메뉴 건너뛰기




Volumn 43, Issue , 2017, Pages 110-119

Transcription factor–DNA binding: beyond binding site motifs

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; DNA; TRANSCRIPTION FACTOR; DNA BINDING PROTEIN; PROTEIN BINDING;

EID: 85016144506     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2017.02.007     Document Type: Review
Times cited : (236)

References (105)
  • 1
    • 84885841612 scopus 로고    scopus 로고
    • Modeling the specificity of protein–DNA interactions
    • 1 Stormo, G.D., Modeling the specificity of protein–DNA interactions. Quant Biol 1 (2013), 115–130.
    • (2013) Quant Biol , vol.1 , pp. 115-130
    • Stormo, G.D.1
  • 3
    • 84946068207 scopus 로고    scopus 로고
    • UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
    • 3 Hume, M.A., Barrera, L.A., Gisselbrecht, S.S., Bulyk, M.L., UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions. Nucleic Acids Res 43 (2015), D117–122.
    • (2015) Nucleic Acids Res , vol.43 , pp. D117-122
    • Hume, M.A.1    Barrera, L.A.2    Gisselbrecht, S.S.3    Bulyk, M.L.4
  • 7
    • 84907413210 scopus 로고    scopus 로고
    • Determination and inference of eukaryotic transcription factor sequence specificity
    • The authors used PBMs to elucidate the DNA binding specificities of more than 1000 TFs from a wide range of organisms; their findings suggest that TF–DNA binding specificity can be inferred from TFs containing highly similar DBDs.
    • 7• Weirauch, M.T., Yang, A., Albu, M., Cote, A.G., Montenegro-Montero, A., Drewe, P., Najafabadi, H.S., Lambert, S.A., Mann, I., Cook, K., et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158 (2014), 1431–1443 The authors used PBMs to elucidate the DNA binding specificities of more than 1000 TFs from a wide range of organisms; their findings suggest that TF–DNA binding specificity can be inferred from TFs containing highly similar DBDs.
    • (2014) Cell , vol.158 , pp. 1431-1443
    • Weirauch, M.T.1    Yang, A.2    Albu, M.3    Cote, A.G.4    Montenegro-Montero, A.5    Drewe, P.6    Najafabadi, H.S.7    Lambert, S.A.8    Mann, I.9    Cook, K.10
  • 8
    • 62549128139 scopus 로고    scopus 로고
    • A census of human transcription factors: function, expression and evolution
    • 8 Vaquerizas, J.M., Kummerfeld, S.K., Teichmann, S.A., Luscombe, N.M., A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10 (2009), 252–263.
    • (2009) Nat Rev Genet , vol.10 , pp. 252-263
    • Vaquerizas, J.M.1    Kummerfeld, S.K.2    Teichmann, S.A.3    Luscombe, N.M.4
  • 12
    • 83755196322 scopus 로고    scopus 로고
    • Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
    • R125-2011-2012-2012-r2125
    • 12 Gordân, R., Murphy, K.F., McCord, R.P., Zhu, C., Vedenko, A., Bulyk, M.L., Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol, 12, 2011 R125-2011-2012-2012-r2125.
    • (2011) Genome Biol , vol.12
    • Gordân, R.1    Murphy, K.F.2    McCord, R.P.3    Zhu, C.4    Vedenko, A.5    Bulyk, M.L.6
  • 13
    • 84895810018 scopus 로고    scopus 로고
    • Protein–DNA binding: complexities and multi-protein codes
    • 13 Siggers, T., Gordân, R., Protein–DNA binding: complexities and multi-protein codes. Nucleic Acids Res 42 (2014), 2099–2111.
    • (2014) Nucleic Acids Res , vol.42 , pp. 2099-2111
    • Siggers, T.1    Gordân, R.2
  • 14
  • 16
    • 84948568467 scopus 로고    scopus 로고
    • Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes
    • 16 Yao, L., Berman, B.P., Farnham, P.J., Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 50 (2015), 550–573.
    • (2015) Crit Rev Biochem Mol Biol , vol.50 , pp. 550-573
    • Yao, L.1    Berman, B.P.2    Farnham, P.J.3
  • 17
    • 84953206812 scopus 로고    scopus 로고
    • The soft touch: low-affinity transcription factor binding sites in development and evolution
    • 17 Crocker, J., Noon, E.P., Stern, D.L., The soft touch: low-affinity transcription factor binding sites in development and evolution. Curr Top Dev Biol 117 (2016), 455–469.
    • (2016) Curr Top Dev Biol , vol.117 , pp. 455-469
    • Crocker, J.1    Noon, E.P.2    Stern, D.L.3
  • 19
    • 84869502241 scopus 로고    scopus 로고
    • ChIP-seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
    • 19 Furey, T.S., ChIP-seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nat Rev Genet 13 (2012), 840–852.
    • (2012) Nat Rev Genet , vol.13 , pp. 840-852
    • Furey, T.S.1
  • 20
  • 21
    • 79958117256 scopus 로고    scopus 로고
    • MEME-ChIP: motif analysis of large DNA datasets
    • 21 Machanick, P., Bailey, T.L., MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27 (2011), 1696–1697.
    • (2011) Bioinformatics , vol.27 , pp. 1696-1697
    • Machanick, P.1    Bailey, T.L.2
  • 22
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • 22 ENCODE Project Consortium, An integrated encyclopedia of DNA elements in the human genome. Nature 489 (2012), 57–74.
    • (2012) Nature , vol.489 , pp. 57-74
    • ENCODE Project Consortium1
  • 23
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein–DNA interactions detected at single-nucleotide resolution
    • 23 Rhee, H.S., Pugh, B.F., Comprehensive genome-wide protein–DNA interactions detected at single-nucleotide resolution. Cell 147 (2011), 1408–1419.
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 24
    • 84926619310 scopus 로고    scopus 로고
    • ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
    • 24 He, Q., Johnston, J., Zeitlinger, J., ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat Biotechnol 33 (2015), 395–401.
    • (2015) Nat Biotechnol , vol.33 , pp. 395-401
    • He, Q.1    Johnston, J.2    Zeitlinger, J.3
  • 26
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • 26 Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10 (2013), 1213–1218.
    • (2013) Nat Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 29
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin
    • 29 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 17 (2007), 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
  • 30
    • 84959449100 scopus 로고    scopus 로고
    • Genome-wide footprinting: ready for prime time?
    • 30 Sung, M.H., Baek, S., Hager, G.L., Genome-wide footprinting: ready for prime time?. Nat Methods 13 (2016), 222–228.
    • (2016) Nat Methods , vol.13 , pp. 222-228
    • Sung, M.H.1    Baek, S.2    Hager, G.L.3
  • 32
    • 84894613651 scopus 로고    scopus 로고
    • Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
    • 32 He, H.H., Meyer, C.A., Hu, S.S., Chen, M.W., Zang, C., Liu, Y., Rao, P.K., Fei, T., Xu, H., Long, H., et al. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods 11 (2014), 73–78.
    • (2014) Nat Methods , vol.11 , pp. 73-78
    • He, H.H.1    Meyer, C.A.2    Hu, S.S.3    Chen, M.W.4    Zang, C.5    Liu, Y.6    Rao, P.K.7    Fei, T.8    Xu, H.9    Long, H.10
  • 33
    • 84922589001 scopus 로고    scopus 로고
    • DNase footprint signatures are dictated by factor dynamics and DNA sequence
    • 33 Sung, M.H., Guertin, M.J., Baek, S., Hager, G.L., DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol Cell 56 (2014), 275–285.
    • (2014) Mol Cell , vol.56 , pp. 275-285
    • Sung, M.H.1    Guertin, M.J.2    Baek, S.3    Hager, G.L.4
  • 34
    • 23444446753 scopus 로고    scopus 로고
    • A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
    • 34 Meng, X., Brodsky, M.H., Wolfe, S.A., A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol 23 (2005), 988–994.
    • (2005) Nat Biotechnol , vol.23 , pp. 988-994
    • Meng, X.1    Brodsky, M.H.2    Wolfe, S.A.3
  • 35
    • 77956654773 scopus 로고    scopus 로고
    • De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
    • 35 Fordyce, P.M., Gerber, D., Tran, D., Zheng, J., Li, H., DeRisi, J.L., Quake, S.R., De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol 28 (2010), 970–975.
    • (2010) Nat Biotechnol , vol.28 , pp. 970-975
    • Fordyce, P.M.1    Gerber, D.2    Tran, D.3    Zheng, J.4    Li, H.5    DeRisi, J.L.6    Quake, S.R.7
  • 36
    • 33846467150 scopus 로고    scopus 로고
    • A systems approach to measuring the binding energy landscapes of transcription factors
    • 36 Maerkl, S.J., Quake, S.R., A systems approach to measuring the binding energy landscapes of transcription factors. Science 315 (2007), 233–237.
    • (2007) Science , vol.315 , pp. 233-237
    • Maerkl, S.J.1    Quake, S.R.2
  • 37
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • 37 Berger, M.F., Philippakis, A.A., Qureshi, A.M., He, F.S., Estep, P.W. 3rd, Bulyk, M.L., Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24 (2006), 1429–1435.
    • (2006) Nat Biotechnol , vol.24 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep, P.W.5    Bulyk, M.L.6
  • 38
    • 84876955991 scopus 로고    scopus 로고
    • Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
    • 38 Gordân, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R., Bulyk, M.L., Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep 3 (2013), 1093–1104.
    • (2013) Cell Rep , vol.3 , pp. 1093-1104
    • Gordân, R.1    Shen, N.2    Dror, I.3    Zhou, T.4    Horton, J.5    Rohs, R.6    Bulyk, M.L.7
  • 40
    • 0036022523 scopus 로고    scopus 로고
    • High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
    • 40 Roulet, E., Busso, S., Camargo, A.A., Simpson, A.J., Mermod, N., Bucher, P., High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 20 (2002), 831–835.
    • (2002) Nat Biotechnol , vol.20 , pp. 831-835
    • Roulet, E.1    Busso, S.2    Camargo, A.A.3    Simpson, A.J.4    Mermod, N.5    Bucher, P.6
  • 42
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein–DNA interactions
    • 42 Stormo, G.D., Zhao, Y., Determining the specificity of protein–DNA interactions. Nat Rev Genet 11 (2010), 751–760.
    • (2010) Nat Rev Genet , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 43
    • 84947717868 scopus 로고    scopus 로고
    • DNA-dependent formation of transcription factor pairs alters their binding specificity
    • CAP-SELEX analyses of TF–TF–DNA interactions revealed roles for DNA in mediating cooperative interactions between TFs and identified hundreds of unique heterodimeric TF binding site motifs.
    • 43•• Jolma, A., Yin, Y., Nitta, K.R., Dave, K., Popov, A., Taipale, M., Enge, M., Kivioja, T., Morgunova, E., Taipale, J., DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 527 (2015), 384–388 CAP-SELEX analyses of TF–TF–DNA interactions revealed roles for DNA in mediating cooperative interactions between TFs and identified hundreds of unique heterodimeric TF binding site motifs.
    • (2015) Nature , vol.527 , pp. 384-388
    • Jolma, A.1    Yin, Y.2    Nitta, K.R.3    Dave, K.4    Popov, A.5    Taipale, M.6    Enge, M.7    Kivioja, T.8    Morgunova, E.9    Taipale, J.10
  • 44
    • 84964312637 scopus 로고    scopus 로고
    • High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding
    • 44 Zuo, Z., Stormo, G.D., High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Genetics 198 (2014), 1329–1343.
    • (2014) Genetics , vol.198 , pp. 1329-1343
    • Zuo, Z.1    Stormo, G.D.2
  • 46
    • 84906790368 scopus 로고    scopus 로고
    • Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding
    • The authors demonstrated that paralogous C2H2 zinc finger TFs can gain novel DNA-binding specificities in a modular fashion, without altering binding to common core sequences recognized by all family members.
    • 46• Siggers, T., Reddy, J., Barron, B., Bulyk, M.L., Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell 55 (2014), 640–648 The authors demonstrated that paralogous C2H2 zinc finger TFs can gain novel DNA-binding specificities in a modular fashion, without altering binding to common core sequences recognized by all family members.
    • (2014) Mol Cell , vol.55 , pp. 640-648
    • Siggers, T.1    Reddy, J.2    Barron, B.3    Bulyk, M.L.4
  • 50
    • 84959450092 scopus 로고    scopus 로고
    • A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity
    • 50 Garton, M., Najafabadi, H.S., Schmitges, F.W., Radovani, E., Hughes, T.R., Kim, P.M., A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Nucleic Acids Res 43 (2015), 9147–9157.
    • (2015) Nucleic Acids Res , vol.43 , pp. 9147-9157
    • Garton, M.1    Najafabadi, H.S.2    Schmitges, F.W.3    Radovani, E.4    Hughes, T.R.5    Kim, P.M.6
  • 51
    • 83455164709 scopus 로고    scopus 로고
    • Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
    • 51 Siggers, T., Duyzend, M.H., Reddy, J., Khan, S., Bulyk, M.L., Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol Syst Biol, 7, 2011, 555.
    • (2011) Mol Syst Biol , vol.7 , pp. 555
    • Siggers, T.1    Duyzend, M.H.2    Reddy, J.3    Khan, S.4    Bulyk, M.L.5
  • 52
    • 85009837028 scopus 로고    scopus 로고
    • Combinatorial function of transcription factors and cofactors
    • 52 Reiter, F., Wienerroither, S., Stark, A., Combinatorial function of transcription factors and cofactors. Curr Opin Genet Dev 43 (2017), 73–81.
    • (2017) Curr Opin Genet Dev , vol.43 , pp. 73-81
    • Reiter, F.1    Wienerroither, S.2    Stark, A.3
  • 53
    • 67749095703 scopus 로고    scopus 로고
    • Hox specificity unique roles for cofactors and collaborators
    • 53 Mann, R.S., Lelli, K.M., Joshi, R., Hox specificity unique roles for cofactors and collaborators. Curr Top Dev Biol 88 (2009), 63–101.
    • (2009) Curr Top Dev Biol , vol.88 , pp. 63-101
    • Mann, R.S.1    Lelli, K.M.2    Joshi, R.3
  • 54
    • 84951325892 scopus 로고    scopus 로고
    • Competition between DNA methylation and transcription factors determines binding of NRF1
    • 54 Domcke, S., Bardet, A.F., Adrian Ginno, P., Hartl, D., Burger, L., Schubeler, D., Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528 (2015), 575–579.
    • (2015) Nature , vol.528 , pp. 575-579
    • Domcke, S.1    Bardet, A.F.2    Adrian Ginno, P.3    Hartl, D.4    Burger, L.5    Schubeler, D.6
  • 55
  • 56
    • 84878716506 scopus 로고    scopus 로고
    • CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo
    • 56 Mann, I.K., Chatterjee, R., Zhao, J., He, X., Weirauch, M.T., Hughes, T.R., Vinson, C., CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. Genome Res 23 (2013), 988–997.
    • (2013) Genome Res , vol.23 , pp. 988-997
    • Mann, I.K.1    Chatterjee, R.2    Zhao, J.3    He, X.4    Weirauch, M.T.5    Hughes, T.R.6    Vinson, C.7
  • 57
    • 84980361817 scopus 로고    scopus 로고
    • Transcription factors as readers and effectors of DNA methylation
    • 57 Zhu, H., Wang, G., Qian, J., Transcription factors as readers and effectors of DNA methylation. Nat Rev Genet 17 (2016), 551–565.
    • (2016) Nat Rev Genet , vol.17 , pp. 551-565
    • Zhu, H.1    Wang, G.2    Qian, J.3
  • 59
    • 84930409407 scopus 로고    scopus 로고
    • Deconvolving the recognition of DNA shape from sequence
    • The authors used targeted mutagenesis and residue swapping experiments to show that shape readout is separable from base readout by the anterior Hox TF Scr.
    • 59•• Abe, N., Dror, I., Yang, L., Slattery, M., Zhou, T., Bussemaker, H.J., Rohs, R., Mann, R.S., Deconvolving the recognition of DNA shape from sequence. Cell 161 (2015), 307–318 The authors used targeted mutagenesis and residue swapping experiments to show that shape readout is separable from base readout by the anterior Hox TF Scr.
    • (2015) Cell , vol.161 , pp. 307-318
    • Abe, N.1    Dror, I.2    Yang, L.3    Slattery, M.4    Zhou, T.5    Bussemaker, H.J.6    Rohs, R.7    Mann, R.S.8
  • 60
    • 84891768983 scopus 로고    scopus 로고
    • TFBSshape: a motif database for DNA shape features of transcription factor binding sites
    • 60 Yang, L., Zhou, T., Dror, I., Mathelier, A., Wasserman, W.W., Gordân, R., Rohs, R., TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res 42 (2014), D148–D155.
    • (2014) Nucleic Acids Res , vol.42 , pp. D148-D155
    • Yang, L.1    Zhou, T.2    Dror, I.3    Mathelier, A.4    Wasserman, W.W.5    Gordân, R.6    Rohs, R.7
  • 61
    • 84928033171 scopus 로고    scopus 로고
    • Quantitative modeling of transcription factor binding specificities using DNA shape
    • Combining DNA shape and base sequence features improved the modeling ofin vitro TF–DNA binding specificities when compared to base sequence-only models.
    • 61• Zhou, T., Shen, N., Yang, L., Abe, N., Horton, J., Mann, R.S., Bussemaker, H.J., Gordân, R., Rohs, R., Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A 112 (2015), 4654–4659 Combining DNA shape and base sequence features improved the modeling ofin vitro TF–DNA binding specificities when compared to base sequence-only models.
    • (2015) Proc Natl Acad Sci U S A , vol.112 , pp. 4654-4659
    • Zhou, T.1    Shen, N.2    Yang, L.3    Abe, N.4    Horton, J.5    Mann, R.S.6    Bussemaker, H.J.7    Gordân, R.8    Rohs, R.9
  • 62
    • 84940998400 scopus 로고    scopus 로고
    • A widespread role of the motif environment in transcription factor binding across diverse protein families
    • 62 Dror, I., Golan, T., Levy, C., Rohs, R., Mandel-Gutfreund, Y., A widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res 25 (2015), 1268–1280.
    • (2015) Genome Res , vol.25 , pp. 1268-1280
    • Dror, I.1    Golan, T.2    Levy, C.3    Rohs, R.4    Mandel-Gutfreund, Y.5
  • 64
    • 84979608897 scopus 로고    scopus 로고
    • The genetics of transcription factor DNA binding variation
    • 64 Deplancke, B., Alpern, D., Gardeux, V., The genetics of transcription factor DNA binding variation. Cell 166 (2016), 538–554.
    • (2016) Cell , vol.166 , pp. 538-554
    • Deplancke, B.1    Alpern, D.2    Gardeux, V.3
  • 69
    • 84963611399 scopus 로고    scopus 로고
    • Pooled ChIP-seq links variation in transcription factor binding to complex disease risk
    • 69 Tehranchi, A.K., Myrthil, M., Martin, T., Hie, B.L., Golan, D., Fraser, H.B., Pooled ChIP-seq links variation in transcription factor binding to complex disease risk. Cell 165 (2016), 730–741.
    • (2016) Cell , vol.165 , pp. 730-741
    • Tehranchi, A.K.1    Myrthil, M.2    Martin, T.3    Hie, B.L.4    Golan, D.5    Fraser, H.B.6
  • 71
    • 84869853147 scopus 로고    scopus 로고
    • Complex effects of nucleotide variants in a mammalian cis-regulatory element
    • 71 Kwasnieski, J.C., Mogno, I., Myers, C.A., Corbo, J.C., Cohen, B.A., Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A 109 (2012), 19498–19503.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 19498-19503
    • Kwasnieski, J.C.1    Mogno, I.2    Myers, C.A.3    Corbo, J.C.4    Cohen, B.A.5
  • 74
    • 84887460044 scopus 로고    scopus 로고
    • Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
    • 74 Mogno, I., Kwasnieski, J.C., Cohen, B.A., Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. Genome Res 23 (2013), 1908–1915.
    • (2013) Genome Res , vol.23 , pp. 1908-1915
    • Mogno, I.1    Kwasnieski, J.C.2    Cohen, B.A.3
  • 75
    • 84956945024 scopus 로고    scopus 로고
    • Massively parallel cis-regulatory analysis in the mammalian central nervous system
    • 75 Shen, S.Q., Myers, C.A., Hughes, A.E., Byrne, L.C., Flannery, J.G., Corbo, J.C., Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res 26 (2016), 238–255.
    • (2016) Genome Res , vol.26 , pp. 238-255
    • Shen, S.Q.1    Myers, C.A.2    Hughes, A.E.3    Byrne, L.C.4    Flannery, J.G.5    Corbo, J.C.6
  • 79
    • 84966297436 scopus 로고    scopus 로고
    • A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface
    • This study integrated MPRAs with orthogonal approaches (e.g., genome editing and genomic data) to dissect the contributions of regulatory variants on TF binding.
    • 79• Ferreira, L.M., Meissner, T.B., Mikkelsen, T.S., Mallard, W., O'Donnell, C.W., Tilburgs, T., Gomes, H.A., Camahort, R., Sherwood, R.I., Gifford, D.K., et al. A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proc Natl Acad Sci U S A 113 (2016), 5364–5369 This study integrated MPRAs with orthogonal approaches (e.g., genome editing and genomic data) to dissect the contributions of regulatory variants on TF binding.
    • (2016) Proc Natl Acad Sci U S A , vol.113 , pp. 5364-5369
    • Ferreira, L.M.1    Meissner, T.B.2    Mikkelsen, T.S.3    Mallard, W.4    O'Donnell, C.W.5    Tilburgs, T.6    Gomes, H.A.7    Camahort, R.8    Sherwood, R.I.9    Gifford, D.K.10
  • 80
    • 84964272066 scopus 로고    scopus 로고
    • Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
    • This study integrated MPRAs with orthogonal approaches (e.g., genome editing and genomic data) to dissect the contributions of regulatory variants on TF binding.
    • 80• Tewhey, R., Kotliar, D., Park, D.S., Liu, B., Winnicki, S., Reilly, S.K., Andersen, K.G., Mikkelsen, T.S., Lander, E.S., Schaffner, S.F., et al. Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay. Cell 165 (2016), 1519–1529 This study integrated MPRAs with orthogonal approaches (e.g., genome editing and genomic data) to dissect the contributions of regulatory variants on TF binding.
    • (2016) Cell , vol.165 , pp. 1519-1529
    • Tewhey, R.1    Kotliar, D.2    Park, D.S.3    Liu, B.4    Winnicki, S.5    Reilly, S.K.6    Andersen, K.G.7    Mikkelsen, T.S.8    Lander, E.S.9    Schaffner, S.F.10
  • 81
    • 84971578930 scopus 로고    scopus 로고
    • Systematic functional dissection of common genetic variation affecting red blood cell traits
    • This study integrated MPRAs with orthogonal approaches (e.g., genome editing and genomic data) to dissect the contributions of regulatory variants on TF binding.
    • 81• Ulirsch, J.C., Nandakumar, S.K., Wang, L., Giani, F.C., Zhang, X., Rogov, P., Melnikov, A., McDonel, P., Do, R., Mikkelsen, T.S., et al. Systematic functional dissection of common genetic variation affecting red blood cell traits. Cell 165 (2016), 1530–1545 This study integrated MPRAs with orthogonal approaches (e.g., genome editing and genomic data) to dissect the contributions of regulatory variants on TF binding.
    • (2016) Cell , vol.165 , pp. 1530-1545
    • Ulirsch, J.C.1    Nandakumar, S.K.2    Wang, L.3    Giani, F.C.4    Zhang, X.5    Rogov, P.6    Melnikov, A.7    McDonel, P.8    Do, R.9    Mikkelsen, T.S.10
  • 82
    • 84946925193 scopus 로고    scopus 로고
    • BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis
    • This study was among the earliest large-scale applications of genome editing methods to dissect regulatory elements in enhancers.
    • 82•• Canver, M.C., Smith, E.C., Sher, F., Pinello, L., Sanjana, N.E., Shalem, O., Chen, D.D., Schupp, P.G., Vinjamur, D.S., Garcia, S.P., et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527 (2015), 192–197 This study was among the earliest large-scale applications of genome editing methods to dissect regulatory elements in enhancers.
    • (2015) Nature , vol.527 , pp. 192-197
    • Canver, M.C.1    Smith, E.C.2    Sher, F.3    Pinello, L.4    Sanjana, N.E.5    Shalem, O.6    Chen, D.D.7    Schupp, P.G.8    Vinjamur, D.S.9    Garcia, S.P.10
  • 83
    • 84959104222 scopus 로고    scopus 로고
    • Functional footprinting of regulatory DNA
    • This study was among the earliest large-scale applications of genome editing methods to dissect regulatory elements in enhancers.
    • 83•• Vierstra, J., Reik, A., Chang, K.H., Stehling-Sun, S., Zhou, Y., Hinkley, S.J., Paschon, D.E., Zhang, L., Psatha, N., Bendana, Y.R., et al. Functional footprinting of regulatory DNA. Nat Methods 12 (2015), 927–930 This study was among the earliest large-scale applications of genome editing methods to dissect regulatory elements in enhancers.
    • (2015) Nat Methods , vol.12 , pp. 927-930
    • Vierstra, J.1    Reik, A.2    Chang, K.H.3    Stehling-Sun, S.4    Zhou, Y.5    Hinkley, S.J.6    Paschon, D.E.7    Zhang, L.8    Psatha, N.9    Bendana, Y.R.10
  • 84
    • 84907257107 scopus 로고    scopus 로고
    • Saturation editing of genomic regions by multiplex homology-directed repair
    • 84 Findlay, G.M., Boyle, E.A., Hause, R.J., Klein, J.C., Shendure, J., Saturation editing of genomic regions by multiplex homology-directed repair. Nature 513 (2014), 120–123.
    • (2014) Nature , vol.513 , pp. 120-123
    • Findlay, G.M.1    Boyle, E.A.2    Hause, R.J.3    Klein, J.C.4    Shendure, J.5
  • 86
    • 84966333766 scopus 로고    scopus 로고
    • Quantification of cooperativity in heterodimer–DNA binding improves the accuracy of binding specificity models
    • 86 Isakova, A., Berset, Y., Hatzimanikatis, V., Deplancke, B., Quantification of cooperativity in heterodimer–DNA binding improves the accuracy of binding specificity models. J Biol Chem 291 (2016), 10293–10306.
    • (2016) J Biol Chem , vol.291 , pp. 10293-10306
    • Isakova, A.1    Berset, Y.2    Hatzimanikatis, V.3    Deplancke, B.4
  • 87
    • 84878683632 scopus 로고    scopus 로고
    • Global analysis of Drosophila Cys(2)-His(2) zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
    • 87 Enuameh, M.S., Asriyan, Y., Richards, A., Christensen, R.G., Hall, V.L., Kazemian, M., Zhu, C., Pham, H., Cheng, Q., Blatti, C., et al. Global analysis of Drosophila Cys(2)-His(2) zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res 23 (2013), 928–940.
    • (2013) Genome Res , vol.23 , pp. 928-940
    • Enuameh, M.S.1    Asriyan, Y.2    Richards, A.3    Christensen, R.G.4    Hall, V.L.5    Kazemian, M.6    Zhu, C.7    Pham, H.8    Cheng, Q.9    Blatti, C.10
  • 89
    • 84962217539 scopus 로고    scopus 로고
    • Survey of variation in human transcription factors reveals prevalent DNA binding changes
    • The authors identified many thousands of naturally occurring human TF DBD missense variants, which were collectively prevalent in humans. They further demonstrated that numerous such variants alterin vitro TF–DNA binding properties.
    • 89• Barrera, L.A., Vedenko, A., Kurland, J.V., Rogers, J.M., Gisselbrecht, S.S., Rossin, E.J., Woodard, J., Mariani, L., Kock, K.H., Inukai, S., et al. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 351 (2016), 1450–1454 The authors identified many thousands of naturally occurring human TF DBD missense variants, which were collectively prevalent in humans. They further demonstrated that numerous such variants alterin vitro TF–DNA binding properties.
    • (2016) Science , vol.351 , pp. 1450-1454
    • Barrera, L.A.1    Vedenko, A.2    Kurland, J.V.3    Rogers, J.M.4    Gisselbrecht, S.S.5    Rossin, E.J.6    Woodard, J.7    Mariani, L.8    Kock, K.H.9    Inukai, S.10
  • 90
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • 90 Schneider, T.D., Stephens, R.M., Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18 (1990), 6097–6100.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 91
    • 84863866025 scopus 로고    scopus 로고
    • Improved models for transcription factor binding site identification using nonindependent interactions
    • 91 Zhao, Y., Ruan, S., Pandey, M., Stormo, G.D., Improved models for transcription factor binding site identification using nonindependent interactions. Genetics 191 (2012), 781–790.
    • (2012) Genetics , vol.191 , pp. 781-790
    • Zhao, Y.1    Ruan, S.2    Pandey, M.3    Stormo, G.D.4
  • 92
    • 84884695174 scopus 로고    scopus 로고
    • The next generation of transcription factor binding site prediction
    • 92 Mathelier, A., Wasserman, W.W., The next generation of transcription factor binding site prediction. PLoS Comput Biol, 9, 2013, e1003214.
    • (2013) PLoS Comput Biol , vol.9 , pp. e1003214
    • Mathelier, A.1    Wasserman, W.W.2
  • 93
    • 84938888109 scopus 로고    scopus 로고
    • Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
    • 93 Alipanahi, B., Delong, A., Weirauch, M.T., Frey, B.J., Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol 33 (2015), 831–838.
    • (2015) Nat Biotechnol , vol.33 , pp. 831-838
    • Alipanahi, B.1    Delong, A.2    Weirauch, M.T.3    Frey, B.J.4
  • 94
    • 84994652021 scopus 로고    scopus 로고
    • Transcription factor-DNA binding motifs in Saccharomyces cerevisiae: tools and resources
    • pdb top080622
    • 94 Schipper, J.L., Gordân, R.M., Transcription factor-DNA binding motifs in Saccharomyces cerevisiae: tools and resources. Cold Spring Harb Protoc, 2016, 2016 pdb top080622.
    • (2016) Cold Spring Harb Protoc , vol.2016
    • Schipper, J.L.1    Gordân, R.M.2
  • 95
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • 95 Stormo, G.D., DNA binding sites: representation and discovery. Bioinformatics 16 (2000), 16–23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 97
    • 46049087782 scopus 로고    scopus 로고
    • The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    • 97 Wingender, E., The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 9 (2008), 326–332.
    • (2008) Brief Bioinform , vol.9 , pp. 326-332
    • Wingender, E.1
  • 99
    • 84898957996 scopus 로고    scopus 로고
    • CCAT: Combinatorial Code Analysis Tool for transcriptional regulation
    • 99 Jiang, P., Singh, M., CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res 42 (2014), 2833–2847.
    • (2014) Nucleic Acids Res , vol.42 , pp. 2833-2847
    • Jiang, P.1    Singh, M.2
  • 101
    • 84979854771 scopus 로고    scopus 로고
    • ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks
    • 101 Wang, P., Qin, J., Qin, Y., Zhu, Y., Wang, L.Y., Li, M.J., Zhang, M.Q., Wang, J., ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Res 43 (2015), W264–269.
    • (2015) Nucleic Acids Res , vol.43 , pp. W264-269
    • Wang, P.1    Qin, J.2    Qin, Y.3    Zhu, Y.4    Wang, L.Y.5    Li, M.J.6    Zhang, M.Q.7    Wang, J.8
  • 102
    • 84861181567 scopus 로고    scopus 로고
    • CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human
    • 102 Qin, B., Zhou, M., Ge, Y., Taing, L., Liu, T., Wang, Q., Wang, S., Chen, J., Shen, L., Duan, X., et al. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics 28 (2012), 1411–1412.
    • (2012) Bioinformatics , vol.28 , pp. 1411-1412
    • Qin, B.1    Zhou, M.2    Ge, Y.3    Taing, L.4    Liu, T.5    Wang, Q.6    Wang, S.7    Chen, J.8    Shen, L.9    Duan, X.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.