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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  
[This corrects the article DOI: 10.1371/journal.pcbi.1007842.].  ...  as Class IV. 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 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

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

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

Poly(A)-binding proteins are required for diverse biological processes in metazoans

Richard W.P. Smith, Tajekesa K.P. Blee, Nicola K. Gray
2014 Biochemical Society Transactions  
The prototypical cytoplasmic member, PABP1, is a multifunctional RNAbinding protein with roles in global and mRNA-specific translation and stability, consistent with a function as a central regulator of  ...  PABPs [poly(A)-binding proteins] bind to the poly(A) tail of eukaryotic mRNAs and are conserved in species ranging from yeast to human.  ...  We thank Matt Brook, Simon Bullock, Lenka Hrabalkova, Judith Kimble, Jessica Scanlon and Gavin Wilkie for critical discussions.  ... 
doi:10.1042/bst20140111 pmid:25110030 pmcid:PMC4128646 fatcat:swrl2nhoobcyrapnlckzuyp2ca

Specificity factors in cytoplasmic polyadenylation

Amanda Charlesworth, Hedda A. Meijer, Cornelia H. de Moor
2013 Wiley Interdisciplinary Reviews - RNA  
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation.  ...  It was first discovered in oocytes and embryos, where it has roles in meiosis and development.  ...  ACKNOWLEDGMENTS Nicola Gray (Edinburgh) and Claudia Bagni (Leuven) are thanked for prompt answers to specific queries. Any remaining errors are entirely our own.  ... 
doi:10.1002/wrna.1171 pmid:23776146 pmcid:PMC3736149 fatcat:pabckljfefgvlg24zmj3qk6ga4

The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells

Elizabeth T. Abshire, Jennifer Chasseur, Jennifer A Bohn, Paul A Del Rizzo, Peter L Freddolino, Aaron C Goldstrohm, Raymond C Trievel
2018 Nucleic Acids Research  
The circadian protein Nocturnin (NOCT) belongs to the exonuclease, endonuclease and phosphatase superfamily and is most similar to the CCR4-class of deadenylases that degrade the poly-adenosine tails of  ...  Together, these data demonstrate that NOCT is an exoribonuclease that can degrade mRNAs to inhibit protein expression, suggesting a molecular mechanism for its regulatory role in lipid metabolism and bone  ...  Hughes for critical reading of the manuscript; J. Wilusz for the MALAT1 sequences; R.  ... 
doi:10.1093/nar/gky412 pmid:29860338 fatcat:bgmr3pzxrjhdbb2c7tdlg2ii2m

The role of AUF1 in regulated mRNA decay

Frances M. Gratacós, Gary Brewer
2010 Wiley Interdisciplinary Reviews - RNA  
This review briefly describes the roles of mRNA decay in gene expression in general and ARE-mediated decay (AMD) in particular, with a focus on AUF1 and the different modes of regulation that govern AUF1  ...  Messenger ribonucleic acid (mRNA) turnover is a major control point in gene expression.  ...  F.M.G. was supported by Integrative Graduate Education and Research Traineeship DGE0333196 from the NSF to Prabhas Moghe (Department of Biomedical Engineering, Rutgers University).  ... 
doi:10.1002/wrna.26 pmid:21956942 pmcid:PMC3608466 fatcat:zgvloai4gvetxcu3ca6fv2zdhu

Messenger RNA Turnover in Eukaryotes: Pathways and Enzymes

Sylke Meyer, Claudia Temme, Elmar Wahle
2004 Critical reviews in biochemistry and molecular biology  
The control of mRNA degradation is an important component of the regulation of gene expression since the steady-state concentration of mRNA is determined both by the rates of synthesis and of decay.  ...  In one pathway, deadenylation is followed by the hydrolysis of the cap and processive degradation of the mRNA body by a 5 exonuclease.  ...  Work in the authors' lab is supported by the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie.  ... 
doi:10.1080/10409230490513991 pmid:15596551 fatcat:mjpac6nuybfodakcgq7vfi5u4y

New Molecular Phenotypes in the dst Mutants of Arabidopsis Revealed by DNA Microarray Analysis

Miguel A. Pérez-Amador, Preetmoninder Lidder, Mark A. Johnson, Jeff Landgraf, Ellen Wisman, Pamela J. Green
2001 The Plant Cell  
Cluster analysis of genes altered in dst1 revealed new coexpression patterns that prompt new hypotheses regarding the nature of the dst1 mutation and a possible role of the DST-mediated mRNA decay pathway  ...  Taylor, C.B., and Green, P.J. (1991). Genes with homology to fungal and S-gene RNases are expressed in Arabidopsis thaliana. Plant Physiol. 96, 980-984. Taylor, C.B., and Green, P.J. (1995).  ...  Christoph Benning for critical reading of the manuscript and members of the Green laboratory for helpful discussions.  ... 
doi:10.1105/tpc.010295 fatcat:h5e5qxbor5gefiw2puzurjejt4

Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana

Christian Kappel, Gerda Trost, Hjördis Czesnick, Anna Ramming, Benjamin Kolbe, Son Lang Vi, Cláudia Bispo, Jörg D. Becker, Cornelia de Moor, Michael Lenhard, Gregory P. Copenhaver
2015 PLoS Genetics  
The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression.  ...  the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis.  ...  We thank Isabel Bäurle and members of the Lenhard lab for critical discussion and suggestions. Author Contributions Conceived and designed the experiments: CK HC ML.  ... 
doi:10.1371/journal.pgen.1005474 pmid:26305463 pmcid:PMC4549238 fatcat:lkz3f2tio5eulfoa3x7buoyv5a

Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress

Rafael Catalá, Cristian Carrasco-López, Carlos Perea-Resa, Tamara Hernández-Verdeja, Julio Salinas
2019 Frontiers in Plant Science  
A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control.  ...  Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress.  ...  ACKNOWLEDGMENTS We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).  ... 
doi:10.3389/fpls.2019.00167 pmid:30873189 pmcid:PMC6401655 fatcat:pb2xuo5ylbcz7jiumfbonj3ina

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

Nick D.L. Owens, Ira L. Blitz, Maura A. Lane, Ilya Patrushev, John D. Overton, Michael J. Gilchrist, Ken W.Y. Cho, Mustafa K. Khokha
2016 Cell Reports  
accumulation rates vary over eight orders of magnitude during development d Temporal synexpression and timescales distinguish gene functions  ...  Graphical Abstract Highlights d Ultra-high temporal resolution RNA-seq reveals smooth expression trajectories d Absolute transcript measurements enable calculation of transcriptome kinetics d Transcript  ...  (D) Dynamics of gene expression of poly(A)+ RNA in transcripts per embryo. Circles mark Clutch A poly(A)+, and triangles mark Clutch B poly(A)+.  ... 
doi:10.1016/j.celrep.2015.12.050 pmid:26774488 pmcid:PMC4731879 fatcat:6qbyegjtyjecnfyk6gbagka7by

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

Ekaterina Samatova, Jan Daberger, Marija Liutkute, Marina V. Rodnina
2021 Frontiers in Microbiology  
Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein.  ...  Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation.  ...  ACKNOWLEDGMENTS We thank Wolfgang Wintermeyer for critical reading of the manuscript.  ... 
doi:10.3389/fmicb.2020.619430 pmid:33505387 pmcid:PMC7829197 fatcat:sudafotarzf4hcs2wypusino3e

Dynamic mRNP Remodeling in Response to Internal and External Stimuli

Kathi Zarnack, Sureshkumar Balasubramanian, Michael P. Gantier, Vladislav Kunetsky, Michael Kracht, M. Lienhard Schmitz, Katja Sträßer
2020 Biomolecules  
RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli.  ...  Signal transduction and the regulation of gene expression are fundamental processes in every cell.  ...  Thus, correct mRNP assembly is crucial for correct gene expression.  ... 
doi:10.3390/biom10091310 pmid:32932892 fatcat:lu5htrfa2zebxoaf6k23zhxaza
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