메뉴 건너뛰기




Volumn 27, Issue 1, 2017, Pages 38-52

Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity (Genome Research (2017) 27 (38 52) DOI: 10.1101/gr.212092.116);A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 85009062687     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.237321.118     Document Type: Erratum
Times cited : (192)

References (69)
  • 1
    • 0025298495 scopus 로고
    • Transient induction of c-jun during hepatic regeneration
    • Alcorn JA, Feitelberg SP, Brenner DA. 1990. Transient induction of c-jun during hepatic regeneration. Hepatology 11: 909-915.
    • (1990) Hepatology , vol.11 , pp. 909-915
    • Alcorn, J.A.1    Feitelberg, S.P.2    Brenner, D.A.3
  • 3
    • 0026506720 scopus 로고
    • Transcription factor loading on the MMTV promoter: A bimodal mechanism for promoter activation
    • Archer TK, Lefebvre P, Wolford RG, Hager GL. 1992. Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science 255: 1573-1576.
    • (1992) Science , vol.255 , pp. 1573-1576
    • Archer, T.K.1    Lefebvre, P.2    Wolford, R.G.3    Hager, G.L.4
  • 4
    • 84874381107 scopus 로고    scopus 로고
    • Genome-wide quantitative enhancer activity maps identified by STARR-seq
    • Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A. 2013. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339: 1074-1077.
    • (2013) Science , vol.339 , pp. 1074-1077
    • Arnold, C.D.1    Gerlach, D.2    Stelzer, C.3    Boryn, L.M.4    Rath, M.5    Stark, A.6
  • 5
    • 84903640603 scopus 로고    scopus 로고
    • Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution
    • Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. 2014. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet 46: 685-692.
    • (2014) Nat Genet , vol.46 , pp. 685-692
    • Arnold, C.D.1    Gerlach, D.2    Spies, D.3    Matts, J.A.4    Sytnikova, Y.A.5    Pagani, M.6    Lau, N.C.7    Stark, A.8
  • 6
    • 0019811465 scopus 로고
    • Expression of a β-globin gene is enhanced by remote SV40 DNA sequences
    • Banerji J, Rusconi S, Schaffner W. 1981. Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell 27(2 Pt 1): 299-308.
    • (1981) Cell , vol.27 , Issue.2 , pp. 299-308
    • Banerji, J.1    Rusconi, S.2    Schaffner, W.3
  • 7
    • 0028813664 scopus 로고
    • A direct physical association between ETS and AP-1 transcription factors in normal human T cells
    • Bassuk AG, Leiden JM. 1995. A direct physical association between ETS and AP-1 transcription factors in normal human T cells. Immunity 3: 223-237.
    • (1995) Immunity , vol.3 , pp. 223-237
    • Bassuk, A.G.1    Leiden, J.M.2
  • 8
    • 0035025888 scopus 로고    scopus 로고
    • A quantitative assay for HIV DNA integration in vivo
    • Butler SL, Hansen MS, Bushman FD. 2001. A quantitative assay for HIV DNA integration in vivo. Nat Med 7: 631-634.
    • (2001) Nat Med , vol.7 , pp. 631-634
    • Butler, S.L.1    Hansen, M.S.2    Bushman, F.D.3
  • 9
    • 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
  • 10
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst J, Kellis M. 2012. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9: 215-216.
    • (2012) Nat Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 16
    • 84905484602 scopus 로고    scopus 로고
    • Enhanced regulatory sequence prediction using gapped k-mer features
    • Ghandi M, Lee D, Mohammad-Noori M, Beer MA. 2014. Enhanced regulatory sequence prediction using gapped k-mer features. PLoS Comput Biol 10: e1003711.
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003711
    • Ghandi, M.1    Lee, D.2    Mohammad-Noori, M.3    Beer, M.A.4
  • 17
    • 79959655657 scopus 로고    scopus 로고
    • DNACLUST: Accurate and efficient clustering of phylogenetic marker genes
    • Ghodsi M, Liu B, Pop M. 2011. DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics 12: 271.
    • (2011) BMC Bioinformatics , vol.12 , pp. 271
    • Ghodsi, M.1    Liu, B.2    Pop, M.3
  • 18
    • 0025878233 scopus 로고
    • Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity
    • Hai T, Curran T. 1991. Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity. Proc Natl Acad Sci 88: 3720-3724.
    • (1991) Proc Natl Acad Sci , vol.88 , pp. 3720-3724
    • Hai, T.1    Curran, T.2
  • 19
    • 34247281521 scopus 로고    scopus 로고
    • Chromatin-dependent cooperativity between site-specific transcription factors in vivo
    • Hebbar PB, Archer TK. 2007. Chromatin-dependent cooperativity between site-specific transcription factors in vivo. J Biol Chem 282: 8284-8291.
    • (2007) J Biol Chem , vol.282 , pp. 8284-8291
    • Hebbar, P.B.1    Archer, T.K.2
  • 20
    • 41949083130 scopus 로고    scopus 로고
    • Altered histone H1 stoichiometry and an absence of nucleosome positioning on transfected DNA
    • Hebbar PB, Archer TK. 2008. Altered histone H1 stoichiometry and an absence of nucleosome positioning on transfected DNA. J Biol Chem 283: 4595-4601.
    • (2008) J Biol Chem , vol.283 , pp. 4595-4601
    • Hebbar, P.B.1    Archer, T.K.2
  • 22
    • 12344252237 scopus 로고    scopus 로고
    • AP-1 subunits: Quarrel and harmony among siblings
    • Hess J, Angel P, Schorpp-Kistner M. 2004. AP-1 subunits: quarrel and harmony among siblings. J Cell Sci 117(Pt 25): 5965-5973.
    • (2004) J Cell Sci , vol.117 , pp. 5965-5973
    • Hess, J.1    Angel, P.2    Schorpp-Kistner, M.3
  • 23
    • 0027242180 scopus 로고
    • C-Jun is essential for normal mouse development and hepatogenesis
    • Hilberg F, Aguzzi A, Howells N, Wagner EF. 1993. c-Jun is essential for normal mouse development and hepatogenesis. Nature 365: 179-181.
    • (1993) Nature , vol.365 , pp. 179-181
    • Hilberg, F.1    Aguzzi, A.2    Howells, N.3    Wagner, E.F.4
  • 24
    • 84862785201 scopus 로고    scopus 로고
    • Unsupervised pattern discovery in human chromatin structure through genomic segmentation
    • Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9: 473-476.
    • (2012) Nat Methods , vol.9 , pp. 473-476
    • Hoffman, M.M.1    Buske, O.J.2    Wang, J.3    Weng, Z.4    Bilmes, J.A.5    Noble, W.S.6
  • 25
    • 0028217604 scopus 로고
    • Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells
    • Jeong S, Stein A. 1994. Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells. Nucleic Acids Res 22: 370-375.
    • (1994) Nucleic Acids Res , vol.22 , pp. 370-375
    • Jeong, S.1    Stein, A.2
  • 26
    • 43449085794 scopus 로고    scopus 로고
    • UShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts
    • Jiang M, Anderson J, Gillespie J, Mayne M. 2008. uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.
    • (2008) BMC Bioinformatics , vol.9 , pp. 192
    • Jiang, M.1    Anderson, J.2    Gillespie, J.3    Mayne, M.4
  • 29
    • 73249129445 scopus 로고    scopus 로고
    • Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection
    • Kantor B, Ma H, Webster-Cyriaque J, Monahan PE, Kafri T. 2009. Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection. Proc Natl Acad Sci 106: 18786-18791.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 18786-18791
    • Kantor, B.1    Ma, H.2    Webster-Cyriaque, J.3    Monahan, P.E.4    Kafri, T.5
  • 31
    • 77952706498 scopus 로고    scopus 로고
    • Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
    • Kinney JB, Murugan A, Callan CG Jr, Cox EC. 2010. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci 107: 9158-9163.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 9158-9163
    • Kinney, J.B.1    Murugan, A.2    Callan, C.G.3    Cox, E.C.4
  • 32
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46: 310-315.
    • (2014) Nat Genet , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 33
    • 33645395980 scopus 로고    scopus 로고
    • In vivo RNA interference demonstrates a role for Nramp1 in modifying susceptibility to type 1 diabetes
    • Kissler S, Stern P, Takahashi K, Hunter K, Peterson LB, Wicker LS. 2006. In vivo RNA interference demonstrates a role for Nramp1 in modifying susceptibility to type 1 diabetes. Nat Genet 38: 479-483.
    • (2006) Nat Genet , vol.38 , pp. 479-483
    • Kissler, S.1    Stern, P.2    Takahashi, K.3    Hunter, K.4    Peterson, L.B.5    Wicker, L.S.6
  • 34
    • 0025869479 scopus 로고
    • Scaffold-attached regions from the human interferon β domain can be used to enhance the stable expression of genes under the control of various promoters
    • Klehr D, Maass K, Bode J. 1991. Scaffold-attached regions from the human interferon β domain can be used to enhance the stable expression of genes under the control of various promoters. Biochemistry 30: 1264-1270.
    • (1991) Biochemistry , vol.30 , pp. 1264-1270
    • Klehr, D.1    Maass, K.2    Bode, J.3
  • 37
  • 38
    • 0030030041 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection
    • Leavitt AD, Robles G, Alesandro N, Varmus HE. 1996. Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection. J Virol 70: 721-728.
    • (1996) J Virol , vol.70 , pp. 721-728
    • Leavitt, A.D.1    Robles, G.2    Alesandro, N.3    Varmus, H.E.4
  • 39
    • 84992435594 scopus 로고    scopus 로고
    • LS-GKM: A new gkm-SVM for large-scale datasets
    • Lee D. 2016. LS-GKM: a new gkm-SVM for large-scale datasets. Bioinformatics 32: 2196-2198.
    • (2016) Bioinformatics , vol.32 , pp. 2196-2198
    • Lee, D.1
  • 40
    • 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
  • 43
    • 0019769520 scopus 로고
    • The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants
    • Moreau P, Hen R, Wasylyk B, Everett R, Gaub MP, Chambon P. 1981. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res 9: 6047-6068.
    • (1981) Nucleic Acids Res , vol.9 , pp. 6047-6068
    • Moreau, P.1    Hen, R.2    Wasylyk, B.3    Everett, R.4    Gaub, M.P.5    Chambon, P.6
  • 44
    • 84883541122 scopus 로고    scopus 로고
    • Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle
    • Munir S, Thierry S, Subra F, Deprez E, Delelis O. 2013. Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle. Retrovirology 10: 87.
    • (2013) Retrovirology , vol.10 , pp. 87
    • Munir, S.1    Thierry, S.2    Subra, F.3    Deprez, E.4    Delelis, O.5
  • 48
    • 71849118573 scopus 로고    scopus 로고
    • Highresolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
    • Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J. 2009. Highresolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol 27: 1173-1175.
    • (2009) Nat Biotechnol , vol.27 , pp. 1173-1175
    • Patwardhan, R.P.1    Lee, C.2    Litvin, O.3    Young, D.L.4    Pe'Er, D.5    Shendure, J.6
  • 50
    • 79961024414 scopus 로고    scopus 로고
    • Recognition and suppression of transfected plasmids by protein ZNF511-PRAP1, a potential molecular barrier to transgene expression
    • Qiu GH, Leung CH, Yun T, Xie X, Laban M, Hooi SC. 2011. Recognition and suppression of transfected plasmids by protein ZNF511-PRAP1, a potential molecular barrier to transgene expression. Mol Ther 19: 1478-1486.
    • (2011) Mol Ther , vol.19 , pp. 1478-1486
    • Qiu, G.H.1    Leung, C.H.2    Yun, T.3    Xie, X.4    Laban, M.5    Hooi, S.C.6
  • 51
    • 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
  • 55
    • 84907527856 scopus 로고    scopus 로고
    • Probing the effect of promoters on noise in gene expression using thousands of designed sequences
    • Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. 2014. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res 24: 1698-1706.
    • (2014) Genome Res , vol.24 , pp. 1698-1706
    • Sharon, E.1    Van Dijk, D.2    Kalma, Y.3    Keren, L.4    Manor, O.5    Yakhini, Z.6    Segal, E.7
  • 57
    • 84899450857 scopus 로고    scopus 로고
    • Transcriptional enhancers: From properties to genome-wide predictions
    • Shlyueva D, Stampfel G, Stark A. 2014. Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet 15: 272-286.
    • (2014) Nat Rev Genet , vol.15 , pp. 272-286
    • Shlyueva, D.1    Stampfel, G.2    Stark, A.3
  • 59
    • 0030836229 scopus 로고    scopus 로고
    • Transcriptional regulation of mammalian genes in vivo. A tale of two templates
    • Smith CL, Hager GL. 1997. Transcriptional regulation of mammalian genes in vivo. A tale of two templates. J Biol Chem 272: 27493-27496.
    • (1997) J Biol Chem , vol.272 , pp. 27493-27496
    • Smith, C.L.1    Hager, G.L.2
  • 61
    • 84921407745 scopus 로고    scopus 로고
    • H2A.Z: A molecular rheostat for transcriptional control
    • Subramanian V, Fields PA, Boyer LA. 2015. H2A.Z: a molecular rheostat for transcriptional control. F1000Prime Rep 7: 01.
    • (2015) F1000Prime Rep , vol.7 , pp. 01
    • Subramanian, V.1    Fields, P.A.2    Boyer, L.A.3
  • 62
    • 84968799957 scopus 로고    scopus 로고
    • Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway
    • Thierry S, Thierry E, Subra F, Deprez E, Leh H, Bury-Moné S, Delelis O. 2016. Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway. Sci Rep 6: 25678.
    • (2016) Sci Rep , vol.6 , pp. 25678
    • Thierry, S.1    Thierry, E.2    Subra, F.3    Deprez, E.4    Leh, H.5    Bury-Moné, S.6    Delelis, O.7
  • 63
    • 79952073585 scopus 로고    scopus 로고
    • The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation
    • Tsukada J, Yoshida Y, Kominato Y, Auron PE. 2011. The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation. Cytokine 54: 6-19.
    • (2011) Cytokine , vol.54 , pp. 6-19
    • Tsukada, J.1    Yoshida, Y.2    Kominato, Y.3    Auron, P.E.4
  • 66
    • 80355136115 scopus 로고    scopus 로고
    • Lentivirus production
    • Wang X, McManus M. 2009. Lentivirus production. J Vis Exp 32: 1499.
    • (2009) J Vis Exp , vol.32 , pp. 1499
    • Wang, X.1    McManus, M.2
  • 67
    • 0038241793 scopus 로고    scopus 로고
    • HNF4: A central regulator of hepatocyte differentiation and function
    • Watt AJ, Garrison WD, Duncan SA. 2003. HNF4: a central regulator of hepatocyte differentiation and function. Hepatology 37: 1249-1253.
    • (2003) Hepatology , vol.37 , pp. 1249-1253
    • Watt, A.J.1    Garrison, W.D.2    Duncan, S.A.3
  • 68
    • 84939265529 scopus 로고    scopus 로고
    • Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences
    • White MA. 2015. Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences. Genomics 106: 165-170.
    • (2015) Genomics , vol.106 , pp. 165-170
    • White, M.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.