • (2006) Nat. Methods , vol.3 , pp. 17-21
    • Dekker, J.1


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