메뉴 건너뛰기




Volumn 2012, Issue 1, 2012, Pages

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

Author keywords

[No Author keywords available]

Indexed keywords

CRYPTOCHROME 1; CRYPTOCHROME 2; MESSENGER RNA; MICRORNA 122; NASCENT RNA; PER1 PROTEIN; PER2 PROTEIN; PROTEIN BMAL1; RNA POLYMERASE II; TRANSCRIPTION FACTOR CLOCK; UNCLASSIFIED DRUG; UNTRANSLATED RNA; ARNTL PROTEIN, MOUSE; CLOCK PROTEIN, MOUSE; DNA; PROTEIN BINDING; TRANSCRIPTION FACTOR ARNTL; TRANSCRIPTOME;

EID: 84881506759     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.00011     Document Type: Article
Times cited : (257)

References (49)
  • 1
    • 81255150242 scopus 로고    scopus 로고
    • Drosophila CLOCK target gene characterization: Implications for circadian tissue-specific gene expression
    • Abruzzi KC, Rodriguez J, Menet JS, Desrochers J, Zadina A, Luo W, et al. 2011. Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression. Genes Dev 25:2374-86.
    • (2011) Genes Dev , vol.25 , pp. 2374-2386
    • Abruzzi, K.C.1    Rodriguez, J.2    Menet, J.S.3    Desrochers, J.4    Zadina, A.5    Luo, W.6
  • 2
    • 84864251757 scopus 로고    scopus 로고
    • Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
    • Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, et al. 2012. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150:279-90.
    • (2012) Cell , vol.150 , pp. 279-290
    • Bhatt, D.M.1    Pandya-Jones, A.2    Tong, A.J.3    Barozzi, I.4    Lissner, M.M.5    Natoli, G.6
  • 5
    • 78649289872 scopus 로고    scopus 로고
    • Global analysis of nascent RNA reveals transcriptional pausing in terminal exons
    • Carrillo Oesterreich F, Preibisch S, Neugebauer KM. 2010. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 40:571-81.
    • (2010) Mol Cell , vol.40 , pp. 571-581
    • Carrillo Oesterreich, F.1    Preibisch, S.2    Neugebauer, K.M.3
  • 6
    • 25444484963 scopus 로고    scopus 로고
    • Control of gene expression during T cell activation: Alternate regulation of mRNA transcription and mRNA stability
    • Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, Do L, et al. 2005. Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability. BMC Genomics 6:75.
    • (2005) BMC Genomics , vol.6 , pp. 75
    • Cheadle, C.1    Fan, J.2    Cho-Chung, Y.S.3    Werner, T.4    Ray, J.5    Do, L.6
  • 7
    • 34247390706 scopus 로고    scopus 로고
    • Molecular circadian rhythms in central and peripheral clocks in mammals
    • Dardente H, Cermakian N. 2007. Molecular circadian rhythms in central and peripheral clocks in mammals. Chronobiol Int 24:195-213.
    • (2007) Chronobiol Int , vol.24 , pp. 195-213
    • Dardente, H.1    Cermakian, N.2
  • 8
    • 79952529158 scopus 로고    scopus 로고
    • A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism
    • Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, et al. 2011. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science 331:1315-19.
    • (2011) Science , vol.331 , pp. 1315-1319
    • Feng, D.1    Liu, T.2    Sun, Z.3    Bugge, A.4    Mullican, S.E.5    Alenghat, T.6
  • 10
    • 0034252265 scopus 로고    scopus 로고
    • RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria
    • Giege P, Hoffmann M, Binder S, Brennicke A. 2000. RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep 1:164-70.
    • (2000) EMBO Rep , vol.1 , pp. 164-170
    • Giege, P.1    Hoffmann, M.2    Binder, S.3    Brennicke, A.4
  • 12
    • 0033557089 scopus 로고    scopus 로고
    • Glucocorticoids stimulate CREB binding to a cyclic-AMP response element in the rat serine dehydratase gene
    • Haas MJ, Pitot HC. 1999. Glucocorticoids stimulate CREB binding to a cyclic-AMP response element in the rat serine dehydratase gene. Arch Biochem Biophys 362:317-24.
    • (1999) Arch Biochem Biophys , vol.362 , pp. 317-324
    • Haas, M.J.1    Pitot, H.C.2
  • 13
    • 60749124122 scopus 로고    scopus 로고
    • The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules
    • Hao S., Baltimore D. 2009. The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules. Nat Immunol 10:281-8.
    • (2009) Nat Immunol , vol.10 , pp. 281-288
    • Hao, S.1    Baltimore, D.2
  • 14
    • 84861441546 scopus 로고    scopus 로고
    • Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
    • Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. 2012. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res 22:1266-81.
    • (2012) Genome Res , vol.22 , pp. 1266-1281
    • Hughes, M.E.1    Grant, G.R.2    Paquin, C.3    Qian, J.4    Nitabach, M.N.5
  • 15
    • 84865973117 scopus 로고    scopus 로고
    • Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals
    • Joshi A, Beck Y, Michoel T. 2012. Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals. FEBS J 279:3501-12.
    • (2012) FEBS J , vol.279 , pp. 3501-3512
    • Joshi, A.1    Beck, Y.2    Michoel, T.3
  • 16
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: Coordination of post-transcriptional events
    • Keene JD. 2007. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8:533-43.
    • (2007) Nat Rev Genet , vol.8 , pp. 533-543
    • Keene, J.D.1
  • 17
    • 84869859046 scopus 로고    scopus 로고
    • Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse
    • Khodor YL, Menet JS, Tolan M, Rosbash M. 2012. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA.
    • (2012) RNA
    • Khodor, Y.L.1    Menet, J.S.2    Tolan, M.3    Rosbash, M.4
  • 19
    • 33749031807 scopus 로고    scopus 로고
    • Molecular components of the mammalian circadian clock
    • Spec No 2
    • Ko CH, Takahashi JS. 2006. Molecular components of the mammalian circadian clock. Hum Mol Genet 15(Spec No 2):R271-7.
    • (2006) Hum Mol Genet , vol.15
    • Ko, C.H.1    Takahashi, J.S.2
  • 20
    • 84867667011 scopus 로고    scopus 로고
    • Transcriptional architecture and chromatin landscape of the core circadian clock in mammals
    • Koike N, Yoo SH, Huang HC, Kumar V, Lee C, Kim TK, et al. 2012. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338:349-54.
    • (2012) Science , vol.338 , pp. 349-354
    • Koike, N.1    Yoo, S.H.2    Huang, H.C.3    Kumar, V.4    Lee, C.5    Kim, T.K.6
  • 21
    • 79551506940 scopus 로고    scopus 로고
    • Post-transcriptional control of circadian rhythms
    • Kojima S, Shingle DL, Green CB. 2011. Post-transcriptional control of circadian rhythms. J Cell Sci 124:311-20.
    • (2011) J Cell Sci , vol.124 , pp. 311-320
    • Kojima, S.1    Shingle, D.L.2    Green, C.B.3
  • 22
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 24
    • 4544362674 scopus 로고    scopus 로고
    • Mammalian circadian biology: Elucidating genome-wide levels of temporal organization
    • Lowrey PL, Takahashi JS. 2004. Mammalian circadian biology: elucidating genome-wide levels of temporal organization. Annu Rev Genomics Hum Genet 5:407-41.
    • (2004) Annu Rev Genomics Hum Genet , vol.5 , pp. 407-441
    • Lowrey, P.L.1    Takahashi, J.S.2
  • 26
    • 65649092633 scopus 로고    scopus 로고
    • The genetic signatures of noncoding RNAs
    • Mattick JS. 2009. The genetic signatures of noncoding RNAs. PLoS Genet 5:e1000459.
    • (2009) PLoS Genet , vol.5
    • Mattick, J.S.1
  • 27
    • 0035977158 scopus 로고    scopus 로고
    • Microarray analysis and organization of circadian gene expression in Drosophila
    • McDonald MJ, Rosbash M. 2001. Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107:567-78.
    • (2001) Cell , vol.107 , pp. 567-578
    • McDonald, M.J.1    Rosbash, M.2
  • 28
  • 29
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets
    • Nicol JW, Helt GA, Blanchard Jnr SG, Raja A, Loraine AE. 2009. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25:2730-1.
    • (2009) Bioinformatics , vol.25 , pp. 2730-2731
    • Nicol, J.W.1    Helt, G.A.2    Blanchard Jr., S.G.3    Raja, A.4    Loraine, A.E.5
  • 30
    • 18444414586 scopus 로고    scopus 로고
    • Coordinated transcription of key pathways in the mouse by the circadian clock
    • Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, et al. 2002. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109:307-20.
    • (2002) Cell , vol.109 , pp. 307-320
    • Panda, S.1    Antoch, M.P.2    Miller, B.H.3    Su, A.I.4    Schook, A.B.5    Straume, M.6
  • 31
    • 79952261359 scopus 로고    scopus 로고
    • Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver
    • Rey G, Cesbron F, Rougemont J, Reinke H, Brunner M, Naef F. 2011. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol 9:e1000595.
    • (2011) PLoS Biol , vol.9
    • Rey, G.1    Cesbron, F.2    Rougemont, J.3    Reinke, H.4    Brunner, M.5    Naef, F.6
  • 32
    • 84863814454 scopus 로고    scopus 로고
    • Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila
    • Rodriguez J, Menet JS, Rosbash M. 2012. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol Cell 47:27-37.
    • (2012) Mol Cell , vol.47 , pp. 27-37
    • Rodriguez, J.1    Menet, J.S.2    Rosbash, M.3
  • 33
    • 67649834440 scopus 로고    scopus 로고
    • ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions
    • Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. 2009. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48:240-8.
    • (2009) Methods , vol.48 , pp. 240-248
    • Schmidt, D.1    Wilson, M.D.2    Spyrou, C.3    Brown, G.D.4    Hadfield, J.5    Odom, D.T.6
  • 34
    • 65249141709 scopus 로고    scopus 로고
    • Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
    • Sharova LV, Sharov AA, Nedorezov T, Piao Y, Shaik N, Ko MS. 2009. Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res 16:45-58.
    • (2009) DNA Res , vol.16 , pp. 45-58
    • Sharova, L.V.1    Sharov, A.A.2    Nedorezov, T.3    Piao, Y.4    Shaik, N.5    Ko, M.S.6
  • 35
    • 0030698128 scopus 로고    scopus 로고
    • Post-transcriptional regulation contributes to Drosophila clock gene mRNA cycling
    • So WV, Rosbash M. 1997. Post-transcriptional regulation contributes to Drosophila clock gene mRNA cycling. EMBO J 16:7146-55.
    • (1997) EMBO J , vol.16 , pp. 7146-7155
    • So, W.V.1    Rosbash, M.2
  • 36
    • 80053318065 scopus 로고    scopus 로고
    • RNA-based regulation in the plant circadian clock
    • Staiger D, Green R. 2011. RNA-based regulation in the plant circadian clock. Trends Plant Sci 16:517-23.
    • (2011) Trends Plant Sci , vol.16 , pp. 517-523
    • Staiger, D.1    Green, R.2
  • 37
    • 78650995766 scopus 로고    scopus 로고
    • Spotlight on post-transcriptional control in the circadian system
    • Staiger D, Koster T. 2011. Spotlight on post-transcriptional control in the circadian system. Cell Mol Life Sci 68:71-83.
    • (2011) Cell Mol Life Sci , vol.68 , pp. 71-83
    • Staiger, D.1    Koster, T.2
  • 39
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-11.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 40
    • 84455200588 scopus 로고    scopus 로고
    • Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast
    • Trcek T, Larson DR, Moldon A, Query CC, Singer RH. 2011. Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147:1484-97.
    • (2011) Cell , vol.147 , pp. 1484-1497
    • Trcek, T.1    Larson, D.R.2    Moldon, A.3    Query, C.C.4    Singer, R.H.5
  • 41
    • 78651491409 scopus 로고    scopus 로고
    • Delay in feedback repression by cryptochrome 1 is required for circadian clock function
    • Ukai-Tadenuma M, Yamada RG, Xu H, Ripperger JA, Liu AC, Ueda HR. 2011. Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell 144:268-81.
    • (2011) Cell , vol.144 , pp. 268-281
    • Ukai-Tadenuma, M.1    Yamada, R.G.2    Xu, H.3    Ripperger, J.A.4    Liu, A.C.5    Ueda, H.R.6
  • 43
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • Wang KC, Chang HY. 2011. Molecular mechanisms of long noncoding RNAs. Mol Cell 43:904-14.
    • (2011) Mol Cell , vol.43 , pp. 904-914
    • Wang, K.C.1    Chang, H.Y.2
  • 44
    • 16844362269 scopus 로고    scopus 로고
    • Molecular and statistical tools for circadian transcript profiling
    • Wijnen H, Naef F, Young MW. 2005. Molecular and statistical tools for circadian transcript profiling. Methods Enzymol 393:341-65.
    • (2005) Methods Enzymol , vol.393 , pp. 341-365
    • Wijnen, H.1    Naef, F.2    Young, M.W.3
  • 45
    • 73549102403 scopus 로고    scopus 로고
    • Circadian amplitude of cryptochrome 1 is modulated by mRNA stability regulation via cytoplasmic hnRNP D oscillation
    • Woo KC, Ha DC, Lee KH, Kim DY, Kim TD, Kim KT. 2010. Circadian amplitude of cryptochrome 1 is modulated by mRNA stability regulation via cytoplasmic hnRNP D oscillation. Mol Cell Biol 30:197-205.
    • (2010) Mol Cell Biol , vol.30 , pp. 197-205
    • Woo, K.C.1    Ha, D.C.2    Lee, K.H.3    Kim, D.Y.4    Kim, T.D.5    Kim, K.T.6
  • 46
    • 58549089726 scopus 로고    scopus 로고
    • Mouse period 2 mRNA circadian oscillation is modulated by PTB-mediated rhythmic mRNA degradation
    • Woo KC, Kim TD, Lee KH, Kim DY, Kim W, Lee KY, et al. 2009. Mouse period 2 mRNA circadian oscillation is modulated by PTB-mediated rhythmic mRNA degradation. Nucleic Acids Res 37:26-37.
    • (2009) Nucleic Acids Res , vol.37 , pp. 26-37
    • Woo, K.C.1    Kim, T.D.2    Lee, K.H.3    Kim, D.Y.4    Kim, W.5    Lee, K.Y.6
  • 47
    • 0028090567 scopus 로고
    • Physical isolation of nascent RNA chains transcribed by RNA polymerase II: Evidence for cotranscriptional splicing
    • Wuarin J, Schibler U. 1994. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol Cell Biol 14:7219-25.
    • (1994) Mol Cell Biol , vol.14 , pp. 7219-7225
    • Wuarin, J.1    Schibler, U.2
  • 48
    • 79955906744 scopus 로고    scopus 로고
    • Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms
    • Zhang L, Weng W, Guo J. 2011. Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms. FEBS Lett 585:1400-5.
    • (2011) FEBS Lett , vol.585 , pp. 1400-1405
    • Zhang, L.1    Weng, W.2    Guo, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.