메뉴 건너뛰기




Volumn 6, Issue , 2015, Pages

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; HISTONE; DNA; GREEN FLUORESCENT PROTEIN;

EID: 84923350477     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7315     Document Type: Article
Times cited : (68)

References (70)
  • 1
    • 0019811465 scopus 로고
    • Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences
    • Banerji, J., Rusconi, S. & Schaffner, W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell 27, 299-308 (1981).
    • (1981) Cell , vol.27 , pp. 299-308
    • Banerji, J.1    Rusconi, S.2    Schaffner, W.3
  • 2
    • 84860443136 scopus 로고    scopus 로고
    • Enhancers: Emerging roles in cell fate specification
    • Ong, C. T. & Corces, V. G. Enhancers: emerging roles in cell fate specification. EMBO Rep. 13, 423-430 (2012).
    • (2012) EMBO Rep. , vol.13 , pp. 423-430
    • Ong, C.T.1    Corces, V.G.2
  • 3
    • 70249088327 scopus 로고    scopus 로고
    • Genomic views of distant-acting enhancers
    • Visel, A., Rubin, E. M. & Pennacchio, L. A. Genomic views of distant-acting enhancers. Nature 461, 199-205 (2009).
    • (2009) Nature , vol.461 , pp. 199-205
    • Visel, A.1    Rubin, E.M.2    Pennacchio, L.A.3
  • 4
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304, 1321-1325 (2004).
    • (2004) Science , vol.304 , pp. 1321-1325
    • Bejerano, G.1
  • 5
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with vertebrate development
    • Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7 (2005).
    • (2005) PLoS Biol. , vol.3 , pp. e7
    • Woolfe, A.1
  • 6
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved noncoding sequences
    • Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved noncoding sequences. Nature 444, 499-502 (2006).
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1
  • 7
    • 77956641239 scopus 로고    scopus 로고
    • ChIP-Seq identification of weakly conserved heart enhancers
    • Blow, M. J. et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 42, 806-810 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 806-810
    • Blow, M.J.1
  • 8
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318 (2007).
    • (2007) Nat. Genet. , vol.39 , pp. 311-318
    • Heintzman, N.D.1
  • 9
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specific activity of enhancers
    • Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
    • (2009) Nature , vol.457 , pp. 854-858
    • Visel, A.1
  • 10
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The 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
  • 11
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 12
    • 33846112470 scopus 로고    scopus 로고
    • VISTA Enhancer Browser-A database of tissue-specific human enhancers
    • Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. D88-D92
    • Visel, A.1    Minovitsky, S.2    Dubchak, I.3    Pennacchio, L.A.4
  • 14
    • 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. Nat. Rev. Genet. 13, 484-492 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 15
    • 33846850155 scopus 로고    scopus 로고
    • Analysis of tissue-specific differentially methylated regions (TDMs) in humans
    • Kitamura, E. et al. Analysis of tissue-specific differentially methylated regions (TDMs) in humans. Genomics 89, 326-337 (2007).
    • (2007) Genomics , vol.89 , pp. 326-337
    • Kitamura, E.1
  • 16
    • 38949212693 scopus 로고    scopus 로고
    • A novel CpG island set identifies tissue-specific methylation at developmental gene loci
    • Illingworth, R. et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6, e22 (2008).
    • (2008) PLoS Biol. , vol.6 , pp. e22
    • Illingworth, R.1
  • 17
    • 0035839126 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mammalian development
    • Reik, W., Dean, W. & Walter, J. Epigenetic reprogramming in mammalian development. Science 293, 1089-1093 (2001).
    • (2001) Science , vol.293 , pp. 1089-1093
    • Reik, W.1    Dean, W.2    Walter, J.3
  • 18
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • Maunakea, A. K. et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253-257 (2010).
    • (2010) Nature , vol.466 , pp. 253-257
    • Maunakea, A.K.1
  • 19
    • 80455176999 scopus 로고    scopus 로고
    • CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    • Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74-79 (2011).
    • (2011) Nature , vol.479 , pp. 74-79
    • Shukla, S.1
  • 20
    • 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
  • 21
    • 79961022522 scopus 로고    scopus 로고
    • DNA methylation status predicts cell type-specific enhancer activity
    • Wiench, M. et al. DNA methylation status predicts cell type-specific enhancer activity. EMBO J. 30, 3028-3039 (2011).
    • (2011) EMBO J. , vol.30 , pp. 3028-3039
    • Wiench, M.1
  • 22
    • 84879611157 scopus 로고    scopus 로고
    • DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    • Xie, M. et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat. Genet. 45, 836-841 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 836-841
    • Xie, M.1
  • 23
    • 84883668746 scopus 로고    scopus 로고
    • Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Zhang, B. et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 23, 1522-1540 (2013).
    • (2013) Genome Res. , vol.23 , pp. 1522-1540
    • Zhang, B.1
  • 24
    • 84878292277 scopus 로고    scopus 로고
    • Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    • Gifford, C. A. et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149-1163 (2013).
    • (2013) Cell , vol.153 , pp. 1149-1163
    • Gifford, C.A.1
  • 25
    • 84878282421 scopus 로고    scopus 로고
    • Epigenomic analysis of multilineage differentiation of human embryonic stem cells
    • Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134-1148 (2013).
    • (2013) Cell , vol.153 , pp. 1134-1148
    • Xie, W.1
  • 27
    • 0033557621 scopus 로고    scopus 로고
    • A role for DNA methylation in gastrulation and somite patterning
    • Martin, C. C., Laforest, L., Akimenko, M. A. & Ekker, M. A role for DNA methylation in gastrulation and somite patterning. Dev. Biol. 206, 189-205 (1999).
    • (1999) Dev. Biol. , vol.206 , pp. 189-205
    • Martin, C.C.1    Laforest, L.2    Akimenko, M.A.3    Ekker, M.4
  • 28
    • 33749179804 scopus 로고    scopus 로고
    • Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development
    • Rai, K. et al. Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Mol. Cell Biol. 26, 7077-7085 (2006).
    • (2006) Mol. Cell Biol. , vol.26 , pp. 7077-7085
    • Rai, K.1
  • 29
    • 77950484579 scopus 로고    scopus 로고
    • Dnmt3 and G9a cooperate for tissue-specific development in zebrafish
    • Rai, K. et al. Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J. Biol. Chem. 285, 4110-4121 (2010).
    • (2010) J. Biol. Chem. , vol.285 , pp. 4110-4121
    • Rai, K.1
  • 30
    • 84877696605 scopus 로고    scopus 로고
    • Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos
    • Jiang, L. et al. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell 153, 773-784 (2013).
    • (2013) Cell , vol.153 , pp. 773-784
    • Jiang, L.1
  • 31
    • 84877711740 scopus 로고    scopus 로고
    • Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern
    • Potok, M. E., Nix, D. A., Parnell, T. J. & Cairns, B. R. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell 153, 759-772 (2013).
    • (2013) Cell , vol.153 , pp. 759-772
    • Potok, M.E.1    Nix, D.A.2    Parnell, T.J.3    Cairns, B.R.4
  • 32
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • Harris, R. A. et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol. 28, 1097-1105 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 1097-1105
    • Harris, R.A.1
  • 33
    • 84883719710 scopus 로고    scopus 로고
    • Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
    • Stevens, M. et al. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res. 23, 1541-1553 (2013).
    • (2013) Genome Res. , vol.23 , pp. 1541-1553
    • Stevens, M.1
  • 34
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322 (2009).
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1
  • 35
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457-466 (2007).
    • (2007) Nat. Genet. , vol.39 , pp. 457-466
    • Weber, M.1
  • 36
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A. et al. 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
  • 37
    • 84875404794 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: Extensions and updates 2013
    • Meyer, L. R. et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, D64-D69 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D64-D69
    • Meyer, L.R.1
  • 38
    • 84867158452 scopus 로고    scopus 로고
    • Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
    • Bogdanovic, O. et al. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res. 22, 2043-2053 (2012).
    • (2012) Genome Res. , vol.22 , pp. 2043-2053
    • Bogdanovic, O.1
  • 39
    • 77952214662 scopus 로고    scopus 로고
    • GREAT improves functional interpretation of cis-regulatory regions
    • McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495-501 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 495-501
    • McLean, C.Y.1
  • 40
    • 84857836107 scopus 로고    scopus 로고
    • Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    • Pauli, A. et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22, 577-591 (2012).
    • (2012) Genome Res. , vol.22 , pp. 577-591
    • Pauli, A.1
  • 41
    • 84887270045 scopus 로고    scopus 로고
    • On and off retinal circuit assembly by divergent molecular mechanisms
    • Sun, L. O. et al. On and off retinal circuit assembly by divergent molecular mechanisms. Science 342, 1241974 (2013).
    • (2013) Science , vol.342 , pp. 1241974
    • Sun, L.O.1
  • 42
    • 84902169937 scopus 로고    scopus 로고
    • Sema6a and Plxna2 mediate spatially regulated repulsion within the developing eye to promote eye vesicle cohesion
    • Ebert, A. M., Childs, S. J., Hehr, C. L., Cechmanek, P. B. & McFarlane, S. Sema6a and Plxna2 mediate spatially regulated repulsion within the developing eye to promote eye vesicle cohesion. Development 141, 2473-2482 (2014).
    • (2014) Development , vol.141 , pp. 2473-2482
    • Ebert, A.M.1    Childs, S.J.2    Hehr, C.L.3    Cechmanek, P.B.4    McFarlane, S.5
  • 43
    • 84903954562 scopus 로고    scopus 로고
    • Cdon acts as a Hedgehog decoy receptor during proximaldistal patterning of the optic vesicle
    • Cardozo, M. J. et al. Cdon acts as a Hedgehog decoy receptor during proximaldistal patterning of the optic vesicle. Nat. Commun. 5, 4272 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 4272
    • Cardozo, M.J.1
  • 44
    • 79960874109 scopus 로고    scopus 로고
    • Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina
    • Brzezinski, 4th J. A., Kim, E. J., Johnson, J. E. & Reh, T. A. Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina. Development 138, 3519-3531 (2011).
    • (2011) Development , vol.138 , pp. 3519-3531
    • Brzezinski, I.V.J.A.1    Kim, E.J.2    Johnson, J.E.3    Reh, T.A.4
  • 45
    • 34347244234 scopus 로고    scopus 로고
    • Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish
    • Fisher, S. et al. Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nat. Protoc. 1, 1297-1305 (2006).
    • (2006) Nat. Protoc. , vol.1 , pp. 1297-1305
    • Fisher, S.1
  • 46
    • 80051683248 scopus 로고    scopus 로고
    • PhiC31 integrase mediates efficient cassette exchange in the zebrafish germline
    • Hu, G., Goll, M. G. & Fisher, S. PhiC31 integrase mediates efficient cassette exchange in the zebrafish germline. Dev. Dyn. 240, 2101-2107 (2011).
    • (2011) Dev. Dyn. , vol.240 , pp. 2101-2107
    • Hu, G.1    Goll, M.G.2    Fisher, S.3
  • 47
    • 79959252336 scopus 로고    scopus 로고
    • Lineage relationship of directdeveloping melanocytes and melanocyte stem cells in the zebrafish
    • Tryon, R. C., Higdon, C. W. & Johnson, S. L. Lineage relationship of directdeveloping melanocytes and melanocyte stem cells in the zebrafish. PLoS ONE 6, e21010 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e21010
    • Tryon, R.C.1    Higdon, C.W.2    Johnson, S.L.3
  • 48
    • 0028019609 scopus 로고
    • Sine oculis is a homeobox gene required for Drosophila visual system development
    • Serikaku, M. A. & O'Tousa, J. E. Sine oculis is a homeobox gene required for Drosophila visual system development. Genetics 138, 1137-1150 (1994).
    • (1994) Genetics , vol.138 , pp. 1137-1150
    • Serikaku, M.A.1    O'Tousa, J.E.2
  • 49
    • 27744534898 scopus 로고    scopus 로고
    • Functions and regulations of fibroblast growth factor signaling during embryonic development
    • Thisse, B. & Thisse, C. Functions and regulations of fibroblast growth factor signaling during embryonic development. Dev. Biol. 287, 390-402 (2005).
    • (2005) Dev. Biol. , vol.287 , pp. 390-402
    • Thisse, B.1    Thisse, C.2
  • 50
    • 84885061881 scopus 로고    scopus 로고
    • De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements
    • Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J. & Hodges, E. De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Res. 23, 1601-1614 (2013).
    • (2013) Genome Res. , vol.23 , pp. 1601-1614
    • Schlesinger, F.1    Smith, A.D.2    Gingeras, T.R.3    Hannon, G.J.4    Hodges, E.5
  • 51
    • 84885021247 scopus 로고    scopus 로고
    • Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
    • Hon, G. C. et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat. Genet. 45, 1198-1206 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1198-1206
    • Hon, G.C.1
  • 52
    • 33745628791 scopus 로고    scopus 로고
    • Close sequence comparisons are sufficient to identify human cis-regulatory elements
    • Prabhakar, S. et al. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res. 16, 855-863 (2006).
    • (2006) Genome Res. , vol.16 , pp. 855-863
    • Prabhakar, S.1
  • 53
    • 38649123306 scopus 로고    scopus 로고
    • Ultraconservation identifies a small subset of extremely constrained developmental enhancers
    • Visel, A. et al. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat. Genet. 40, 158-160 (2008).
    • (2008) Nat. Genet. , vol.40 , pp. 158-160
    • Visel, A.1
  • 54
    • 0031104930 scopus 로고    scopus 로고
    • DNA methylation directs a timedependent repression of transcription initiation
    • Kass, S. U., Landsberger, N. & Wolffe, A. P. DNA methylation directs a timedependent repression of transcription initiation. Curr. Biol. 7, 157-165 (1997).
    • (1997) Curr. Biol. , vol.7 , pp. 157-165
    • Kass, S.U.1    Landsberger, N.2    Wolffe, A.P.3
  • 55
    • 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
  • 56
    • 79959209733 scopus 로고    scopus 로고
    • 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
    • Stroud, H., Feng, S., Kinney, S. M., Pradhan, S. & Jacobsen, S. E. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 12, R54 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R54
    • Stroud, H.1    Feng, S.2    Kinney, S.M.3    Pradhan, S.4    Jacobsen, S.E.5
  • 57
    • 79956302047 scopus 로고    scopus 로고
    • TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
    • Williams, K. et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473, 343-348 (2011).
    • (2011) Nature , vol.473 , pp. 343-348
    • Williams, K.1
  • 58
    • 78651364359 scopus 로고    scopus 로고
    • ZFIN: Enhancements and updates to the Zebrafish Model Organism Database
    • Bradford, Y. et al. ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res. 39, D822-D829 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D822-D829
    • Bradford, Y.1
  • 59
    • 84923330760 scopus 로고    scopus 로고
    • Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation
    • Li, D., Zhang, B., Xing, X. & Wang, T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods 72, 29-40 (2014).
    • (2014) Methods , vol.72 , pp. 29-40
    • Li, D.1    Zhang, B.2    Xing, X.3    Wang, T.4
  • 60
    • 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
  • 61
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 62
    • 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. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1
  • 63
    • 84891808382 scopus 로고    scopus 로고
    • JASPAR 2014: An extensively expanded and updated openaccess database of transcription factor binding profiles
    • Mathelier, A. et al. JASPAR 2014: an extensively expanded and updated openaccess database of transcription factor binding profiles. Nucleic Acids Res. 42, D14-147 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D14-147
    • Mathelier, A.1
  • 64
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, D. W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 65
    • 84883564514 scopus 로고    scopus 로고
    • The UCSC Interaction Browser: Multidimensional data views in pathway context
    • Wong, C. K. et al. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 41, W218-W224 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. W218-W224
    • Wong, C.K.1
  • 66
    • 84923292574 scopus 로고    scopus 로고
    • Regulatory network decoded from epigenomes of surface ectoderm-derived cell types
    • Lowdon, R. F. et al. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nat. Commun. 5, 5442 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 5442
    • Lowdon, R.F.1
  • 67
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith, J. J. et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5, e8 (2007).
    • (2007) PLoS Biol. , vol.5 , pp. e8
    • Faith, J.J.1
  • 68
    • 77957243164 scopus 로고    scopus 로고
    • ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
    • Lachmann, A. et al. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26, 2438-2444 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2438-2444
    • Lachmann, A.1
  • 69
    • 82355171753 scopus 로고    scopus 로고
    • The human epigenome browser at Washington University
    • Zhou, X. et al. The Human Epigenome Browser at Washington University. Nat. Methods 8, 989-990 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 989-990
    • Zhou, X.1
  • 70
    • 84877296402 scopus 로고    scopus 로고
    • Exploring long-range genome interactions using the WashU Epigenome Browser
    • Zhou, X. et al. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat. Methods 10, 375-376 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 375-376
    • Zhou, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.