RNA around the clock – regulation at the RNA level in biological timing

Nolte C, Staiger D (2015)
Frontiers in Plant Science 6: 311.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.
RNA-binding protein; post-transcriptional regulation; circadian oscillation
Frontiers in Plant Science
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI


Nolte C, Staiger D. RNA around the clock – regulation at the RNA level in biological timing. Frontiers in Plant Science. 2015;6: 311.
Nolte, C., & Staiger, D. (2015). RNA around the clock – regulation at the RNA level in biological timing. Frontiers in Plant Science, 6, 311. doi:10.3389/fpls.2015.00311
Nolte, Christine, and Staiger, Dorothee. 2015. “RNA around the clock – regulation at the RNA level in biological timing”. Frontiers in Plant Science 6: 311.
Nolte, C., and Staiger, D. (2015). RNA around the clock – regulation at the RNA level in biological timing. Frontiers in Plant Science 6:311.
Nolte, C., & Staiger, D., 2015. RNA around the clock – regulation at the RNA level in biological timing. Frontiers in Plant Science, 6: 311.
C. Nolte and D. Staiger, “RNA around the clock – regulation at the RNA level in biological timing”, Frontiers in Plant Science, vol. 6, 2015, : 311.
Nolte, C., Staiger, D.: RNA around the clock – regulation at the RNA level in biological timing. Frontiers in Plant Science. 6, : 311 (2015).
Nolte, Christine, and Staiger, Dorothee. “RNA around the clock – regulation at the RNA level in biological timing”. Frontiers in Plant Science 6 (2015): 311.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Access Level
OA Open Access
Zuletzt Hochgeladen
MD5 Prüfsumme

13 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Cardinal Epigenetic Role of non-coding Regulatory RNAs in Circadian Rhythm.
Bhadra U, Patra P, Pal-Bhadra M., Mol Neurobiol 55(4), 2018
PMID: 28516429
What makes ribosomes tick?
Mills SC, Enganti R, von Arnim AG., RNA Biol 15(1), 2018
PMID: 29099307
Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation.
Mateos JL, de Leone MJ, Torchio J, Reichel M, Staiger D., Genes (Basel) 9(12), 2018
PMID: 30544736
PIF-mediated sucrose regulation of the circadian oscillator is light quality and temperature dependent.
Shor E, Potavskaya R, Kurtz A, Paik I, Huq E, Green R., Genes (Basel) 9(12), 2018
PMID: 30551669
Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris.
Saitua F, Torres P, Pérez-Correa JR, Agosin E., BMC Syst Biol 11(1), 2017
PMID: 28222737
Up-Frameshift Protein UPF1 Regulates Neurospora crassa Circadian and Diurnal Growth Rhythms.
Wu Y, Zhang Y, Sun Y, Yu J, Wang P, Ma H, Chen S, Ma L, Zhang D, He Q, Guo J., Genetics 206(4), 2017
PMID: 28600326
Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE.
Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE., Front Plant Sci 7(), 2016
PMID: 27462335
In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings.
Reichel M, Liao Y, Rettel M, Ragan C, Evers M, Alleaume AM, Horos R, Hentze MW, Preiss T, Millar AA., Plant Cell 28(10), 2016
PMID: 27729395
The Plant Circadian Clock: From a Simple Timekeeper to a Complex Developmental Manager.
Sanchez SE, Kay SA., Cold Spring Harb Perspect Biol 8(12), 2016
PMID: 27663772
Molecular mechanisms at the core of the plant circadian oscillator.
Nohales MA, Kay SA., Nat Struct Mol Biol 23(12), 2016
PMID: 27922614
Integrating circadian dynamics with physiological processes in plants.
Greenham K, McClung CR., Nat Rev Genet 16(10), 2015
PMID: 26370901

76 References

Daten bereitgestellt von Europe PubMed Central.

Pseudomonas HopU1 modulates plant immune receptor levels by blocking the interaction of their mRNAs with GRP7.
Nicaise V, Joe A, Jeong BR, Korneli C, Boutrot F, Westedt I, Staiger D, Alfano JR, Zipfel C., EMBO J. 32(5), 2013
PMID: 23395902
Expansion of the eukaryotic proteome by alternative splicing.
Nilsen TW, Graveley BR., Nature 463(7280), 2010
PMID: 20110989
Molecular architecture of the mammalian circadian clock.
Partch CL, Green CB, Takahashi JS., Trends Cell Biol. 24(2), 2013
PMID: 23916625
Role for LSM genes in the regulation of circadian rhythms.
Perez-Santangelo S, Mancini E, Francey LJ, Schlaen RG, Chernomoretz A, Hogenesch JB, Yanovsky MJ., Proc. Natl. Acad. Sci. U.S.A. 111(42), 2014
PMID: 25288739
Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis.
Piques M, Schulze WX, Hohne M, Usadel B, Gibon Y, Rohwer J, Stitt M., Mol. Syst. Biol. 5(), 2009
PMID: 19888209
Ending the message: poly(A) signals then and now.
Proudfoot NJ., Genes Dev. 25(17), 2011
PMID: 21896654
The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames.
Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, Von Arnim AG., RNA 16(4), 2010
PMID: 20179149
Translational Regulation of Cytoplasmic mRNAs.
Roy B, von Arnim AG., Arabidopsis Book 11(), 2013
PMID: 23908601
Alternative splicing at the right time.
Sanchez SE, Petrillo E, Kornblihtt AR, Yanovsky MJ., RNA Biol 8(6), 2011
PMID: 21941124
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.
Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL., Genome Biol. 9(8), 2008
PMID: 18710561
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.
Sherstnev A, Duc C, Cole C, Zacharaki V, Hornyik C, Ozsolak F, Milos PM, Barton GJ, Simpson GG., Nat. Struct. Mol. Biol. 19(8), 2012
PMID: 22820990
RNA-binding proteins and circadian rhythms in Arabidopsis thaliana.
Staiger D., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 356(1415), 2001
PMID: 11710982
The circadian clock goes genomic.
Staiger D, Shin J, Johansson M, Davis SJ., Genome Biol. 14(6), 2013
PMID: 23796230
Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7.
Streitner C, Hennig L, Korneli C, Staiger D., BMC Plant Biol. 10(), 2010
PMID: 20946635
An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana.
Streitner C, Koster T, Simpson CG, Shaw P, Danisman S, Brown JW, Staiger D., Nucleic Acids Res. 40(22), 2012
PMID: 23042250
Alternative splicing in plants--coming of age.
Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW., Trends Plant Sci. 17(10), 2012
PMID: 22743067
Ribonucleoprotein complexes that control circadian clocks.
Wang D, Liang X, Chen X, Guo J., Int J Mol Sci 14(5), 2013
PMID: 23698761
Rhythmic expression of Nocturnin mRNA in multiple tissues of the mouse.
Wang Y, Osterbur DL, Megaw PL, Tosini G, Fukuhara C, Green CB, Besharse JC., BMC Dev. Biol. 1(), 2001
PMID: 11394964
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., Mol. Cell. Biol. 30(1), 2010
PMID: 19858287
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, Kim KT., Nucleic Acids Res. 37(1), 2008
PMID: 19010962
The role of the transcriptional activator protein DBP in circadian liver gene expression.
Wuarin J, Falvey E, Lavery D, Talbot D, Schmidt E, Ossipow V, Fonjallaz P, Schibler U., J. Cell Sci. Suppl. 16(), 1992
PMID: 1297647
Transcriptional interference by antisense RNA is required for circadian clock function.
Xue Z, Ye Q, Anson SR, Yang J, Xiao G, Kowbel D, Glass NL, Crosthwaite SK, Liu Y., Nature 514(7524), 2014
PMID: 25132551
Light modulation of Rubisco in Arabidopsis requires a capacity for redox regulation of the larger Rubisco activase isoform.
Zhang N, Kallis RP, Ewy RG, Portis AR Jr., Proc. Natl. Acad. Sci. U.S.A. 99(5), 2002
PMID: 11854454
The circadian RNA-binding protein CHLAMY 1 represents a novel type heteromer of RNA recognition motif and lysine homology domain-containing subunits.
Zhao B, Schneid C, Iliev D, Schmidt EM, Wagner V, Wollnik F, Mittag M., Eukaryotic Cell 3(3), 2004
PMID: 15190002
Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing.
Deng X, Gu L, Liu C, Lu T, Lu F, Lu Z, Cui P, Pei Y, Wang B, Hu S, Cao X., Proc. Natl. Acad. Sci. U.S.A. 107(44), 2010
PMID: 20956294
Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis.
Dixon LE, Knox K, Kozma-Bognar L, Southern MM, Pokhilko A, Millar AJ., Curr. Biol. 21(2), 2011
PMID: 21236675
Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.
Filichkin SA, Cumbie JS, Dharmawadhana JP, Jaiswal P, Chang JH, Palusa SG, Reddy AS, Megraw M, Mockler TC., Mol Plant (), 2014
PMID: 25366180
Genome-wide mapping of alternative splicing in Arabidopsis thaliana.
Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC., Genome Res. 20(1), 2009
PMID: 19858364
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor.
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SE, Kay SA., Proc. Natl. Acad. Sci. U.S.A. 109(8), 2012
PMID: 22315425
Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation.
Golisz A, Sikorski PJ, Kruszka K, Kufel J., Nucleic Acids Res. 41(12), 2013
PMID: 23620288
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.
Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA., Genome Biol. 10(2), 2009
PMID: 19210792
LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.
Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, Kay SA., Curr. Biol. 21(2), 2011
PMID: 21236673
Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit.
Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Buhlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W., Mol. Syst. Biol. 8(), 2012
PMID: 22929616
Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana.
Hong S, Song HR, Lutz K, Kerstetter RA, Michael TP, McClung CR., Proc. Natl. Acad. Sci. U.S.A. 107(49), 2010
PMID: 21097700
Wheels within wheels: the plant circadian system.
Hsu PY, Harmer SL., Trends Plant Sci. 19(4), 2013
PMID: 24373845
Mutation of Arabidopsis spliceosomal timekeeper locus1 causes circadian clock defects.
Jones MA, Williams BA, McNicol J, Simpson CG, Brown JW, Harmer SL., Plant Cell 24(10), 2012
PMID: 23110899
The circadian clock coordinates ribosome biogenesis.
Jouffe C, Cretenet G, Symul L, Martin E, Atger F, Naef F, Gachon F., PLoS Biol. 11(1), 2013
PMID: 23300384
Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.
Kim JS, Park SJ, Kwak KJ, Kim YO, Kim JY, Song J, Jang B, Jung CH, Kang H., Nucleic Acids Res. 35(2), 2006
PMID: 17169986
Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY.
Kim JY, Song HR, Taylor BL, Carre IA., EMBO J. 22(4), 2003
PMID: 12574129
Transcriptional architecture and chromatin landscape of the core circadian clock in mammals.
Koike N, Yoo SH, Huang HC, Kumar V, Lee C, Kim TK, Takahashi JS., Science 338(6105), 2012
PMID: 22936566
LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1.
Kojima S, Matsumoto K, Hirose M, Shimada M, Nagano M, Shigeyoshi Y, Hoshino S, Ui-Tei K, Saigo K, Green CB, Sakaki Y, Tei H., Proc. Natl. Acad. Sci. U.S.A. 104(6), 2007
PMID: 17264215
Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression.
Kojima S, Sher-Chen EL, Green CB., Genes Dev. 26(24), 2012
PMID: 23249735
Post-transcriptional control of circadian rhythms.
Kojima S, Shingle DL, Green CB., J. Cell. Sci. 124(Pt 3), 2011
PMID: 21242310
The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator.
Koncz C, Dejong F, Villacorta N, Szakonyi D, Koncz Z., Front Plant Sci 3(), 2012
PMID: 22639636
Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis.
Koster T, Meyer K, Weinholdt C, Smith LM, Lummer M, Speth C, Grosse I, Weigel D, Staiger D., Nucleic Acids Res. 42(15), 2014
PMID: 25104024
Circadian rhythms from multiple oscillators: lessons from diverse organisms.
Bell-Pedersen D, Cassone VM, Earnest DJ, Golden SS, Hardin PE, Thomas TL, Zoran MJ., Nat. Rev. Genet. 6(7), 2005
PMID: 15951747
AUF1 contributes to Cryptochrome1 mRNA degradation and rhythmic translation.
Lee KH, Kim SH, Kim HJ, Kim W, Lee HR, Jung Y, Choi JH, Hong KY, Jang SK, Kim KT., Nucleic Acids Res. 42(6), 2014
PMID: 24423872
Rhythmic interaction between Period1 mRNA and hnRNP Q leads to circadian time-dependent translation.
Lee KH, Woo KC, Kim DY, Kim TD, Shin J, Park SM, Jang SK, Kim KT., Mol. Cell. Biol. 32(3), 2011
PMID: 22124155
Plant SILAC: stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics.
Lewandowska D, ten Have S, Hodge K, Tillemans V, Lamond AI, Brown JW., PLoS ONE 8(8), 2013
PMID: 23977254
MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis.
Li S, Liu L, Zhuang X, Yu Y, Liu X, Cui X, Ji L, Pan Z, Cao X, Mo B, Zhang F, Raikhel N, Jiang L, Chen X., Cell 153(3), 2013
PMID: 23622241
Adenosine Methylation in Arabidopsis mRNA is Associated with the 3' End and Reduced Levels Cause Developmental Defects.
Bodi Z, Zhong S, Mehra S, Song J, Graham N, Li H, May S, Fray RG., Front Plant Sci 3(), 2012
PMID: 22639649
Rhythmic degradation explains and unifies circadian transcriptome and proteome data.
Luck S, Thurley K, Thaben PF, Westermark PO., Cell Rep 9(2), 2014
PMID: 25373909
Ordered changes in histone modifications at the core of the Arabidopsis circadian clock.
Malapeira J, Khaitova LC, Mas P., Proc. Natl. Acad. Sci. U.S.A. 109(52), 2012
PMID: 23236129
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis.
Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M., Genome Res. 22(6), 2012
PMID: 22391557
A systematic forward genetic analysis identified components of the Chlamydomonas circadian system.
Matsuo T, Okamoto K, Onai K, Niwa Y, Shimogawara K, Ishiura M., Genes Dev. 22(7), 2008
PMID: 18334618
Post-translational modifications in circadian rhythms.
Mehra A, Baker CL, Loros JJ, Dunlap JC., Trends Biochem. Sci. 34(10), 2009
PMID: 19740663
Nascent-Seq reveals novel features of mouse circadian transcriptional regulation.
Menet JS, Rodriguez J, Abruzzi KC, Rosbash M., Elife 1(), 2012
PMID: 23150795
Complexity in the wiring and regulation of plant circadian networks.
Nagel DH, Kay SA., Curr. Biol. 22(16), 2012
PMID: 22917516

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 25999975
PubMed | Europe PMC

Suchen in

Google Scholar