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Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression

Xiangyu Yao, Shihoko Kojima, Jing Chen
2021 PLoS Computational Biology  
as Class IV. https://doi.org/10.1371/journal.pcbi.1009065.g001 Yao X, Kojima S, Chen J (2021) Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression.  ...  (E) Distributions of peak phase differences (i) between deadenylation and degradation, (ii) between polyadenylation and degradation, and (iii) between deadenylation and polyadenylation for the two classes.Results  ... 
doi:10.1371/journal.pcbi.1009065 pmid:34038419 fatcat:lmaboaaw3neu5e3i4oxeuld55q

Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression

Xiangyu Yao, Shihoko Kojima, Jing Chen, Attila Csikász-Nagy
2020 PLoS Computational Biology  
Our findings highlight the critical role of rhythmic deadenylation in regulating poly(A) rhythms and circadian gene expression.  ...  To understand the role of rhythmic poly(A) regulation in circadian gene expression, we constructed a parsimonious model that depicts rhythmic control imposed upon basic mRNA expression and poly(A) regulation  ...  Xi Chen (Virginia Tech) for helpful discussion of the Sobol method.  ... 
doi:10.1371/journal.pcbi.1007842 pmid:32339166 fatcat:46zxjpy7bjcqzdcgzthuau4ehu

Critical role of rhythmic poly(A) tail regulation in circadian gene expression [article]

Xiangyu Yao, Shihoko Kojima, Jing Chen
2019 bioRxiv   pre-print
A recent study particularly highlighted rhythmic control of poly(A) tail lengths in hundreds of genes in mouse liver and a strong correlation of poly(A) rhythm with protein expression rhythm.  ...  The circadian rhythmicity is deeply rooted in rhythmic regulation of gene expression.  ...  A recent study particularly highlighted rhythmic control of poly(A) tail lengths in hundreds of genes in mouse liver and a strong correlation of poly(A) rhythm with protein expression rhythm.  ... 
doi:10.1101/700443 fatcat:yf2xatx5f5cjzmog5thsud2eua

Nocturnin, a Deadenylase in Xenopus laevis Retina

Julie E Baggs, Carla B Green
2003 Current Biology  
[16, 17] and express Xenopus hoclock-related transcripts in a novel mechanism for postmologs of known clock genes [18, 19]. transcriptional regulation in the circadian clock or its A mouse homolog of  ...  The rhythmicity of clock gene mRNA levels, a be involved in such circadian control identified nocturhallmark of circadian systems, implies that the half-lives nin, a novel gene that displays high-amplitude  ...  Extensive and divergent circadian gene expression in liver and heart. Nature 417, 78-83. 45.  ... 
doi:10.1016/s0960-9822(03)00014-9 pmid:12573214 fatcat:orrhx7jouvbwbeota6twnarieq

AtHESPERIN: a novel regulator of circadian rhythms with poly(A)-degrading activity in plants

Costas Delis, Afrodite Krokida, Anastasia Tomatsidou, Daniela Tsikou, Rafailia A.A. Beta, Maria Tsioumpekou, Julietta Moustaka, Georgios Stravodimos, Demetres D. Leonidas, Nikolaos A. A. Balatsos, Kalliope K. Papadopoulou
2015 RNA Biology  
This study demonstrates an evolutionary conserved poly(A)-degrading activity in plants and suggests deadenylation as a mechanism involved in the regulation of the circadian clock.  ...  The gene is under circadian clock-gene regulation and has similarity to the mammalian Nocturnin. AtHESP can efficiently degrade poly(A) substrates exhibiting allosteric kinetics.  ...  Kontopidis (University of Thessaly) and kindly providing the Tricorn Superose 12 10/300 GL column, and Eirini Papanastasi for valuable help in DIG-assays.  ... 
doi:10.1080/15476286.2015.1119363 pmid:26619288 pmcid:PMC4829295 fatcat:lfdiwu3hhbf2thlnywo4dz6bce

Circadian Post-transcriptional Control of Metabolism [chapter]

Carla B. Green
2016 Research and Perspectives in Endocrine Interactions  
Circadian clocks control thousands of genes, which ultimately generate rhythms in signaling pathways, metabolism, tissue physiology and behavior.  ...  Although rhythmic transcription plays a critical role in generating these rhythmic gene expression patterns, recent evidence has shown that post-transcriptional mechanisms are also important.  ...  Introduction Circadian clocks regulate and coordinate rhythms in behavior, physiology, biochemistry and gene expression in mammals (Pittendrigh 1981a, b; Akhtar et al. 2002; Panda et al. 2002; Storch  ... 
doi:10.1007/978-3-319-27069-2_5 fatcat:6akg3vz3mjgehflrefseidnsmu

Circadian Posttranscriptional Regulatory Mechanisms in Mammals

Carla B. Green
2017 Cold Spring Harbor Perspectives in Biology  
The circadian clock drives rhythms in the levels of thousands of proteins in the mammalian cell, arising in part from rhythmic transcriptional regulation of the genes that encode them.  ...  have been shown to be important for producing the final rhythms in protein levels critical for proper circadian rhythmicity.  ...  ACKNOWLEDGMENTS I thank the National Institutes of Health (NIH) for funding support (R01 GM112991, R01 GM111387, and R01 AG045795).  ... 
doi:10.1101/cshperspect.a030692 pmid:28778869 fatcat:kbgvcvyuqzdqngf4qm5w3ed4ym

Direct evidence that Ataxin-2 is a translational activator mediating cytoplasmic polyadenylation

Hiroto Inagaki, Nao Hosoda, Hitomi Tsuiji, Shin-ichi Hoshino
2020 Journal of Biological Chemistry  
Ataxin-2 is additionally involved in several processes requiring translation such as germline formation, long term habituation and circadian rhythm formation.  ...  Ataxin-2 is known to be a potent modifier of TDP-43 proteinopathies and to play a causative role in the neurodegenerative disease Spinocerebellar ataxia type 2, so these findings suggest that Ataxin-2-  ...  Acknowledgments-We thank the members of the Hoshino laboratory for technical assistance, reagents, and helpful discussions.  ... 
doi:10.1074/jbc.ra120.013835 pmid:32989052 pmcid:PMC7681009 fatcat:xxl4g7q755edtbadbbcrcxmzty

Ribonucleoprotein Complexes That Control Circadian Clocks

Dongni Wang, Xiaodi Liang, Xianyun Chen, Jinhu Guo
2013 International Journal of Molecular Sciences  
Herein, we summarize the advances in the current knowledge on the role of RNP complexes in circadian clock regulation.  ...  Post-transcriptional regulation and translational regulation of circadian clocks have been extensively investigated.  ...  In addition, studies of the roles of SNPs in circadian clocks will no doubt help in revision of the basic model of the generation of circadian rhythms.  ... 
doi:10.3390/ijms14059018 pmid:23698761 pmcid:PMC3676770 fatcat:5gnbo62sl5cevpmi3e2wpisdei

A panoramic view of RNA modifications: exploring new frontiers

Zijun Zhang, Eddie Park, Lan Lin, Yi Xing
2018 Genome Biology  
Meeting report on the Cold Spring Harbor Asia conference on RNA Modifications and Epitranscriptomics,  ...  Acknowledgements We thank conference speakers for their helpful feedback and comments on the meeting report.  ...  Ramesh Pillai (University of Geneva, Switzerland) introduced a critical role of the m 6 A reader YTHDC2 in facilitating the meiotic gene expression program during mouse spermatogenesis.  ... 
doi:10.1186/s13059-018-1394-4 pmid:29382368 pmcid:PMC5791362 fatcat:wdppgu6t6bfk7lnlcdvjctzybq

Determinants and implications of mRNA poly(A) tail size – Does this protein make my tail look big?

Aimee L. Jalkanen, Stephen J. Coleman, Jeffrey Wilusz
2014 Seminars in Cell and Developmental Biology  
This could open up new angles of regulation in the post-transcriptional control of gene expression throughout development, differentiation and cancer.  ...  While the phenomenon of polyadenylation has been well-studied, the dynamics of poly(A) tail size and its impact on transcript function and cell biology are less well-appreciated.  ...  Acknowledgments Studies on RNA stability and polyadenylation in the Wilusz laboratory have been funded by the NIH (GM072481) and NSF (MCB-1301983).  ... 
doi:10.1016/j.semcdb.2014.05.018 pmid:24910447 pmcid:PMC4163081 fatcat:zjbs2d2xtzhlpjm32r6aaqrfd4

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Jérôme Mermet, Jake Yeung, Felix Naef
2016 Cold Spring Harbor Perspectives in Biology  
ACKNOWLEDGMENTS We thank Eric Paquet and Jingkui Wang for critical reading and informative discussions. We thank Laura Symul for illustrations and discussions.  ...  Circadian rhythms in poly(A) tail lengths have been known for a long time (Robinson et al. 1988) .  ...  (B) Recent advances highlighted the role of chromatin conformation in regulating circadian genes.  ... 
doi:10.1101/cshperspect.a028720 pmid:27920039 fatcat:jrjoqvsl7nh3bmx4bvuasanxia

Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms

Lin Zhang, Wenya Weng, Jinhu Guo
2011 FEBS Letters  
Though it remains poorly understood, a growing body of evidence has shown that posttranscriptional regulation controls the expression of both circadian oscillator and output gene transcripts at a number  ...  In a highly conserved fashion, the circadian clock is primarily controlled by multiple positive and negative molecular circuitries that control gene expression.  ...  However, DART5/CSU1 also plays an important role in regulating the circadian clock through splicing of clock-associated genes and expression of a subset of ccgs.  ... 
doi:10.1016/j.febslet.2011.03.018 pmid:21414314 fatcat:uttqqvfa6jghnlnkvrfvir3cnq

The Circadian Deadenylase Nocturnin Is Necessary for Stabilization of the iNOS mRNA in Mice

Shuang Niu, Danielle L. Shingle, Eduardo Garbarino-Pico, Shihoko Kojima, Misty Gilbert, Carla B. Green, Shin Yamazaki
2011 PLoS ONE  
Because it can remove poly(A) tails from mRNAs, it is presumed to play a role in post-transcriptional control of circadian gene expression, but its target mRNAs are not known.  ...  Nocturnin is a member of the CCR4 deadenylase family, and its expression is under circadian control with peak levels at night.  ...  Nancy Kedersha and Dr. Paul Anderson for expression clones and Dr. Todd Stukenberg and John Tooley for use of the Gradient Station for the polysome analysis. Author Contributions  ... 
doi:10.1371/journal.pone.0026954 pmid:22073225 pmcid:PMC3206874 fatcat:pr2jw27xvja7paeogo4llkljau

Immediate early response of the circadian polyA ribonuclease nocturnin to two extracellular stimuli

E. Garbarino-Pico, S. Niu, M. D. Rollag, C. A. Strayer, J. C. Besharse, C. B. Green
2007 RNA: A publication of the RNA Society  
NOC may act in turning off the expression of genes that are required to be silenced as a response to these extracellular signals.  ...  Our data show that in addition to its robust circadian regulation, Noc expression can be regulated acutely, and imply that it can respond directly and specifically to physiological cues.  ...  ACKNOWLEDGMENTS We thank Mike Wormington (University of Virginia) for helpful discussion, criticism of the manuscript, and for providing the PARN antibody and plasmid.  ... 
doi:10.1261/rna.286507 pmid:17400819 pmcid:PMC1852813 fatcat:rot3e5hl4zh3do5xb73gxvyyfi
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