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Volumn 27, Issue 10, 2013, Pages 1146-1158

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

Author keywords

Axis patterning; Dpp signaling pathway; Drosophila embryo; GRO seq BMP; Promoter proximal pausing; Zygotic transcription

Indexed keywords

BONE MORPHOGENETIC PROTEIN; RNA POLYMERASE;

EID: 84877975516     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.215459.113     Document Type: Article
Times cited : (70)

References (58)
  • 1
    • 84871699564 scopus 로고    scopus 로고
    • Promoter-proximal pausing of RNA polymerase II: Emerging roles in metazoans
    • Adelman K., Lis JT. 2012. Promoter-proximal pausing of RNA polymerase II: Emerging roles in metazoans. Nat Rev Genet 13: 720-731.
    • (2012) Nat Rev Genet , vol.13 , pp. 720-731
    • Adelman, K.1    Lis, J.T.2
  • 2
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S., Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 4
    • 0028135238 scopus 로고
    • The screw gene encodes a ubiquitously expressed member of the TGF-b family required for specification of dorsal cell fates in the Drosophila embryo
    • Arora K., Levine MS, O'Connor MB. 1994. The screw gene encodes a ubiquitously expressed member of the TGF-b family required for specification of dorsal cell fates in the Drosophila embryo. Genes Dev 8: 2588-2601.
    • (1994) Genes Dev , vol.8 , pp. 2588-2601
    • Arora, K.1    Levine, M.S.2    O'Connor, M.B.3
  • 5
    • 0022461818 scopus 로고
    • A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells
    • Bentley D.L., Groudine M. 1986. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells. Nature 321: 702-706.
    • (1986) Nature , vol.321 , pp. 702-706
    • Bentley, D.L.1    Groudine, M.2
  • 6
    • 67749106610 scopus 로고    scopus 로고
    • Synchronous and stochastic patterns of gene activation in the Drosophila embryo
    • Boettiger A.N., Levine M. 2009. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 325: 471-473.
    • (2009) Science , vol.325 , pp. 471-473
    • Boettiger, A.N.1    Levine, M.2
  • 7
    • 80053330640 scopus 로고    scopus 로고
    • The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo
    • Bothma J.P., Magliocco J, Levine M. 2011. The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo. Curr Biol 21: 1571-1577.
    • (2011) Curr Biol , vol.21 , pp. 1571-1577
    • Bothma, J.P.1    Magliocco, J.2    Levine, M.3
  • 8
    • 65049091772 scopus 로고    scopus 로고
    • Regulation of Hox gene activity by transcriptional elongation in Drosophila
    • Chopra V.S., Hong JW, Levine M. 2009. Regulation of Hox gene activity by transcriptional elongation in Drosophila. Curr Biol 19: 688-693.
    • (2009) Curr Biol , vol.19 , pp. 688-693
    • Chopra, V.S.1    Hong, J.W.2    Levine, M.3
  • 9
    • 79959348134 scopus 로고    scopus 로고
    • The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo
    • Chopra V.S., Hendrix DA, Core LJ, Tsui C, Lis JT, Levine M. 2011. The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Mol Cell 42: 837-844.
    • (2011) Mol Cell , vol.42 , pp. 837-844
    • Chopra, V.S.1    Hendrix, D.A.2    Core, L.J.3    Tsui, C.4    Lis, J.T.5    Levine, M.6
  • 10
    • 78751659330 scopus 로고    scopus 로고
    • Nascent transcript sequencing visualizes transcription at nucleotide resolution
    • Churchman LS, Weissman JS. 2011. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469: 368-373.
    • (2011) Nature , vol.469 , pp. 368-373
    • Churchman, L.S.1    Weissman, J.S.2
  • 11
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core L.J., Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 13
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R., Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 14
    • 0029895007 scopus 로고    scopus 로고
    • A group of genes required for maintenance of the amnioserosa tissue in Drosophila
    • Frank L.H., Rushlow C. 1996. A group of genes required for maintenance of the amnioserosa tissue in Drosophila. Development 122: 1343-1352.
    • (1996) Development , vol.122 , pp. 1343-1352
    • Frank, L.H.1    Rushlow, C.2
  • 15
    • 70249104647 scopus 로고    scopus 로고
    • Defining mechanisms that regulate RNA polymerase II transcription in vivo
    • Fuda N.J., Ardehali MB, Lis JT. 2009. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461: 186-192.
    • (2009) Nature , vol.461 , pp. 186-192
    • Fuda, N.J.1    Ardehali, M.B.2    Lis, J.T.3
  • 17
    • 47549090254 scopus 로고    scopus 로고
    • NELF-mediated stalling of Pol II can enhance gene expression by blocking promoterproximal nucleosome assembly
    • Gilchrist D.A., Nechaev S, Lee C, Ghosh SK, Collins JB, Li L, Gilmour D.S., Adelman K. 2008. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoterproximal nucleosome assembly. Genes Dev 22: 1921-1933.
    • (2008) Genes Dev , vol.22 , pp. 1921-1933
    • Gilchrist, D.A.1    Nechaev, S.2    Lee, C.3    Ghosh, S.K.4    Collins, J.B.5    Li, L.6    Gilmour, D.S.7    Adelman, K.8
  • 18
    • 78149477660 scopus 로고    scopus 로고
    • Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    • Gilchrist D.A., Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. 2010. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143: 540-551.
    • (2010) Cell , vol.143 , pp. 540-551
    • Gilchrist, D.A.1    Dos Santos, G.2    Fargo, D.C.3    Xie, B.4    Gao, Y.5    Li, L.6    Adelman, K.7
  • 20
    • 0022817308 scopus 로고
    • RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells
    • Gilmour D.S., Lis JT. 1986. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol Cell Biol 6: 3984-3989.
    • (1986) Mol Cell Biol , vol.6 , pp. 3984-3989
    • Gilmour, D.S.1    Lis, J.T.2
  • 22
    • 79955836460 scopus 로고    scopus 로고
    • A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells
    • Hah N., Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. 2011. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145: 622-634.
    • (2011) Cell , vol.145 , pp. 622-634
    • Hah, N.1    Danko, C.G.2    Core, L.3    Waterfall, J.J.4    Siepel, A.5    Lis, J.T.6    Kraus, W.L.7
  • 23
    • 80055073174 scopus 로고    scopus 로고
    • Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-tozygotic transition
    • Harrison M.M., Li XY, Kaplan T, Botchan MR, Eisen MB. 2011. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-tozygotic transition. PLoS Genet 7: e1002266.
    • (2011) PLoS Genet , vol.7
    • Harrison, M.M.1    Li, X.Y.2    Kaplan, T.3    Botchan, M.R.4    Eisen, M.B.5
  • 25
    • 0842265974 scopus 로고    scopus 로고
    • Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors
    • Kadonaga J.T. 2004. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116: 247-257.
    • (2004) Cell , vol.116 , pp. 247-257
    • Kadonaga, J.T.1
  • 26
    • 0023513563 scopus 로고
    • Antitermination of transcription within the long terminal repeat of HIV-1 by tat gene product
    • Kao S.Y., Calman AF, Luciw PA, Peterlin BM. 1987. Antitermination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature 330: 489-493.
    • (1987) Nature , vol.330 , pp. 489-493
    • Kao, S.Y.1    Calman, A.F.2    Luciw, P.A.3    Peterlin, B.M.4
  • 28
    • 84874175008 scopus 로고    scopus 로고
    • Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
    • Kwak H., Fuda NJ, Core LJ, Lis JT. 2013. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339: 950-953.
    • (2013) Science , vol.339 , pp. 950-953
    • Kwak, H.1    Fuda, N.J.2    Core, L.J.3    Lis, J.T.4
  • 29
    • 79955795581 scopus 로고    scopus 로고
    • Paused RNA polymerase II as a developmental checkpoint
    • Levine M. 2011. Paused RNA polymerase II as a developmental checkpoint. Cell 145: 502-511.
    • (2011) Cell , vol.145 , pp. 502-511
    • Levine, M.1
  • 30
    • 79952360918 scopus 로고    scopus 로고
    • Long-and short-range transcriptional repressors induce distinct chromatin states on repressed genes
    • Li L.M., Arnosti DN. 2011. Long-and short-range transcriptional repressors induce distinct chromatin states on repressed genes. Curr Biol 21: 406-412.
    • (2011) Curr Biol , vol.21 , pp. 406-412
    • Li, L.M.1    Arnosti, D.N.2
  • 31
    • 79953164741 scopus 로고    scopus 로고
    • Promoter proximal pausing and the control of gene expression
    • Li J., Gilmour DS. 2011. Promoter proximal pausing and the control of gene expression. Curr Opin Genet Dev 21: 231-235.
    • (2011) Curr Opin Genet Dev , vol.21 , pp. 231-235
    • Li, J.1    Gilmour, D.S.2
  • 32
    • 56749183626 scopus 로고    scopus 로고
    • The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila
    • Liang H.L., Nien CY, Liu HY, Metzstein MM, Kirov N, Rushlow C. 2008. The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature 456: 400-403.
    • (2008) Nature , vol.456 , pp. 400-403
    • Liang, H.L.1    Nien, C.Y.2    Liu, H.Y.3    Metzstein, M.M.4    Kirov, N.5    Rushlow, C.6
  • 33
    • 79952256180 scopus 로고    scopus 로고
    • Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq
    • Lott S.E., Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB. 2011. Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 9: e1000590.
    • (2011) PLoS Biol , vol.9
    • Lott, S.E.1    Villalta, J.E.2    Schroth, G.P.3    Luo, S.4    Tonkin, L.A.5    Eisen, M.B.6
  • 34
    • 84865419994 scopus 로고    scopus 로고
    • The super elongation complex (SEC) family in transcriptional control
    • Luo Z., Lin C, Shilatifard A. 2012. The super elongation complex (SEC) family in transcriptional control. Nat Rev Mol Cell Biol 13: 543-547.
    • (2012) Nat Rev Mol Cell Biol , vol.13 , pp. 543-547
    • Luo, Z.1    Lin, C.2    Shilatifard, A.3
  • 35
    • 84881506759 scopus 로고    scopus 로고
    • Nascent-Seq reveals novel features of mouse circadian transcriptional regulation
    • Menet J.S., Rodriguez J, Abruzzi KC, Rosbash M. 2012. Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. eLife 1: e00011.
    • (2012) eLife , vol.1
    • Menet, J.S.1    Rodriguez, J.2    Abruzzi, K.C.3    Rosbash, M.4
  • 36
    • 79954562232 scopus 로고    scopus 로고
    • Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
    • Min I.M., Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT. 2011. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev 25: 742-754.
    • (2011) Genes Dev , vol.25 , pp. 742-754
    • Min, I.M.1    Waterfall, J.J.2    Core, L.J.3    Munroe, R.J.4    Schimenti, J.5    Lis, J.T.6
  • 40
    • 74549132843 scopus 로고    scopus 로고
    • Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
    • Nechaev S., Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. 2010. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327: 335-338.
    • (2010) Science , vol.327 , pp. 335-338
    • Nechaev, S.1    Fargo, D.C.2    dos Santos, G.3    Liu, L.4    Gao, Y.5    Adelman, K.6
  • 42
    • 32244437156 scopus 로고    scopus 로고
    • Shaping BMP morphogen gradients in the Drosophila embryo and pupal wing
    • O'Connor MB, Umulis D, Othmer HG, Blair SS. 2006. Shaping BMP morphogen gradients in the Drosophila embryo and pupal wing. Development 133: 183-193.
    • (2006) Development , vol.133 , pp. 183-193
    • O'Connor, M.B.1    Umulis, D.2    Othmer, H.G.3    Blair, S.S.4
  • 43
    • 0033214367 scopus 로고    scopus 로고
    • Morphogen gradients: New insights from DPP
    • Podos S.D., Ferguson EL. 1999. Morphogen gradients: New insights from DPP. Trends Genet 15: 396-402.
    • (1999) Trends Genet , vol.15 , pp. 396-402
    • Podos, S.D.1    Ferguson, E.L.2
  • 44
    • 10644234650 scopus 로고    scopus 로고
    • Visualization of trans-homolog enhancer-promoter interactions at the Abd-B Hox locus in the Drosophila embryo
    • Ronshaugen M., Levine M. 2004. Visualization of trans-homolog enhancer-promoter interactions at the Abd-B Hox locus in the Drosophila embryo. Dev Cell 7: 925-932.
    • (2004) Dev Cell , vol.7 , pp. 925-932
    • Ronshaugen, M.1    Levine, M.2
  • 45
    • 0024282827 scopus 로고
    • The RNA polymerase II molecule at the 59 end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged
    • Rougvie A.E., Lis JT. 1988. The RNA polymerase II molecule at the 59 end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54: 795-804.
    • (1988) Cell , vol.54 , pp. 795-804
    • Rougvie, A.E.1    Lis, J.T.2
  • 46
    • 0035680634 scopus 로고    scopus 로고
    • Generating patterns from fields of cells. Examples from Drosophila segmentation
    • Sanson B. 2001. Generating patterns from fields of cells. Examples from Drosophila segmentation. EMBO Rep 2: 1083-1088.
    • (2001) EMBO Rep , vol.2 , pp. 1083-1088
    • Sanson, B.1
  • 48
    • 5444257285 scopus 로고    scopus 로고
    • Whole-genome analysis of Drosophila gastrulation
    • Stathopoulos A., Levine M. 2004. Whole-genome analysis of Drosophila gastrulation. Curr Opin Genet Dev 14: 477-484.
    • (2004) Curr Opin Genet Dev , vol.14 , pp. 477-484
    • Stathopoulos, A.1    Levine, M.2
  • 49
    • 0035109375 scopus 로고    scopus 로고
    • A screen for modifiers of decapentaplegic mutant phenotypes identifies lilliputian, the only member of the Fragile-X/Burkitt's Lymphoma family of transcription factors in Drosophila melanogaster
    • Su M.A., Wisotzkey RG, Newfeld SJ. 2001. A screen for modifiers of decapentaplegic mutant phenotypes identifies lilliputian, the only member of the Fragile-X/Burkitt's Lymphoma family of transcription factors in Drosophila melanogaster. Genetics 157: 717-725.
    • (2001) Genetics , vol.157 , pp. 717-725
    • Su, M.A.1    Wisotzkey, R.G.2    Newfeld, S.J.3
  • 50
    • 0035093076 scopus 로고    scopus 로고
    • Transcriptional regulation of cytoskeletal functions and segmentation by a novel maternal pair-rule gene, lilliputian
    • Tang A.H., Neufeld TP, Rubin GM, Muller HA. 2001. Transcriptional regulation of cytoskeletal functions and segmentation by a novel maternal pair-rule gene, lilliputian. Development 128: 801-813.
    • (2001) Development , vol.128 , pp. 801-813
    • Tang, A.H.1    Neufeld, T.P.2    Rubin, G.M.3    Muller, H.A.4
  • 51
    • 79957990336 scopus 로고    scopus 로고
    • STAT is an essential activator of the zygotic genome in the early Drosophila embryo
    • Tsurumi A., Xia F, Li J, Larson K, LaFrance R, Li WX. 2011. STAT is an essential activator of the zygotic genome in the early Drosophila embryo. PLoS Genet 7: e1002086.
    • (2011) PLoS Genet , vol.7
    • Tsurumi, A.1    Xia, F.2    Li, J.3    Larson, K.4    LaFrance, R.5    Li, W.X.6
  • 52
    • 14444275279 scopus 로고    scopus 로고
    • DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs
    • Wada T., Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S., Yano K, Hartzog GA, Winston F, et al. 1998. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev 12: 343-356.
    • (1998) Genes Dev , vol.12 , pp. 343-356
    • Wada, T.1    Takagi, T.2    Yamaguchi, Y.3    Ferdous, A.4    Imai, T.5    Hirose, S.6    Sugimoto, S.7    Yano, K.8    Hartzog, G.A.9    Winston, F.10
  • 53
    • 34247627984 scopus 로고    scopus 로고
    • Transcription elongation controls cell fate specification in the Drosophila embryo
    • Wang X., Lee C, Gilmour DS, Gergen JP. 2007. Transcription elongation controls cell fate specification in the Drosophila embryo. Genes Dev 21: 1031-1036.
    • (2007) Genes Dev , vol.21 , pp. 1031-1036
    • Wang, X.1    Lee, C.2    Gilmour, D.S.3    Gergen, J.P.4
  • 54
    • 77955367829 scopus 로고    scopus 로고
    • NELF potentiates gene transcription in the Drosophila embryo
    • Wang X., Hang S, Prazak L, Gergen JP. 2010. NELF potentiates gene transcription in the Drosophila embryo. PLoS ONE 5: e11498.
    • (2010) PLoS ONE , vol.5
    • Wang, X.1    Hang, S.2    Prazak, L.3    Gergen, J.P.4
  • 56
    • 80455144479 scopus 로고    scopus 로고
    • Pioneer transcription factors: Establishing competence for gene expression
    • Zaret K.S., Carroll JS. 2011. Pioneer transcription factors: Establishing competence for gene expression. Genes Dev 25: 2227-2241.
    • (2011) Genes Dev , vol.25 , pp. 2227-2241
    • Zaret, K.S.1    Carroll, J.S.2
  • 57
    • 0034657415 scopus 로고    scopus 로고
    • The roles of the Drosophila JAK/STAT pathway
    • Zeidler M.P., Bach EA, Perrimon N. 2000. The roles of the Drosophila JAK/STAT pathway. Oncogene 19: 2598-2606.
    • (2000) Oncogene , vol.19 , pp. 2598-2606
    • Zeidler, M.P.1    Bach, E.A.2    Perrimon, N.3


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