메뉴 건너뛰기




Volumn 15, Issue 7, 2014, Pages 453-468

In pursuit of design principles of regulatory sequences

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; ENHANCEOSOME; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

EID: 84902810053     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg3684     Document Type: Review
Times cited : (169)

References (151)
  • 1
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961).
    • (1961) J. Mol. Biol , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 2
    • 77956495708 scopus 로고    scopus 로고
    • Transcriptional enhancers in animal development and evolution
    • Levine, M. Transcriptional enhancers in animal development and evolution. Curr. Biol. 20, R754-R763 (2010).
    • (2010) Curr. Biol , vol.20
    • Levine, M.1
  • 3
    • 79960261434 scopus 로고    scopus 로고
    • Enhancers: From developmental genetics to the genetics of common human disease
    • Williamson, I., Hill, R. E. & Bickmore, W. A. Enhancers: from developmental genetics to the genetics of common human disease. Dev. Cell 21, 17-19 (2011).
    • (2011) Dev. Cell , vol.21 , pp. 17-19
    • Williamson, I.1    Hill, R.E.2    Bickmore, W.A.3
  • 4
    • 84891375981 scopus 로고    scopus 로고
    • Functional anatomy of distant-acting mammalian enhancers
    • Dickel, D. E., Visel, A. & Pennacchio, L. A. Functional anatomy of distant-acting mammalian enhancers. Phil. Trans. R. Soc. B 368, 20120359 (2013).
    • (2013) Phil. Trans. R. Soc. B , vol.368 , pp. 20120359
    • Dickel, D.E.1    Visel, A.2    Pennacchio, L.A.3
  • 5
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
    • (2012) Science , vol.337 , pp. 1190-1195
    • Maurano, M.T.1
  • 6
    • 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
  • 7
    • 84855720966 scopus 로고    scopus 로고
    • Transcriptional enhancers in development and disease
    • Sakabe, N. J., Savic, D. & Nobrega, M. A. Transcriptional enhancers in development and disease. Genome Biol. 13, 238 (2012).
    • (2012) Genome Biol , vol.13 , Issue.238
    • Sakabe, N.J.1    Savic, D.2    Nobrega, M.A.3
  • 8
    • 84868198825 scopus 로고    scopus 로고
    • Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression
    • Cowper-Sal lari, R. et al. Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nature Genet. 44, 1191-1198 (2012).
    • (2012) Nature Genet , vol.44 , pp. 1191-1198
    • Cowper-Sal Lari, R.1
  • 9
    • 84880870139 scopus 로고    scopus 로고
    • Lessons from functional analysis of genome-wide association studies
    • Sur, I., Tuupanen, S., Whitington, T., Aaltonen, L. A. & Taipale, J. Lessons from functional analysis of genome-wide association studies. Cancer Res. 73, 4180-4184 (2013).
    • (2013) Cancer Res , vol.73 , pp. 4180-4184
    • Sur, I.1    Tuupanen, S.2    Whitington, T.3    Aaltonen, L.A.4    Taipale, J.5
  • 10
    • 0029559463 scopus 로고
    • Yeast transcriptional regulatory mechanisms
    • Struhl, K. Yeast transcriptional regulatory mechanisms. Annu. Rev. Genet. 29, 651-674 (1995).
    • (1995) Annu. Rev. Genet , vol.29 , pp. 651-674
    • Struhl, K.1
  • 11
    • 0030960672 scopus 로고    scopus 로고
    • Transcriptional activation by recruitment
    • Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569-577 (1997).
    • (1997) Nature , vol.386 , pp. 569-577
    • Ptashne, M.1    Gann, A.2
  • 12
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1
  • 13
    • 79951493843 scopus 로고    scopus 로고
    • A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces
    • Venters, B. J. et al. A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol. Cell 41, 480-492 (2011).
    • (2011) Mol. Cell , vol.41 , pp. 480-492
    • Venters, B.J.1
  • 14
    • 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 316, 1497-1502 (2007).
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 15
    • 84865856641 scopus 로고    scopus 로고
    • Sequence and chromatin determinants of cell-type-specific transcription factor binding
    • Arvey, A., Agius, P., Noble, W. S. & Leslie, C. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res. 22, 1723-1734 (2012).
    • (2012) Genome Res , vol.22 , pp. 1723-1734
    • Arvey, A.1    Agius, P.2    Noble, W.S.3    Leslie, C.4
  • 16
    • 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 147, 1408-1419 (2011).
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 17
    • 63849308888 scopus 로고    scopus 로고
    • Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
    • Hesselberth, J. R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods 6, 283-289 (2009).
    • (2009) Nature Methods , vol.6 , pp. 283-289
    • Hesselberth, J.R.1
  • 18
    • 84865708757 scopus 로고    scopus 로고
    • An expansive human regulatory lexicon encoded in transcription factor footprints
    • Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012).
    • (2012) Nature , vol.489 , pp. 83-90
    • Neph, S.1
  • 19
    • 84859582058 scopus 로고    scopus 로고
    • Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
    • Lickwar, C. R., Mueller, F., Hanlon, S. E., McNally, J. G. & Lieb, J. D. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484, 251-255 (2012).
    • (2012) Nature , vol.484 , pp. 251-255
    • Lickwar, C.R.1    Mueller, F.2    Hanlon, S.E.3    McNally, J.G.4    Lieb, J.D.5
  • 20
    • 84885853740 scopus 로고    scopus 로고
    • Measuring chromatin interaction dynamics on the second time scale at single-copy genes
    • Poorey, K. et al. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science 342, 369-372 (2013).
    • (2013) Science , vol.342 , pp. 369-372
    • Poorey, K.1
  • 21
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions
    • Stormo, G. D. & Zhao, Y. Determining the specificity of protein-DNA interactions. Nature Rev. Genet. 11, 751-760 (2010).
    • (2010) Nature Rev. Genet , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 22
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for saccharomyces cerevisiae
    • MacIsaac, K. D. et al. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7, 113 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • Macisaac, K.D.1
  • 23
    • 59949083631 scopus 로고    scopus 로고
    • Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors
    • Berger, M. F. & Bulyk, M. L. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protoc. 4, 393-411 (2009).
    • (2009) Nature Protoc , vol.4 , pp. 393-411
    • Berger, M.F.1    Bulyk, M.L.2
  • 24
    • 74549209548 scopus 로고    scopus 로고
    • Inferring binding energies from selected binding sites
    • Zhao, Y., Granas, D. & Stormo, G. D. Inferring binding energies from selected binding sites. PLoS Comput. Biol. 5, e1000590 (2009).
    • (2009) PLoS Comput. Biol , vol.5
    • Zhao, Y.1    Granas, D.2    Stormo, G.D.3
  • 25
    • 84872540994 scopus 로고    scopus 로고
    • DNA-binding specificities of human transcription factors
    • Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013).
    • (2013) Cell , vol.152 , pp. 327-339
    • Jolma, A.1
  • 26
    • 33846467150 scopus 로고    scopus 로고
    • A systems approach to measuring the binding energy landscapes of transcription factors
    • Maerkl, S. J. & Quake, S. R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233-237 (2007).
    • (2007) Science , vol.315 , pp. 233-237
    • Maerkl, S.J.1    Quake, S.R.2
  • 27
    • 77956654773 scopus 로고    scopus 로고
    • De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
    • Fordyce, P. M. et al. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nature Biotech. 28, 970-975 (2010).
    • (2010) Nature Biotech , vol.28 , pp. 970-975
    • Fordyce, P.M.1
  • 28
    • 79960277492 scopus 로고    scopus 로고
    • Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
    • Nutiu, R. et al. Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nature Biotech. 29, 659-664 (2011).
    • (2011) Nature Biotech , vol.29 , pp. 659-664
    • Nutiu, R.1
  • 29
    • 57749121616 scopus 로고    scopus 로고
    • A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
    • Badis, G. et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol. Cell 32, 878-887 (2008).
    • (2008) Mol. Cell , vol.32 , pp. 878-887
    • Badis, G.1
  • 30
    • 63849315606 scopus 로고    scopus 로고
    • High-resolution DNA-binding specificity analysis of yeast transcription factors
    • Zhu, C. et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 19, 556-566 (2009).
    • (2009) Genome Res , vol.19 , pp. 556-566
    • Zhu, C.1
  • 31
    • 67650594823 scopus 로고    scopus 로고
    • A multiparameter network reveals extensive divergence between C elegans bHLH transcription factors
    • Grove, C. A. et al. A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 138, 314-327 (2009).
    • (2009) Cell , vol.138 , pp. 314-327
    • Grove, C.A.1
  • 32
    • 67649982744 scopus 로고    scopus 로고
    • Diversity and complexity in DNA recognition by transcription factors
    • Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723 (2009).
    • (2009) Science , vol.324 , pp. 1720-1723
    • Badis, G.1
  • 33
    • 30544449081 scopus 로고    scopus 로고
    • Quantitative protein interaction network for the ErbB receptors using protein microarrays
    • Jones, R. B., Gordus, A., Krall, J. A. & MacBeath, G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439, 168-174 (2006).
    • (2006) Nature , vol.439 , pp. 168-174
    • Jones, R.B.1    Gordus, A.2    Krall, J.A.3    Macbeath, G.A.4
  • 34
    • 83455164709 scopus 로고    scopus 로고
    • Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
    • 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, 555 (2011).
    • (2011) Mol. Syst. Biol , vol.7 , Issue.555
    • Siggers, T.1    Duyzend, M.H.2    Reddy, J.3    Khan, S.4    Bulyk, M.L.5
  • 35
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium et al.
    • ENCODE Project Consortium et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
  • 36
    • 84862002321 scopus 로고    scopus 로고
    • Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
    • Sharon, E. et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nature Biotech. 30, 521-530 (2012).
    • (2012) Nature Biotech , vol.30 , pp. 521-530
    • Sharon, E.1
  • 37
    • 84885018787 scopus 로고    scopus 로고
    • Mapping the fine structure of a eukaryotic promoter input-output function
    • Rajkumar, A. S., Denervaud, N. & Maerkl, S. J. Mapping the fine structure of a eukaryotic promoter input-output function. Nature Genet. 45, 1207-1215 (2013).
    • (2013) Nature Genet , vol.45 , pp. 1207-1215
    • Rajkumar, A.S.1    Denervaud, N.2    Maerkl, S.J.3
  • 38
    • 84887460044 scopus 로고    scopus 로고
    • Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
    • 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, 1908-1915 (2013).
    • (2013) Genome Res , vol.23 , pp. 1908-1915
    • Mogno, I.1    Kwasnieski, J.C.2    Cohen, B.A.3
  • 39
    • 84877147962 scopus 로고    scopus 로고
    • Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
    • Kheradpour, P. et al. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res. 23, 800-811 (2013).
    • (2013) Genome Res , vol.23 , pp. 800-811
    • Kheradpour, P.1
  • 40
    • 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 451, 535-540 (2008).
    • (2008) Nature , vol.451 , pp. 535-540
    • Segal, E.1    Raveh-Sadka, T.2    Schroeder, M.3    Unnerstall, U.4    Gaul, U.5
  • 41
    • 84881442078 scopus 로고    scopus 로고
    • Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos
    • Gisselbrecht, S. S. et al. Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nature Methods 10, 774-780 (2013).
    • (2013) Nature Methods , vol.10 , pp. 774-780
    • Gisselbrecht, S.S.1
  • 42
    • 33749381311 scopus 로고    scopus 로고
    • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    • Liu, X., Lee, C. K., Granek, J. A., Clarke, N. D. & Lieb, J. D. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res. 16, 1517-1528 (2006).
    • (2006) Genome Res , vol.16 , pp. 1517-1528
    • Liu, X.1    Lee, C.K.2    Granek, J.A.3    Clarke, N.D.4    Lieb, J.D.5
  • 43
    • 84859230739 scopus 로고    scopus 로고
    • Accurate prediction of inducible transcription factor binding intensities
    • Guertin, M. J., Martins, A. L., Siepel, A. & Lis, J. T. Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet. 8, e1002610 (2012).
    • (2012) Vivo. PLoS Genet , vol.8
    • Guertin, M.J.1    Martins, A.L.2    Siepel, A.3    Lis, J.T.4
  • 44
    • 79959359483 scopus 로고    scopus 로고
    • Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
    • Zhou, X. & O'Shea, E. K. Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol. Cell 42, 826-836 (2011).
    • (2011) Mol. Cell , vol.42 , pp. 826-836
    • Zhou, X.1    O'shea, E.K.2
  • 45
    • 84876955991 scopus 로고    scopus 로고
    • Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
    • Gordan, R. et al. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep. 3, 1093-1104 (2013).
    • (2013) Cell Rep , vol.3 , pp. 1093-1104
    • Gordan, R.1
  • 46
    • 84863649033 scopus 로고    scopus 로고
    • Master regulatory GATA transcription factors: Mechanistic principles and emerging links to hematologic malignancies
    • Bresnick, E. H., Katsumura, K. R., Lee, H. Y., Johnson, K. D. & Perkins, A. S. Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies. Nucleic Acids Res. 40, 5819-5831 (2012).
    • (2012) Nucleic Acids Res , vol.40 , pp. 5819-5831
    • Bresnick, E.H.1    Katsumura, K.R.2    Lee, H.Y.3    Johnson, K.D.4    Perkins, A.S.5
  • 47
    • 84895810018 scopus 로고    scopus 로고
    • Protein-DNA binding: Complexities and multi-protein codes
    • Siggers, T. & Gordan, R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res. 42, 2099-2111 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. 2099-2111
    • Siggers, T.1    Gordan, R.2
  • 48
    • 83255188878 scopus 로고    scopus 로고
    • Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
    • Slattery, M. et al. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147, 1270-1282 (2011).
    • (2011) Cell , vol.147 , pp. 1270-1282
    • Slattery, M.1
  • 49
    • 84870222914 scopus 로고    scopus 로고
    • Disentangling the many layers of eukaryotic transcriptional regulation
    • Lelli, K. M., Slattery, M. & Mann, R. S. Disentangling the many layers of eukaryotic transcriptional regulation. Annu. Rev. Genet. 46, 43-68 (2012).
    • (2012) Annu. Rev. Genet , vol.46 , pp. 43-68
    • Lelli, K.M.1    Slattery, M.2    Mann, R.S.3
  • 50
    • 80054728495 scopus 로고    scopus 로고
    • Animal transcription networks as highly connected, quantitative continua
    • Biggin, M. D. Animal transcription networks as highly connected, quantitative continua. Dev. Cell 21, 611-626 (2011).
    • (2011) Dev. Cell , vol.21 , pp. 611-626
    • Biggin, M.D.1
  • 51
    • 84865249952 scopus 로고    scopus 로고
    • Transcription factors: From enhancer binding to developmental control
    • Spitz, F. & Furlong, E. E. Transcription factors: from enhancer binding to developmental control. Nature Rev. Genet. 13, 613-626 (2012).
    • (2012) Nature Rev. Genet , vol.13 , pp. 613-626
    • Spitz, F.1    Furlong, E.E.2
  • 52
    • 70549090448 scopus 로고    scopus 로고
    • Organization of developmental enhancers in the Drosophila embryo
    • Papatsenko, D., Goltsev, Y. & Levine, M. Organization of developmental enhancers in the Drosophila embryo. Nucleic Acids Res. 37, 5665-5677 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. 5665-5677
    • Papatsenko, D.1    Goltsev, Y.2    Levine, M.3
  • 53
    • 1642289044 scopus 로고    scopus 로고
    • Coordinate enhancers share common organizational features in the Drosophila genome
    • Erives, A. & Levine, M. Coordinate enhancers share common organizational features in the Drosophila genome. Proc. Natl Acad. Sci. USA 101, 3851-3856 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 3851-3856
    • Erives, A.1    Levine, M.2
  • 54
    • 44349089659 scopus 로고    scopus 로고
    • The words of the regulatory code are arranged in a variable manner in highly conserved enhancers
    • Rastegar, S. et al. The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev. Biol. 318, 366-377 (2008).
    • (2008) Dev. Biol , vol.318 , pp. 366-377
    • Rastegar, S.1
  • 55
    • 76749088015 scopus 로고    scopus 로고
    • Evolutionary mirages: Selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers
    • Lusk, R. W. & Eisen, M. B. Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet. 6, e1000829 (2010).
    • (2010) PLoS Genet , vol.6
    • Lusk, R.W.1    Eisen, M.B.2
  • 56
    • 46249134068 scopus 로고    scopus 로고
    • Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
    • Hare, E. E., Peterson, B. K., Iyer, V. N., Meier, R. & Eisen, M. B. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet. 4, e1000106 (2008).
    • (2008) PLoS Genet , vol.4
    • Hare, E.E.1    Peterson, B.K.2    Iyer, V.N.3    Meier, R.4    Eisen, M.B.5
  • 57
    • 75149143994 scopus 로고    scopus 로고
    • Conserved expression without conserved regulatory sequence: The more things change, the more they stay the same
    • Weirauch, M. T. & Hughes, T. R. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet. 26, 66-74 (2010).
    • (2010) Trends Genet , vol.26 , pp. 66-74
    • Weirauch, M.T.1    Hughes, T.R.2
  • 58
    • 70449132583 scopus 로고    scopus 로고
    • Combinatorial binding predicts spatio-temporal cis-regulatory activity
    • Zinzen, R. P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E. E. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462, 65-70 (2009).
    • (2009) Nature , vol.462 , pp. 65-70
    • Zinzen, R.P.1    Girardot, C.2    Gagneur, J.3    Braun, M.4    Furlong, E.E.5
  • 59
    • 34548690542 scopus 로고    scopus 로고
    • Functional architecture and evolution of transcriptional elements that drive gene coexpression
    • Brown, C. D., Johnson, D. S. & Sidow, A. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 317, 1557-1560 (2007).
    • (2007) Science , vol.317 , pp. 1557-1560
    • Brown, C.D.1    Johnson, D.S.2    Sidow, A.3
  • 60
    • 84883457107 scopus 로고    scopus 로고
    • Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
    • Smith, R. P. et al. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nature Genet. 45, 1021-1028 (2013).
    • (2013) Nature Genet , vol.45 , pp. 1021-1028
    • Smith, R.P.1
  • 61
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • Tanay, A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res. 16, 962-972 (2006).
    • (2006) Genome Res , vol.16 , pp. 962-972
    • Tanay, A.1
  • 62
    • 84856425002 scopus 로고    scopus 로고
    • Sparkling insights into enhancer structure, function, and evolution
    • Evans, N. C., Swanson, C. I. & Barolo, S. Sparkling insights into enhancer structure, function, and evolution. Curr. Top. Dev. Biol. 98, 97-120 (2012).
    • (2012) Curr. Top. Dev. Biol , vol.98 , pp. 97-120
    • Evans, N.C.1    Swanson, C.I.2    Barolo, S.3
  • 63
    • 79958204355 scopus 로고    scopus 로고
    • The cis-regulatory logic of Hedgehog gradient responses: Key roles for gli binding affinity, competition, and cooperativity
    • Parker, D. S., White, M. A., Ramos, A. I., Cohen, B. A. & Barolo, S. The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity. Sci Signal 4, ra38 (2011).
    • (2011) Sci Signal , vol.4
    • Parker, D.S.1    White, M.A.2    Ramos, A.I.3    Cohen, B.A.4    Barolo, S.5
  • 64
    • 80054020133 scopus 로고    scopus 로고
    • Morphogen gradients: From generation to interpretation
    • Rogers, K. W. & Schier, A. F. Morphogen gradients: from generation to interpretation. Annu. Rev. Cell Dev. Biol. 27, 377-407 (2011).
    • (2011) Annu. Rev. Cell Dev. Biol , vol.27 , pp. 377-407
    • Rogers, K.W.1    Schier, A.F.2
  • 65
    • 80455144479 scopus 로고    scopus 로고
    • Pioneer transcription factors: Establishing competence for gene expression
    • Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227-2241 (2011).
    • (2011) Genes Dev , vol.25 , pp. 2227-2241
    • Zaret, K.S.1    Carroll, J.S.2
  • 66
    • 17644397256 scopus 로고    scopus 로고
    • Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?
    • Arnosti, D. N. & Kulkarni, M. M. Transcriptional enhancers: intelligent enhanceosomes or flexible billboards? J. Cell Biochem. 94, 890-898 (2005).
    • (2005) J. Cell Biochem , vol.94 , pp. 890-898
    • Arnosti, D.N.1    Kulkarni, M.M.2
  • 67
    • 0030030902 scopus 로고    scopus 로고
    • The eve stripe 2 enhancer employs multiple modes of transcriptional synergy
    • Arnosti, D. N., Barolo, S., Levine, M. & Small, S. The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122, 205-214 (1996).
    • (1996) Development , vol.122 , pp. 205-214
    • Arnosti, D.N.1    Barolo, S.2    Levine, M.3    Small, S.4
  • 68
    • 84864595830 scopus 로고    scopus 로고
    • Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules
    • Liu, F. & Posakony, J. W. Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules. PLoS Genet. 8, e1002796 (2012).
    • (2012) PLoS Genet , vol.8
    • Liu, F.1    Posakony, J.W.2
  • 69
    • 1642368138 scopus 로고    scopus 로고
    • Immunity regulatory DNAs share common organizational features in
    • Senger, K. et al. Immunity regulatory DNAs share common organizational features in Drosophila. Mol. Cell 13, 19-32 (2004).
    • (2004) Drosophila. Mol. Cell , vol.13 , pp. 19-32
    • Senger, K.1
  • 70
    • 56849103052 scopus 로고    scopus 로고
    • Evolution acts on enhancer organization to fine-tune gradient threshold readouts
    • Crocker, J., Tamori, Y. & Erives, A. Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol. 6, e263 (2008).
    • (2008) PLoS Biol , vol.6
    • Crocker, J.1    Tamori, Y.2    Erives, A.3
  • 71
    • 77950580571 scopus 로고    scopus 로고
    • Structural rules and complex regulatory circuitry constrain expression of a Notch-and EGFR-regulated eye enhancer
    • Swanson, C. I., Evans, N. C. & Barolo, S. Structural rules and complex regulatory circuitry constrain expression of a Notch-and EGFR-regulated eye enhancer. Dev. Cell 18, 359-370 (2010).
    • (2010) Dev. Cell , vol.18 , pp. 359-370
    • Swanson, C.I.1    Evans, N.C.2    Barolo, S.3
  • 72
    • 34250017968 scopus 로고    scopus 로고
    • An atomic model of the interferon-? Enhanceosome
    • Panne, D., Maniatis, T. & Harrison, S. C. An atomic model of the interferon-? enhanceosome. Cell 129, 1111-1123 (2007).
    • (2007) Cell , vol.129 , pp. 1111-1123
    • Panne, D.1    Maniatis, T.2    Harrison, S.C.3
  • 73
    • 0029617947 scopus 로고
    • Virus induction of human IFN? Gene expression requires the assembly of an enhanceosome
    • Thanos, D. & Maniatis, T. Virus induction of human IFN? gene expression requires the assembly of an enhanceosome. Cell 83, 1091-1100 (1995).
    • (1995) Cell , vol.83 , pp. 1091-1100
    • Thanos, D.1    Maniatis, T.2
  • 74
    • 84856704764 scopus 로고    scopus 로고
    • A transcription factor collective defines cardiac cell fate and reflects lineage history
    • Junion, G. et al. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 148, 473-486 (2012).
    • (2012) Cell , vol.148 , pp. 473-486
    • Junion, G.1
  • 75
    • 84863229330 scopus 로고    scopus 로고
    • Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
    • Melnikov, A. et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature Biotech. 30, 271-277 (2012).
    • (2012) Nature Biotech , vol.30 , pp. 271-277
    • Melnikov, A.1
  • 76
    • 84863230316 scopus 로고    scopus 로고
    • Massively parallel functional dissection of mammalian enhancers
    • Patwardhan, R. P. et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotech. 30, 265-270 (2012).
    • (2012) Vivo. Nature Biotech , vol.30 , pp. 265-270
    • Patwardhan, R.P.1
  • 78
    • 84863882671 scopus 로고    scopus 로고
    • Mechanisms of transcriptional precision in animal development
    • Lagha, M., Bothma, J. P. & Levine, M. Mechanisms of transcriptional precision in animal development. Trends Genet. 28, 409-416 (2012).
    • (2012) Trends Genet , vol.28 , pp. 409-416
    • Lagha, M.1    Bothma, J.P.2    Levine, M.3
  • 79
    • 84866086842 scopus 로고    scopus 로고
    • High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    • Guo, Y., Mahony, S. & Gifford, D. K. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput. Biol. 8, e1002638 (2012).
    • (2012) PLoS Comput. Biol , vol.8
    • Guo, Y.1    Mahony, S.2    Gifford, D.K.3
  • 80
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • Tirosh, I. & Barkai, N. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 18, 1084-1091 (2008).
    • (2008) Genome Res , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 81
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • Field, Y. et al. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 4, e1000216 (2008).
    • (2008) PLoS Comput. Biol , vol.4
    • Field, Y.1
  • 82
    • 84858165145 scopus 로고    scopus 로고
    • Genome-wide structure and organization of eukaryotic pre-initiation complexes
    • Rhee, H. S. & Pugh, B. F. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483, 295-301 (2012).
    • (2012) Nature , vol.483 , pp. 295-301
    • Rhee, H.S.1    Pugh, B.F.2
  • 83
    • 0030946251 scopus 로고    scopus 로고
    • Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun
    • Leonard, D. A., Rajaram, N. & Kerppola, T. K. Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun. Proc. Natl Acad. Sci. USA 94, 4913-4918 (1997).
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 4913-4918
    • Leonard, D.A.1    Rajaram, N.2    Kerppola, T.K.3
  • 84
    • 33745070996 scopus 로고    scopus 로고
    • Flanking sequence composition differentially affects the binding and functional characteristics of glucocorticoid receptor homo-and heterodimers
    • Morin, B., Nichols, L. A. & Holland, L. J. Flanking sequence composition differentially affects the binding and functional characteristics of glucocorticoid receptor homo-and heterodimers. Biochemistry 45, 7299-7306 (2006).
    • (2006) Biochemistry , vol.45 , pp. 7299-7306
    • Morin, B.1    Nichols, L.A.2    Holland, L.J.3
  • 85
    • 0035945263 scopus 로고    scopus 로고
    • Selected base sequence outside the target binding site of zinc finger protein Sp1
    • Nagaoka, M., Shiraishi, Y. & Sugiura, Y. Selected base sequence outside the target binding site of zinc finger protein Sp1. Nucleic Acids Res. 29, 4920-4929 (2001).
    • (2001) Nucleic Acids Res , vol.29 , pp. 4920-4929
    • Nagaoka, M.1    Shiraishi, Y.2    Sugiura, Y.3
  • 86
    • 84877247171 scopus 로고    scopus 로고
    • Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal
    • Aow, J. S. et al. Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal. Nucleic Acids Res. 41, 4877-4887 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. 4877-4887
    • Aow, J.S.1
  • 87
    • 77950519937 scopus 로고    scopus 로고
    • Origins of specificity in protein-DNA recognition
    • Rohs, R. et al. Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem. 79, 233-269 (2010).
    • (2010) Annu. Rev. Biochem , vol.79 , pp. 233-269
    • Rohs, R.1
  • 88
    • 0033529565 scopus 로고    scopus 로고
    • Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome
    • Kornberg, R. D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294 (1999).
    • (1999) Cell , vol.98 , pp. 285-294
    • Kornberg, R.D.1    Lorch, Y.2
  • 89
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi, R. et al. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21, 447-455 (2011).
    • (2011) Genome Res , vol.21 , pp. 447-455
    • Pique-Regi, R.1
  • 90
    • 79952273012 scopus 로고    scopus 로고
    • Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
    • Kaplan, T. et al. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 7, e1001290 (2011).
    • (2011) PLoS Genet , vol.7
    • Kaplan, T.1
  • 91
    • 79952184341 scopus 로고    scopus 로고
    • Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
    • John, S. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nature Genet. 43, 264-268 (2011).
    • (2011) Nature Genet , vol.43 , pp. 264-268
    • John, S.1
  • 92
    • 84875196326 scopus 로고    scopus 로고
    • Determinants of nucleosome positioning
    • Struhl, K. & Segal, E. Determinants of nucleosome positioning. Nature Struct. Mol. Biol. 20, 267-273 (2013).
    • (2013) Nature Struct. Mol. Biol , vol.20 , pp. 267-273
    • Struhl, K.1    Segal, E.2
  • 93
    • 48249153426 scopus 로고    scopus 로고
    • The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome
    • Fu, Y., Sinha, M., Peterson, C. L. & Weng, Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008).
    • (2008) PLoS Genet , vol.4
    • Fu, Y.1    Sinha, M.2    Peterson, C.L.3    Weng, Z.4
  • 94
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • Tillo, D. & Hughes, T. R. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10, 442 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 95
    • 36949023082 scopus 로고    scopus 로고
    • A nucleosome-guided map of transcription factor binding sites in yeast
    • Narlikar, L., Gordan, R. & Hartemink, A. J. A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput. Biol. 3, e215 (2007).
    • (2007) PLoS Comput. Biol , vol.3
    • Narlikar, L.1    Gordan, R.2    Hartemink, A.J.3
  • 96
    • 68049083831 scopus 로고    scopus 로고
    • Incorporating nucleosomes into thermodynamic models of transcription regulation
    • Raveh-Sadka, T., Levo, M. & Segal, E. Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res. 19, 1480-1496 (2009).
    • (2009) Genome Res , vol.19 , pp. 1480-1496
    • Raveh-Sadka, T.1    Levo, M.2    Segal, E.3
  • 97
    • 70350741354 scopus 로고    scopus 로고
    • An ensemble model of competitive multi-factor binding of the genome
    • Wasson, T. & Hartemink, A. J. An ensemble model of competitive multi-factor binding of the genome. Genome Res. 19, 2101-2112 (2009).
    • (2009) Genome Res , vol.19 , pp. 2101-2112
    • Wasson, T.1    Hartemink, A.J.2
  • 98
    • 84862979650 scopus 로고    scopus 로고
    • A map of nucleosome positions in yeast at base-pair resolution
    • Brogaard, K., Xi, L., Wang, J. P. & Widom, J. A map of nucleosome positions in yeast at base-pair resolution. Nature 486, 496-501 (2012).
    • (2012) Nature , vol.486 , pp. 496-501
    • Brogaard, K.1    Xi, L.2    Wang, J.P.3    Widom, J.4
  • 99
    • 77953132064 scopus 로고    scopus 로고
    • A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites
    • Khoueiry, P. et al. A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr. Biol. 20, 792-802 (2010).
    • (2010) Curr. Biol , vol.20 , pp. 792-802
    • Khoueiry, P.1
  • 100
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: Major determinants of nucleosome organization
    • Segal, E. & Widom, J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 19, 65-71 (2009).
    • (2009) Curr. Opin. Struct. Biol , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 101
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer, V. & Struhl, K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14, 2570-2579 (1995).
    • (1995) EMBO J , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 102
    • 84862984796 scopus 로고    scopus 로고
    • Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
    • Raveh-Sadka, T. et al. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nature Genet. 44, 743-750 (2012).
    • (2012) Nature Genet , vol.44 , pp. 743-750
    • Raveh-Sadka, T.1
  • 103
    • 77949393272 scopus 로고    scopus 로고
    • High nucleosome occupancy is encoded at human regulatory sequences
    • Tillo, D. et al. High nucleosome occupancy is encoded at human regulatory sequences. PLoS ONE 5, e9129 (2010).
    • (2010) PLoS ONE , vol.5
    • Tillo, D.1
  • 104
    • 84872269321 scopus 로고    scopus 로고
    • Nucleosome-driven transcription factor binding and gene regulation
    • Ballare, C. et al. Nucleosome-driven transcription factor binding and gene regulation. Mol. Cell 49, 67-79 (2013).
    • (2013) Mol. Cell , vol.49 , pp. 67-79
    • Ballare, C.1
  • 105
    • 84880362638 scopus 로고    scopus 로고
    • Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
    • White, M. A., Myers, C. A., Corbo, J. C. & Cohen, B. A. Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc. Natl Acad. Sci. USA 110, 11952-11957 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 11952-11957
    • White, M.A.1    Myers, C.A.2    Corbo, J.C.3    Cohen, B.A.4
  • 106
    • 84857111200 scopus 로고    scopus 로고
    • DNase i sensitivity QTLs are a major determinant of human expression variation
    • Degner, J. F. et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390-394 (2012).
    • (2012) Nature , vol.482 , pp. 390-394
    • Degner, J.F.1
  • 107
    • 84865777825 scopus 로고    scopus 로고
    • Linking disease associations with regulatory information in the human genome
    • Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012).
    • (2012) Genome Res , vol.22 , pp. 1748-1759
    • Schaub, M.A.1    Boyle, A.P.2    Kundaje, A.3    Batzoglou, S.4    Snyder, M.5
  • 108
    • 84856321864 scopus 로고    scopus 로고
    • Dissecting the regulatory architecture of gene expression QTLs
    • Gaffney, D. J. et al. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 13, R7 (2012).
    • (2012) Genome Biol , vol.13
    • Gaffney, D.J.1
  • 109
    • 59249086642 scopus 로고    scopus 로고
    • Learning a prior on regulatory potential from eQTL data
    • Lee, S. I. et al. Learning a prior on regulatory potential from eQTL data. PLoS Genet. 5, e1000358 (2009).
    • (2009) PLoS Genet , vol.5
    • Lee, S.I.1
  • 110
    • 84875980888 scopus 로고    scopus 로고
    • Robust prediction of expression differences among human individuals using only genotype information
    • Manor, O. & Segal, E. Robust prediction of expression differences among human individuals using only genotype information. PLoS Genet. 9, e1003396 (2013).
    • (2013) PLoS Genet , vol.9
    • Manor, O.1    Segal, E.2
  • 111
    • 15744387380 scopus 로고    scopus 로고
    • Transcriptional regulation by the numbers: Models
    • Bintu, L. et al. Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116-124 (2005).
    • (2005) Curr. Opin. Genet. Dev , vol.15 , pp. 116-124
    • Bintu, L.1
  • 112
    • 67649826220 scopus 로고    scopus 로고
    • From DNA sequence to transcriptional behaviour: A quantitative approach
    • Segal, E. & Widom, J. From DNA sequence to transcriptional behaviour: a quantitative approach. Nature Rev. Genet. 10, 443-456 (2009).
    • (2009) Nature Rev. Genet , vol.10 , pp. 443-456
    • Segal, E.1    Widom, J.2
  • 113
    • 84858444088 scopus 로고    scopus 로고
    • Perspectives on the RNA polymerase II core promoter
    • Kadonaga, J. T. Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip. Rev. Dev. Biol. 1, 40-51 (2012).
    • (2012) Wiley Interdiscip. Rev. Dev. Biol , vol.1 , pp. 40-51
    • Kadonaga, J.T.1
  • 114
    • 78649298722 scopus 로고    scopus 로고
    • TATA is a modular component of synthetic promoters
    • Mogno, I., Vallania, F., Mitra, R. D. & Cohen, B. A. TATA is a modular component of synthetic promoters. Genome Res. 20, 1391-1397 (2010).
    • (2010) Genome Res , vol.20 , pp. 1391-1397
    • Mogno, I.1    Vallania, F.2    Mitra, R.D.3    Cohen, B.A.4
  • 115
    • 84878869936 scopus 로고    scopus 로고
    • Sequence features of yeast and human core promoters that are predictive of maximal promoter activity
    • Lubliner, S., Keren, L. & Segal, E. Sequence features of yeast and human core promoters that are predictive of maximal promoter activity. Nucleic Acids Res. 41, 5569-5581 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. 5569-5581
    • Lubliner, S.1    Keren, L.2    Segal, E.3
  • 116
    • 84858446718 scopus 로고    scopus 로고
    • Regulation of cytoplasmic mRNA decay
    • Schoenberg, D. R. & Maquat, L. E. Regulation of cytoplasmic mRNA decay. Nature Rev. Genet. 13, 246-259 (2012).
    • (2012) Nature Rev. Genet , vol.13 , pp. 246-259
    • Schoenberg, D.R.1    Maquat, L.E.2
  • 117
    • 84902812930 scopus 로고    scopus 로고
    • Global analyses of determinants of RNA decay
    • Burgess, D. J. Global analyses of determinants of RNA decay. Nature Rev. Genet. http://dx.doi.org/10.1038/nrg3710 (2014).
    • (2014) Nature Rev. Genet
    • Burgess, D.J.1
  • 118
    • 84875444381 scopus 로고    scopus 로고
    • Alternative splicing: A pivotal step between eukaryotic transcription and translation
    • Kornblihtt, A. R. et al. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nature Rev. Mol. Cell Biol. 14, 153-165 (2013).
    • (2013) Nature Rev. Mol. Cell Biol , vol.14 , pp. 153-165
    • Kornblihtt, A.R.1
  • 119
    • 84894318608 scopus 로고    scopus 로고
    • Ribosome profiling: New views of translation, from single codons to genome scale
    • Ingolia, N. T. Ribosome profiling: new views of translation, from single codons to genome scale. Nature Rev. Genet. 15, 205-213 (2014).
    • (2014) Nature Rev. Genet , vol.15 , pp. 205-213
    • Ingolia, N.T.1
  • 120
    • 84870182699 scopus 로고    scopus 로고
    • Noncoding transcription at enhancers: General principles and functional models
    • Natoli, G. & Andrau, J. C. Noncoding transcription at enhancers: general principles and functional models. Annu. Rev. Genet. 46, 1-19 (2012).
    • (2012) Annu. Rev. Genet , vol.46 , pp. 1-19
    • Natoli, G.1    Andrau, J.C.2
  • 121
    • 84897446230 scopus 로고    scopus 로고
    • Enhancer RNAs and regulated transcriptional programs
    • Lam, M. T., Li, W., Rosenfeld, M. G. & Glass, C. K. Enhancer RNAs and regulated transcriptional programs. Trends Biochem. Sci. 39, 170-182 (2014).
    • (2014) Trends Biochem. Sci , vol.39 , pp. 170-182
    • Lam, M.T.1    Li, W.2    Rosenfeld, M.G.3    Glass, C.K.4
  • 122
    • 84897459814 scopus 로고    scopus 로고
    • An atlas of active enhancers across human cell types and tissues
    • Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461 (2014).
    • (2014) Nature , vol.507 , pp. 455-461
    • Andersson, R.1
  • 123
    • 84862180741 scopus 로고    scopus 로고
    • A tunable zinc finger-based framework for Boolean logic computation in mammalian cells
    • Lohmueller, J. J., Armel, T. Z. & Silver, P. A. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res. 40, 5180-5187 (2012).
    • (2012) Nucleic Acids Res , vol.40 , pp. 5180-5187
    • Lohmueller, J.J.1    Armel, T.Z.2    Silver, P.A.3
  • 124
    • 84888055306 scopus 로고    scopus 로고
    • Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter in
    • Teo, W. S. & Chang, M. W. Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter in Saccharomyces cerevisiae. Biotechnol. Bioeng. 111, 144-151 (2013).
    • (2013) Saccharomyces Cerevisiae. Biotechnol. Bioeng , vol.111 , pp. 144-151
    • Teo, W.S.1    Chang, M.W.2
  • 125
    • 84874616818 scopus 로고    scopus 로고
    • Synergistic and tunable human gene activation by combinations of synthetic transcription factors
    • Perez-Pinera, P. et al. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nature Methods 10, 239-242 (2013).
    • (2013) Nature Methods , vol.10 , pp. 239-242
    • Perez-Pinera, P.1
  • 126
    • 84879264708 scopus 로고    scopus 로고
    • 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
    • Gaj, T., Gersbach, C. A. & Barbas, C. F. 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31, 397-405 (2013).
    • (2013) Trends Biotechnol , vol.31 , pp. 397-405
    • Gaj, T.1    Gersbach, C.A.2    Barbas, C.F.3
  • 127
    • 84895072244 scopus 로고    scopus 로고
    • High-resolution mapping of transcription factor binding sites on native chromatin
    • Kasinathan, S., Orsi, G. A., Zentner, G. E., Ahmad, K. & Henikoff, S. High-resolution mapping of transcription factor binding sites on native chromatin. Nature Methods 11, 203-209 (2014).
    • (2014) Nature Methods , vol.11 , pp. 203-209
    • Kasinathan, S.1    Orsi, G.A.2    Zentner, G.E.3    Ahmad, K.4    Henikoff, S.5
  • 128
    • 84894651254 scopus 로고    scopus 로고
    • Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH
    • Vierstra, J., Wang, H., John, S., Sandstrom, R. & Stamatoyannopoulos, J. A. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nature Methods 11, 66-72 (2014).
    • (2014) Nature Methods , vol.11 , pp. 66-72
    • Vierstra, J.1    Wang, H.2    John, S.3    Sandstrom, R.4    Stamatoyannopoulos, J.A.5
  • 129
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • 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. Nature Methods 10, 1213-1218 (2013).
    • (2013) Nature 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
  • 130
    • 2942576308 scopus 로고    scopus 로고
    • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
    • Rajewsky, N., Vergassola, M., Gaul, U. & Siggia, E. D. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3, 30 (2002).
    • (2002) BMC Bioinformatics , vol.3 , pp. 30
    • Rajewsky, N.1    Vergassola, M.2    Gaul, U.3    Siggia, E.D.4
  • 131
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • Berman, B. P. et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA 99, 757-762 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 757-762
    • Berman, B.P.1
  • 132
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009).
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 133
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 134
    • 84861733509 scopus 로고    scopus 로고
    • Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA
    • Simon, J. M., Giresi, P. G., Davis, I. J. & Lieb, J. D. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature Protoc. 7, 256-267 (2012).
    • (2012) Nature Protoc , vol.7 , pp. 256-267
    • Simon, J.M.1    Giresi, P.G.2    Davis, I.J.3    Lieb, J.D.4
  • 135
    • 0038824733 scopus 로고    scopus 로고
    • Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay
    • Khambata-Ford, S. et al. Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Genome Res. 13, 1765-1774 (2003).
    • (2003) Genome Res , vol.13 , pp. 1765-1774
    • Khambata-Ford, S.1
  • 136
    • 84868088171 scopus 로고    scopus 로고
    • A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of
    • Jory, A. et al. A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Rep. 2, 1014-1024 (2012).
    • (2012) Drosophila Melanogaster. Cell Rep , vol.2 , pp. 1014-1024
    • Jory, A.1
  • 137
    • 84868114222 scopus 로고    scopus 로고
    • A GAL4-driver line resource for Drosophila neurobiology
    • Jenett, A. et al. A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2, 991-1001 (2012).
    • (2012) Cell Rep , vol.2 , pp. 991-1001
    • Jenett, A.1
  • 138
    • 84868097251 scopus 로고    scopus 로고
    • A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS
    • Manning, L. et al. A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS. Cell Rep. 2, 1002-1013 (2012).
    • (2012) Cell Rep , vol.2 , pp. 1002-1013
    • Manning, L.1
  • 139
    • 84874381107 scopus 로고    scopus 로고
    • Genome-wide quantitative enhancer activity maps identified by STARR-seq
    • Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074-1077 (2013).
    • (2013) Science , vol.339 , pp. 1074-1077
    • Arnold, C.D.1
  • 140
    • 84899692444 scopus 로고    scopus 로고
    • Function-based identification of mammalian enhancers using site-specific integration
    • Dickel, D. E. et al. Function-based identification of mammalian enhancers using site-specific integration. Nature Methods 11, 566-571 (2014).
    • (2014) Nature Methods , vol.11 , pp. 566-571
    • Dickel, D.E.1
  • 141
    • 84899670369 scopus 로고    scopus 로고
    • FIREWACh: High-throughput functional detection of transcriptional regulatory modules in mammalian cells
    • Murtha, M. et al. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nature Methods 11, 559-565 (2014).
    • (2014) Nature Methods , vol.11 , pp. 559-565
    • Murtha, M.1
  • 142
    • 77952706498 scopus 로고    scopus 로고
    • Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
    • Kinney, J. B., Murugan, A., Callan, C. G. Jr & Cox, E. C. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc. Natl Acad. Sci. USA 107, 9158-9163 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 9158-9163
    • Kinney, J.B.1    Murugan, A.2    Callan Jr., C.G.3    Cox, E.C.4
  • 143
    • 84882777421 scopus 로고    scopus 로고
    • Composability of regulatory sequences controlling transcription and translation in
    • Kosuri, S. et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc. Natl Acad. Sci. USA 110, 14024-14029 (2013).
    • (2013) Escherichia Coli. Proc. Natl Acad. Sci. USA , vol.110 , pp. 14024-14029
    • Kosuri, S.1
  • 144
    • 71849118573 scopus 로고    scopus 로고
    • High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
    • Patwardhan, R. P. et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nature Biotech. 27, 1173-1175 (2009).
    • (2009) Nature Biotech , vol.27 , pp. 1173-1175
    • Patwardhan, R.P.1
  • 145
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • Kleinjan, D. A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32 (2005).
    • (2005) Am. J. Hum. Genet , vol.76 , pp. 8-32
    • Kleinjan, D.A.1    Van Heyningen, V.2
  • 146
    • 84876838711 scopus 로고    scopus 로고
    • The hierarchy of the 3D genome
    • Gibcus, J. H. & Dekker, J. The hierarchy of the 3D genome. Mol. Cell 49, 773-782 (2013).
    • (2013) Mol. Cell , vol.49 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 147
    • 84879232679 scopus 로고    scopus 로고
    • Genome organization and long-range regulation of gene expression by enhancers
    • Smallwood, A. & Ren, B. Genome organization and long-range regulation of gene expression by enhancers. Curr. Opin. Cell Biol. 25, 387-394 (2013).
    • (2013) Curr. Opin. Cell Biol , vol.25 , pp. 387-394
    • Smallwood, A.1    Ren, B.2
  • 148
    • 84885617426 scopus 로고    scopus 로고
    • Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
    • Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59-64 (2013).
    • (2013) Nature , vol.502 , pp. 59-64
    • Nagano, T.1
  • 149
    • 84890432056 scopus 로고    scopus 로고
    • Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations
    • Zhang, Y. et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504, 306-310 (2013).
    • (2013) Nature , vol.504 , pp. 306-310
    • Zhang, Y.1
  • 150
    • 84878860751 scopus 로고    scopus 로고
    • Architectural protein subclasses shape 3D organization of genomes during lineage commitment
    • Phillips-Cremins, J. E. et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153, 1281-1295 (2013).
    • (2013) Cell , vol.153 , pp. 1281-1295
    • Phillips-Cremins, J.E.1
  • 151
    • 84855804140 scopus 로고    scopus 로고
    • Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy
    • Barolo, S. Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy. Bioessays 34, 135-141 (2012).
    • (2012) Bioessays , vol.34 , pp. 135-141
    • Barolo, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.