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Volumn 518, Issue 7540, 2015, Pages 556-559

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA PROTEIN; RIBOSOME PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DREF; TRANSCRIPTION FACTOR TRI; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; DREF PROTEIN, DROSOPHILA; TRL PROTEIN, DROSOPHILA;

EID: 84925543087     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13994     Document Type: Article
Times cited : (339)

References (45)
  • 1
    • 84897138228 scopus 로고    scopus 로고
    • Looping back to leap forward: Transcription enters a new era
    • Levine, M., Cattoglio, C. & Tjian, R. Looping back to leap forward: transcription enters a new era. Cell 157, 13-25 (2014).
    • (2014) Cell , vol.157 , pp. 13-25
    • Levine, M.1    Cattoglio, C.2    Tjian, R.3
  • 2
    • 0028123693 scopus 로고
    • Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo
    • Li, X. & Noll, M. Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo. EMBO J. 13, 400-406 (1994).
    • (1994) EMBO J. , vol.13 , pp. 400-406
    • Li, X.1    Noll, M.2
  • 3
    • 0032519586 scopus 로고    scopus 로고
    • Different core promoters possess distinct regulatory activities in the Drosophila embryo
    • Ohtsuki, S., Levine, M. & Cai, H. N. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev. 12, 547-556 (1998).
    • (1998) Genes Dev. , vol.12 , pp. 547-556
    • Ohtsuki, S.1    Levine, M.2    Cai, H.N.3
  • 4
    • 0032536818 scopus 로고    scopus 로고
    • Selectivity, sharing and competitive interactions in the regulation of Hoxb genes
    • Sharpe, J., Nonchev, S., Gould, A.,Whiting, J.& Krumlauf, R. Selectivity, sharing and competitive interactions in the regulation of Hoxb genes. EMBO J. 17, 1788-1798 (1998).
    • (1998) EMBO J. , vol.17 , pp. 1788-1798
    • Sharpe, J.1    Nonchev, S.2    Gould, A.3    Whiting, J.4    Krumlauf, R.5
  • 5
    • 0029973108 scopus 로고    scopus 로고
    • Promoter specificity mediates the independent regulation of neighboring genes
    • Merli, C., Bergstrom, D. E., Cygan, J. A. & Blackman, R. K. Promoter specificity mediates the independent regulation of neighboring genes. Genes Dev. 10, 1260-1270 (1996).
    • (1996) Genes Dev. , vol.10 , pp. 1260-1270
    • Merli, C.1    Bergstrom, D.E.2    Cygan, J.A.3    Blackman, R.K.4
  • 6
    • 0035477093 scopus 로고    scopus 로고
    • Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs
    • Butler, J. E. & Kadonaga, J. T. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 15, 2515-2519 (2001).
    • (2001) Genes Dev. , vol.15 , pp. 2515-2519
    • Butler, J.E.1    Kadonaga, J.T.2
  • 7
    • 84858444088 scopus 로고    scopus 로고
    • Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip
    • Kadonaga, J. T. Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip. Rev. Dev. Biol. 1, 40-51 (2012).
    • (2012) Rev. Dev. Biol. , vol.1 , pp. 40-51
    • Kadonaga, J.T.1
  • 8
    • 77956842987 scopus 로고    scopus 로고
    • The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery
    • Parry, T. J. et al. The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes Dev. 24, 2013-2018 (2010).
    • (2010) Genes Dev. , vol.24 , pp. 2013-2018
    • Parry, T.J.1
  • 9
    • 38849112675 scopus 로고    scopus 로고
    • Genomic regulatory blocks underlie extensive microsynteny conservation in insects
    • Engström, P. G., Ho Sui, S. J., Drivenes, O., Becker, T. S. & Lenhard, B. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17, 1898-1908 (2007).
    • (2007) Genome Res. , vol.17 , pp. 1898-1908
    • Engström, P.G.1    Ho Sui, S.J.2    Drivenes, O.3    Becker, T.S.4    Lenhard, B.5
  • 11
    • 47749087494 scopus 로고    scopus 로고
    • Tools for neuroanatomy and neurogenetics in Drosophila
    • Pfeiffer, B. D. et al. Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl Acad. Sci. USA 105, 9715-9720 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 9715-9720
    • Pfeiffer, B.D.1
  • 12
    • 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
  • 13
    • 84898025687 scopus 로고    scopus 로고
    • Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin
    • Shlyueva, D. et al. Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. Mol. Cell 54, 180-192 (2014).
    • (2014) Mol. Cell , vol.54 , pp. 180-192
    • Shlyueva, D.1
  • 14
    • 0019811465 scopus 로고
    • Expression of a b-globin gene isenhanced by remote SV40 DNA sequences
    • Banerji, J., Rusconi,S. & Schaffner, W. Expression of a b-globin gene isenhanced by remote SV40 DNA sequences. Cell 27, 299-308 (1981).
    • (1981) Cell , vol.27 , pp. 299-308
    • Banerji, J.1    Rusconi, S.2    Schaffner, W.3
  • 15
    • 84858440747 scopus 로고    scopus 로고
    • Metazoan promoters: Emerging characteristics and insights into transcriptional regulation
    • Lenhard, B., Sandelin, A. & Carninci, P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nature Rev. Genet. 13, 233-245 (2012).
    • (2012) Nature Rev. Genet. , vol.13 , pp. 233-245
    • Lenhard, B.1    Sandelin, A.2    Carninci, P.3
  • 16
    • 0012253746 scopus 로고    scopus 로고
    • Computational analysis of core promoters in the Drosophila genome
    • research0087.1-0087.12
    • Ohler, U., Liao, G.-C., Niemann, H. & Rubin, G. M. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3, research0087.1-0087.12 (2002).
    • (2002) Genome Biol. , vol.3
    • Ohler, U.1    Liao, G.-C.2    Niemann, H.3    Rubin, G.M.4
  • 17
    • 0027333369 scopus 로고
    • Hobo enhancer trappingmutagenesis in Drosophila reveals an insertion specificity different fromP elements
    • Smith, D., Wohlgemuth, J., Calvi, B. R., Franklin, I. & Gelbart, W. M. hobo enhancer trappingmutagenesis in Drosophila reveals an insertion specificity different fromP elements. Genetics 135, 1063-1076 (1993).
    • (1993) Genetics , vol.135 , pp. 1063-1076
    • Smith, D.1    Wohlgemuth, J.2    Calvi, B.R.3    Franklin, I.4    Gelbart, W.M.5
  • 18
    • 0034081817 scopus 로고    scopus 로고
    • The downstreampromoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters
    • Kutach, A. K.& Kadonaga, J. T. The downstreampromoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20, 4754-4764 (2000).
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 4754-4764
    • Kutach, A.K.1    Kadonaga, J.T.2
  • 19
    • 84865257761 scopus 로고    scopus 로고
    • Uncovering cisregulatory sequence requirements for context-specific transcription factor binding
    • Yáñ ez-Cuna, J. O., Dinh, H. Q., Kvon, E. Z., Shlyueva, D. & Stark, A. Uncovering cisregulatory sequence requirements for context-specific transcription factor binding. Genome Res. 22, 2018-2030 (2012).
    • (2012) Genome Res. , vol.22 , pp. 2018-2030
    • Yáñ Ez-Cuna, J.O.1    Dinh, H.Q.2    Kvon, E.Z.3    Shlyueva, D.4    Stark, A.5
  • 20
    • 84901804887 scopus 로고    scopus 로고
    • Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
    • Yáñ ez-Cuna, J. O. et al. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res. 24, 1147-1156 (2014).
    • (2014) Genome Res. , vol.24 , pp. 1147-1156
    • Yáñ Ez-Cuna, J.O.1
  • 21
    • 84877934795 scopus 로고    scopus 로고
    • Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle
    • Gurudatta, B. V., Yang, J., Van Bortle, K., Donlin-Asp, P. G. & Corces, V. G. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle. Cell Cycle 12, 1605-1615 (2013).
    • (2013) Cell Cycle , vol.12 , pp. 1605-1615
    • Gurudatta, B.V.1    Yang, J.2    Van Bortle, K.3    Donlin-Asp, P.G.4    Corces, V.G.5
  • 22
    • 78650331647 scopus 로고    scopus 로고
    • ModENCODE Consortium Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • modENCODE Consortium Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (2010).
    • (2010) Science , vol.330 , pp. 1787-1797
  • 23
    • 73649105501 scopus 로고    scopus 로고
    • Promoting developmental transcription
    • Ohler, U. & Wassarman, D. A. Promoting developmental transcription. Development 137, 15-26 (2010).
    • (2010) Development , vol.137 , pp. 15-26
    • Ohler, U.1    Wassarman, D.A.2
  • 24
    • 84927641804 scopus 로고    scopus 로고
    • In search of the determinants of enhancer-promoter interaction specificity
    • van Arensbergen, J., van Steensel, B. & Bussemaker, H. J. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol. http://dx.doi.org/10.1016/j.tcb.2014.07.004 (2014).
    • (2014) Trends Cell Biol.
    • Van Arensbergen, J.1    Van Steensel, B.2    Bussemaker, H.J.3
  • 25
    • 84904332607 scopus 로고    scopus 로고
    • TRF2, but not TBP, mediates the transcription of ribosomal protein genes
    • Wang, Y.-L. et al. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev. 28, 1550-1555 (2014).
    • (2014) Genes Dev. , vol.28 , pp. 1550-1555
    • Wang, Y.-L.1
  • 26
    • 36249011467 scopus 로고    scopus 로고
    • Transcription of histone gene cluster by differential core-promoter factors
    • Isogai, Y., Keles, S., Prestel, M., Hochheimer, A. & Tjian, R. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev. 21, 2936-2949 (2007).
    • (2007) Genes Dev. , vol.21 , pp. 2936-2949
    • Isogai, Y.1    Keles, S.2    Prestel, M.3    Hochheimer, A.4    Tjian, R.5
  • 27
    • 0037191755 scopus 로고    scopus 로고
    • TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila
    • Hochheimer, A., Zhou, S., Zheng, S., Holmes, M. C. & Tjian, R. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420, 439-445 (2002).
    • (2002) Nature , vol.420 , pp. 439-445
    • Hochheimer, A.1    Zhou, S.2    Zheng, S.3    Holmes, M.C.4    Tjian, R.5
  • 28
    • 34548427818 scopus 로고    scopus 로고
    • Switching of the core transcription machinery during myogenesis
    • Deato, M. D. E. & Tjian, R. Switching of the core transcription machinery during myogenesis. Genes Dev. 21, 2137-2149 (2007).
    • (2007) Genes Dev. , vol.21 , pp. 2137-2149
    • Deato, M.D.E.1    Tjian, R.2
  • 29
    • 72149130298 scopus 로고    scopus 로고
    • Shifting players and paradigms in cellspecific transcription
    • D?Alessio, J. A., Wright, K. J. & Tjian, R. Shifting players and paradigms in cellspecific transcription. Mol. Cell 36, 924-931 (2009).
    • (2009) Mol. Cell , vol.36 , pp. 924-931
    • Dalessio, J.A.1    Wright, K.J.2    Tjian, R.3
  • 30
    • 77956649878 scopus 로고    scopus 로고
    • Developmental regulation of transcription initiation: More than just changing the actors
    • Müller, F., Zaucker, A. & Tora, L. Developmental regulation of transcription initiation: more than just changing the actors. Curr. Opin. Genet. Dev. 20, 533-540 (2010).
    • (2010) Curr. Opin. Genet. Dev. , vol.20 , pp. 533-540
    • Müller, F.1    Zaucker, A.2    Tora, L.3
  • 31
    • 70449519397 scopus 로고    scopus 로고
    • A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila
    • Saito, K. et al. A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 461, 1296-1299 (2009).
    • (2009) Nature , vol.461 , pp. 1296-1299
    • Saito, K.1
  • 32
    • 84903640603 scopus 로고    scopus 로고
    • Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution
    • Arnold, C. D. et al. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nature Genet. 46, 685-692 (2014).
    • (2014) Nature Genet. , vol.46 , pp. 685-692
    • Arnold, C.D.1
  • 33
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25-29 (2000).
    • (2000) Nature Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 34
    • 38349127974 scopus 로고    scopus 로고
    • Globalanalysis ofpatterns of gene expressionduring Drosophila embryogenesis
    • Tomancak, P. et al. Globalanalysis ofpatterns of gene expressionduring Drosophila embryogenesis. Genome Biol. 8, R145 (2007).
    • (2007) Genome Biol. , vol.8 , pp. R145
    • Tomancak, P.1
  • 35
    • 34249804498 scopus 로고    scopus 로고
    • Using FlyAtlas to identify better Drosophila melanogaster models of human disease
    • Chintapalli, V. R., Wang, J. & Dow, J. A. T. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nature Genet. 39, 715-720 (2007).
    • (2007) Nature Genet. , vol.39 , pp. 715-720
    • Chintapalli, V.R.1    Wang, J.2    Dow, J.A.T.3
  • 36
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: Application to sequence homology searches
    • Bailey, T. L. & Gribskov, M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54 (1998).
    • (1998) Bioinformatics , vol.14 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 37
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 40
    • 76949094155 scopus 로고    scopus 로고
    • Developmental gene regulation in the era of genomics
    • Zeitlinger, J. & Stark, A. Developmental gene regulation in the era of genomics. Dev. Biol. 339, 230-239 (2010).
    • (2010) Dev. Biol. , vol.339 , pp. 230-239
    • Zeitlinger, J.1    Stark, A.2
  • 41
    • 84905642951 scopus 로고    scopus 로고
    • Genome-scale functional characterization of Drosophila developmental enhancers in vivo
    • Kvon, E. Z. et al. Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512, 91-95 (2014).
    • (2014) Nature , vol.512 , pp. 91-95
    • Kvon, E.Z.1
  • 42
    • 76149089221 scopus 로고    scopus 로고
    • The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation
    • Soler, E. et al. The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes Dev. 24, 277-289 (2010).
    • (2010) Genes Dev. , vol.24 , pp. 277-289
    • Soler, E.1
  • 43
    • 84881591218 scopus 로고    scopus 로고
    • A global change in RNA polymerase II pausing during the Drosophila midblastula transition
    • Chen, K. et al. A global change in RNA polymerase II pausing during the Drosophila midblastula transition. eLife 2, e00861 (2013).
    • (2013) ELife , vol.2 , pp. e00861
    • Chen, K.1
  • 44
    • 84878318299 scopus 로고    scopus 로고
    • Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo
    • Lagha, M. et al. Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell 153, 976-987 (2013).
    • (2013) Cell , vol.153 , pp. 976-987
    • Lagha, M.1
  • 45
    • 84874175008 scopus 로고    scopus 로고
    • Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
    • Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950-953 (2013).
    • (2013) Science , vol.339 , pp. 950-953
    • Kwak, H.1    Fuda, N.J.2    Core, L.J.3    Lis, J.T.4


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