메뉴 건너뛰기




Volumn 110, Issue 4, 2013, Pages

Nascent-Seq analysis of Drosophila cycling gene expression

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 84872840475     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1219969110     Document Type: Article
Times cited : (74)

References (52)
  • 1
    • 77955829612 scopus 로고    scopus 로고
    • Surprising gene expression patterns within and between pdfcontaining circadian neurons in drosophila
    • Kula-Eversole E, et al. (2010) Surprising gene expression patterns within and between PDFcontaining circadian neurons in Drosophila. Proc Natl Acad Sci USA 107(30):13497-13502.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.30 , pp. 13497-13502
    • Kula-Eversole, E.1
  • 2
    • 66349107101 scopus 로고    scopus 로고
    • Harmonics of circadian gene transcription in mammals
    • Hughes ME, et al. (2009) Harmonics of circadian gene transcription in mammals. PLoS Genet 5(4):e1000442.
    • (2009) PLoS Genet , vol.5 , Issue.4
    • Hughes, M.E.1
  • 3
    • 33846944676 scopus 로고    scopus 로고
    • System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock
    • Kornmann B, Schaad O, Bujard H, Takahashi JS, Schibler U (2007) System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock. PLoS Biol 5(2):e34.
    • (2007) PLoS Biol , vol.5 , Issue.2
    • Kornmann, B.1    Schaad, O.2    Bujard, H.3    Takahashi, J.S.4    Schibler, U.5
  • 4
    • 0037007625 scopus 로고    scopus 로고
    • Extensive and divergent circadian gene expression in liver and heart
    • Storch KF, et al. (2002) Extensive and divergent circadian gene expression in liver and heart. Nature 417(6884):78-83.
    • (2002) Nature , vol.417 , Issue.6884 , pp. 78-83
    • Storch, K.F.1
  • 5
    • 18444414586 scopus 로고    scopus 로고
    • Coordinated transcription of key pathways in the mouse by the circadian clock
    • Panda S, et al. (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109(3):307-320.
    • (2002) Cell , vol.109 , Issue.3 , pp. 307-320
    • Panda, S.1
  • 6
    • 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(5):567-578.
    • (2001) Cell , vol.107 , Issue.5 , pp. 567-578
    • McDonald, M.J.1    Rosbash, M.2
  • 7
    • 0035923746 scopus 로고    scopus 로고
    • Circadian regulation of gene expression systems in the drosophila head
    • Claridge-Chang A, et al. (2001) Circadian regulation of gene expression systems in the Drosophila head. Neuron 32(4):657-671.
    • (2001) Neuron , vol.32 , Issue.4 , pp. 657-671
    • Claridge-Chang, A.1
  • 8
    • 81255150242 scopus 로고    scopus 로고
    • Drosophila clock target gene characterization: Implications for circadian tissue-specific gene expression
    • Abruzzi KC, et al. (2011) Drosophila CLOCK target gene characterization: Implications for circadian tissue-specific gene expression. Genes Dev 25(22):2374-2386.
    • (2011) Genes Dev , vol.25 , Issue.22 , pp. 2374-2386
    • Abruzzi, K.C.1
  • 9
    • 0032486432 scopus 로고    scopus 로고
    • Closing the circadian loop: Clock-induced transcription of its own inhibitors per and tim
    • 5 June
    • Darlington TK, et al. (1998) Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science 280(5 June 1998):1599-1603.
    • (1998) Science , vol.1998 , Issue.280 , pp. 1599-1603
    • Darlington, T.K.1
  • 10
    • 0025044560 scopus 로고
    • Feedback of the drosophila period gene product on circadian cycling of its messenger rna levels
    • Hardin PE, Hall JC, Rosbash M (1990) Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature 343(6258):536-540.
    • (1990) Nature , vol.343 , Issue.6258 , pp. 536-540
    • Hardin, P.E.1    Hall, J.C.2    Rosbash, M.3
  • 11
    • 76749085755 scopus 로고    scopus 로고
    • Dynamic per repression mechanisms in the drosophila circadian clock: From on-dna to off-dna
    • Menet JS, Abruzzi KC, Desrochers J, Rodriguez J, Rosbash M (2010) Dynamic PER repression mechanisms in the Drosophila circadian clock: From on-DNA to off-DNA. Genes Dev 24(4):358-367.
    • (2010) Genes Dev , vol.24 , Issue.4 , pp. 358-367
    • Menet, J.S.1    Abruzzi, K.C.2    Desrochers, J.3    Rodriguez, J.4    Rosbash, M.5
  • 12
    • 24044444531 scopus 로고    scopus 로고
    • The circadian timekeeping system of drosophila
    • Hardin PE (2005) The circadian timekeeping system of Drosophila. Curr Biol 15(17): R714-R722.
    • (2005) Curr Biol , vol.15 , Issue.17
    • Hardin, P.E.1
  • 13
    • 1342285689 scopus 로고    scopus 로고
    • Posttranslational regulation of drosophila period protein by protein phosphatase 2a
    • Sathyanarayanan S, Zheng X, Xiao R, Sehgal A (2004) Posttranslational regulation of Drosophila PERIOD protein by protein phosphatase 2A. Cell 116(4):603-615.
    • (2004) Cell , vol.116 , Issue.4 , pp. 603-615
    • Sathyanarayanan, S.1    Zheng, X.2    Xiao, R.3    Sehgal, A.4
  • 14
    • 34250790719 scopus 로고    scopus 로고
    • Post-translational regulation of the drosophila circadian clock requires protein phosphatase 1 (pp1)
    • Fang Y, Sathyanarayanan S, Sehgal A (2007) Post-translational regulation of the Drosophila circadian clock requires protein phosphatase 1 (PP1). Genes Dev 21(12): 1506-1518.
    • (2007) Genes Dev , vol.21 , Issue.12 , pp. 1506-1518
    • Fang, Y.1    Sathyanarayanan, S.2    Sehgal, A.3
  • 15
    • 0037187636 scopus 로고    scopus 로고
    • Drosophila clock protein is under posttranscriptional control and influences light-induced activity
    • Kim EY, et al. (2002) Drosophila CLOCK protein is under posttranscriptional control and influences light-induced activity. Neuron 34(1):69-81.
    • (2002) Neuron , vol.34 , Issue.1 , pp. 69-81
    • Kim, E.Y.1
  • 16
    • 46249098507 scopus 로고    scopus 로고
    • The phospho-occupancy of an atypical slimb-binding site on period that is phosphorylated by doubletime controls the pace of the clock
    • Chiu JC, Vanselow JT, Kramer A, Edery I (2008) The phospho-occupancy of an atypical SLIMB-binding site on PERIOD that is phosphorylated by DOUBLETIME controls the pace of the clock. Genes Dev 22(13):1758-1772.
    • (2008) Genes Dev , vol.22 , Issue.13 , pp. 1758-1772
    • Chiu, J.C.1    Vanselow, J.T.2    Kramer, A.3    Edery, I.4
  • 17
    • 79955540602 scopus 로고    scopus 로고
    • Nemo/nlk phosphorylates period to initiate a timedelay phosphorylation circuit that sets circadian clock speed
    • Chiu JC, Ko HW, Edery I (2011) NEMO/NLK phosphorylates PERIOD to initiate a timedelay phosphorylation circuit that sets circadian clock speed. Cell 145(3):357-370.
    • (2011) Cell , vol.145 , Issue.3 , pp. 357-370
    • Chiu, J.C.1    Ko, H.W.2    Edery, I.3
  • 18
    • 12244296161 scopus 로고    scopus 로고
    • No transcription-translation feedback in circadian rhythm of kaic phosphorylation
    • Tomita J, Nakajima M, Kondo T, Iwasaki H (2005) No transcription- translation feedback in circadian rhythm of KaiC phosphorylation. Science 307(5707):251-254.
    • (2005) Science , vol.307 , Issue.5707 , pp. 251-254
    • Tomita, J.1    Nakajima, M.2    Kondo, T.3    Iwasaki, H.4
  • 19
    • 0032503969 scopus 로고    scopus 로고
    • Double-time is a novel drosophila clock gene that regulates period protein accumulation
    • Price JL, et al. (1998) double-time is a novel Drosophila clock gene that regulates PERIOD protein accumulation. Cell 94(1):83-95.
    • (1998) Cell , vol.94 , Issue.1 , pp. 83-95
    • Price, J.L.1
  • 20
    • 45149085615 scopus 로고    scopus 로고
    • Circadian transcription contributes to core period determination in drosophila
    • Kadener S, Menet JS, Schoer R, Rosbash M (2008) Circadian transcription contributes to core period determination in Drosophila. PLoS Biol 6(5):e119.
    • (2008) PLoS Biol , vol.6 , Issue.5
    • Kadener, S.1    Menet, J.S.2    Schoer, R.3    Rosbash, M.4
  • 21
    • 82955247079 scopus 로고    scopus 로고
    • Nascent-seq indicates widespread cotranscriptional premrna splicing in drosophila
    • Khodor YL, et al. (2011) Nascent-seq indicates widespread cotranscriptional premRNA splicing in Drosophila. Genes Dev 25(23):2502-2512.
    • (2011) Genes Dev , vol.25 , Issue.23 , pp. 2502-2512
    • Khodor, Y.L.1
  • 22
    • 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(1):27-37.
    • (2012) Mol Cell , vol.47 , Issue.1 , pp. 27-37
    • Rodriguez, J.1    Menet, J.S.2    Rosbash, M.3
  • 23
    • 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(11): 7219-7225.
    • (1994) Mol Cell Biol , vol.14 , Issue.11 , pp. 7219-7225
    • Wuarin, J.1    Schibler, U.2
  • 24
    • 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(4):571-581.
    • (2010) Mol Cell , vol.40 , Issue.4 , pp. 571-581
    • Carrillo Oesterreich, F.1    Preibisch, S.2    Neugebauer, K.M.3
  • 25
    • 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(9):1105-1111.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 26
    • 0033544692 scopus 로고    scopus 로고
    • Cycling vrille expression is required for a functional drosophila clock
    • Blau J, Young MW (1999) Cycling vrille expression is required for a functional Drosophila clock. Cell 99(6):661-671.
    • (1999) Cell , vol.99 , Issue.6 , pp. 661-671
    • Blau, J.1    Young, M.W.2
  • 27
    • 33645766967 scopus 로고    scopus 로고
    • Control of daily transcript oscillations in drosophila by light and the circadian clock
    • Wijnen H, Naef F, Boothroyd C, Claridge-Chang A, Young MW (2006) Control of daily transcript oscillations in Drosophila by light and the circadian clock. PLoS Genet 2(3):e39.
    • (2006) PLoS Genet , vol.2 , Issue.3
    • Wijnen, H.1    Naef, F.2    Boothroyd, C.3    Claridge-Chang, A.4    Young, M.W.5
  • 28
    • 0037134445 scopus 로고    scopus 로고
    • Genome-wide transcriptional orchestration of circadian rhythms in drosophila
    • Ueda HR, et al. (2002) Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J Biol Chem 277(16):14048-14052.
    • (2002) J Biol Chem , vol.277 , Issue.16 , pp. 14048-14052
    • Ueda, H.R.1
  • 29
    • 0036848612 scopus 로고    scopus 로고
    • Genome-wide expression analysis in drosophila reveals genes controlling circadian behavior
    • Ceriani MF, et al. (2002) Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J Neurosc 22(21):9305-9319.
    • (2002) J Neurosc , vol.22 , Issue.21 , pp. 9305-9319
    • Ceriani, M.F.1
  • 30
    • 0027079975 scopus 로고
    • Circadian oscillations in period gene mrna levels are transcriptionally regulated
    • Hardin PE, Hall JC, Rosbash M (1992) Circadian oscillations in period gene mRNA levels are transcriptionally regulated. Proc Natl Acad Sci USA 89(24):11711-11715.
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.24 , pp. 11711-11715
    • Hardin, P.E.1    Hall, J.C.2    Rosbash, M.3
  • 31
    • 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(23):7146-7155.
    • (1997) EMBO J , vol.16 , Issue.23 , pp. 7146-7155
    • So, W.V.1    Rosbash, M.2
  • 32
    • 0028838668 scopus 로고
    • Rhythmic expression of timeless: A basis for promoting circadian cycles in period gene autoregulation
    • Sehgal A, et al. (1995) Rhythmic expression of timeless: A basis for promoting circadian cycles in period gene autoregulation. Science 270:808-810.
    • (1995) Science , vol.270 , pp. 808-810
    • Sehgal, A.1
  • 33
    • 0037423224 scopus 로고    scopus 로고
    • Vrille, pdp1, and dclock form a second feedback loop in the drosophila circadian clock
    • Cyran SA, et al. (2003) vrille, Pdp1, and dClock form a second feedback loop in the Drosophila circadian clock. Cell 112(3):329-341.
    • (2003) Cell , vol.112 , Issue.3 , pp. 329-341
    • Cyran, S.A.1
  • 34
    • 17044451254 scopus 로고    scopus 로고
    • A mutant drosophila homolog of mammalian clock disrupts circadian rhythms and transcription of period and timeless
    • Allada R, White NE, So WV, Hall JC, Rosbash M (1998) A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell 93(5):791-804.
    • (1998) Cell , vol.93 , Issue.5 , pp. 791-804
    • Allada, R.1    White, N.E.2    So, W.V.3    Hall, J.C.4    Rosbash, M.5
  • 35
    • 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(7): 1266-1281.
    • (2012) Genome Res , vol.22 , Issue.7 , pp. 1266-1281
    • Hughes, M.E.1    Grant, G.R.2    Paquin, C.3    Qian, J.4    Nitabach, M.N.5
  • 36
    • 84881506759 scopus 로고    scopus 로고
    • Nascent-seq reveals novel features of mouse circadian transcriptional regulation
    • Menet JS, Rodriguez J, Abruzzi KC, Rosbash M (2012) Nascent-seq reveals novel features of mouse circadian transcriptional regulation. elife. 1:e00011.
    • (2012) Elife. , Issue.1
    • Menet, J.S.1    Rodriguez, J.2    Abruzzi, K.C.3    Rosbash, M.4
  • 37
    • 84867667011 scopus 로고    scopus 로고
    • Transcriptional architecture and chromatin landscape of the core circadian clock in mammals
    • Koike N, et al. (2012) Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338(6105):349-354.
    • (2012) Science , vol.338 , Issue.6105 , pp. 349-354
    • Koike, N.1
  • 38
    • 55849117380 scopus 로고    scopus 로고
    • At least four distinct circadian regulatory mechanisms are required for all phases of rhythms in mrna amount
    • Jacobshagen S, Kessler B, Rinehart CA (2008) At least four distinct circadian regulatory mechanisms are required for all phases of rhythms in mRNA amount. J Biol Rhythms 23(6):511-524.
    • (2008) J Biol Rhythms , vol.23 , Issue.6 , pp. 511-524
    • Jacobshagen, S.1    Kessler, B.2    Rinehart, C.A.3
  • 39
    • 0025630643 scopus 로고
    • Expression of the liver-enriched transcriptional activator protein dbp follows a stringent circadian rhythm
    • Wuarin J, Schibler U (1990) Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 63(6):1257-1266.
    • (1990) Cell , vol.63 , Issue.6 , pp. 1257-1266
    • Wuarin, J.1    Schibler, U.2
  • 40
    • 0027023614 scopus 로고
    • The role of the transcriptional activator protein dbp in circadian liver gene expression
    • Wuarin J, et al. (1992) The role of the transcriptional activator protein DBP in circadian liver gene expression. J Cell Sci Suppl 16:123-127.
    • (1992) J Cell Sci Suppl , vol.16 , pp. 123-127
    • Wuarin, J.1
  • 41
    • 70349093118 scopus 로고    scopus 로고
    • A role for micrornas in the drosophila circadian clock
    • Kadener S, et al. (2009) A role for microRNAs in the Drosophila circadian clock. Genes Dev 23(18):2179-2191.
    • (2009) Genes Dev , vol.23 , Issue.18 , pp. 2179-2191
    • Kadener, S.1
  • 42
    • 70349245117 scopus 로고    scopus 로고
    • The mirna-192/194 cluster regulates the period gene family and the circadian clock
    • Nagel R, Clijsters L, Agami R (2009) The miRNA-192/194 cluster regulates the Period gene family and the circadian clock. FEBS J 276(19):5447-5455.
    • (2009) FEBS J , vol.276 , Issue.19 , pp. 5447-5455
    • Nagel, R.1    Clijsters, L.2    Agami, R.3
  • 43
    • 40549096693 scopus 로고    scopus 로고
    • Circadian regulation of a limited set of conserved micrornas in drosophila
    • Yang M, Lee JE, Padgett RW, Edery I (2008) Circadian regulation of a limited set of conserved microRNAs in Drosophila. BMC Genomics 9:83.
    • (2008) BMC Genomics , vol.9 , pp. 83
    • Yang, M.1    Lee, J.E.2    Padgett, R.W.3    Edery, I.4
  • 44
    • 70350038002 scopus 로고    scopus 로고
    • Rhythmic expression of microrna-26a regulates the l-type voltage-gated calcium channel alpha1c subunit in chicken cone photoreceptors
    • Shi L, Ko ML, Ko GY (2009) Rhythmic expression of microRNA-26a regulates the L-type voltage-gated calcium channel alpha1C subunit in chicken cone photoreceptors. J Biol Chem 284(38):25791-25803.
    • (2009) J Biol Chem , vol.284 , Issue.38 , pp. 25791-25803
    • Shi, L.1    Ko, M.L.2    Ko, G.Y.3
  • 45
    • 77956197958 scopus 로고    scopus 로고
    • Microrna-122 modulates the rhythmic expression profile of the circadian deadenylase nocturnin in mouse liver
    • Kojima S, Gatfield D, Esau CC, Green CB (2010) MicroRNA-122 modulates the rhythmic expression profile of the circadian deadenylase Nocturnin in mouse liver. PLoS ONE 5(6):e11264.
    • (2010) PLoS ONE , vol.5 , Issue.6
    • Kojima, S.1    Gatfield, D.2    Esau, C.C.3    Green, C.B.4
  • 46
    • 70149093861 scopus 로고    scopus 로고
    • The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop
    • Guo J, Cheng P, Yuan H, Liu Y (2009) The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop. Cell 138(6):1236-1246.
    • (2009) Cell , vol.138 , Issue.6 , pp. 1236-1246
    • Guo, J.1    Cheng, P.2    Yuan, H.3    Liu, Y.4
  • 47
    • 58549089726 scopus 로고    scopus 로고
    • Mouse period 2 mrna circadian oscillation is modulated by ptbmediated rhythmic mrna degradation
    • Woo KC, et al. (2009) Mouse period 2 mRNA circadian oscillation is modulated by PTBmediated rhythmic mRNA degradation. Nucleic Acids Res 37(1):26-37.
    • (2009) Nucleic Acids Res , vol.37 , Issue.1 , pp. 26-37
    • Woo, K.C.1
  • 48
    • 73549102403 scopus 로고    scopus 로고
    • Circadian amplitude of cryptochrome 1 is modulated by mrna stability regulation via cytoplasmic hnrnp d oscillation
    • Woo KC, et al. (2010) Circadian amplitude of cryptochrome 1 is modulated by mRNA stability regulation via cytoplasmic hnRNP D oscillation. Mol Cell Biol 30(1):197-205.
    • (2010) Mol Cell Biol , vol.30 , Issue.1 , pp. 197-205
    • Woo, K.C.1
  • 49
    • 40249091049 scopus 로고    scopus 로고
    • The lark rna-binding protein selectively regulates the circadian eclosion rhythm by controlling e74 protein expression
    • Huang Y, Genova G, Roberts M, Jackson FR (2007) The LARK RNA-binding protein selectively regulates the circadian eclosion rhythm by controlling E74 protein expression. PLoS ONE 2(10):e1107.
    • (2007) PLoS ONE , vol.2 , Issue.10
    • Huang, Y.1    Genova, G.2    Roberts, M.3    Jackson, F.R.4
  • 50
    • 33846907098 scopus 로고    scopus 로고
    • Lark activates posttranscriptional expression of an essential mammalian clock protein, period1
    • Kojima S, et al. (2007) LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc Natl Acad Sci USA 104(6):1859-1864.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.6 , pp. 1859-1864
    • Kojima, S.1
  • 51
    • 80052266532 scopus 로고    scopus 로고
    • Micrornas can generate thresholds in target gene expression
    • Mukherji S, et al. (2011) MicroRNAs can generate thresholds in target gene expression. Nat Genet 43(9):854-859.
    • (2011) Nat Genet , vol.43 , Issue.9 , pp. 854-859
    • Mukherji, S.1
  • 52
    • 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 393:341-365.
    • (2005) Methods Enzymol , vol.393 , pp. 341-365
    • Wijnen, H.1    Naef, F.2    Young, M.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.