Literature DB >> 26285676

Transcriptome-wide dynamics of RNA pseudouridylation.

John Karijolich1, Chengqi Yi2, Yi-Tao Yu3.   

Abstract

Pseudouridylation is the most abundant internal post-transcriptional modification of stable RNAs, with fundamental roles in the biogenesis and function of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs). Recently, the first transcriptome-wide maps of RNA pseudouridylation were published, greatly expanding the catalogue of known pseudouridylated RNAs. These data have further implicated RNA pseudouridylation in the cellular stress response and, moreover, have established that mRNAs are also targets of pseudouridine synthases, potentially representing a novel mechanism for expanding the complexity of the cellular proteome.

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Year:  2015        PMID: 26285676      PMCID: PMC5694666          DOI: 10.1038/nrm4040

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  38 in total

1.  Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs.

Authors:  Xavier Darzacq; Beáta E Jády; Céline Verheggen; Arnold M Kiss; Edouard Bertrand; Tamás Kiss
Journal:  EMBO J       Date:  2002-06-03       Impact factor: 11.598

2.  Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons.

Authors:  Marc Parisien; Chengqi Yi; Tao Pan
Journal:  RNA       Date:  2012-01-26       Impact factor: 4.942

3.  A pseudouridine residue in the spliceosome core is part of the filamentous growth program in yeast.

Authors:  Anindita Basak; Charles C Query
Journal:  Cell Rep       Date:  2014-08-07       Impact factor: 9.423

4.  Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

Authors:  Kate D Meyer; Yogesh Saletore; Paul Zumbo; Olivier Elemento; Christopher E Mason; Samie R Jaffrey
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

5.  Loss of function of the tumor suppressor DKC1 perturbs p27 translation control and contributes to pituitary tumorigenesis.

Authors:  Cristian Bellodi; Olya Krasnykh; Nikesha Haynes; Marily Theodoropoulou; Guang Peng; Lorenzo Montanaro; Davide Ruggero
Journal:  Cancer Res       Date:  2010-06-29       Impact factor: 12.701

Review 6.  Pseudouridine: still mysterious, but never a fake (uridine)!

Authors:  Felix Spenkuch; Yuri Motorin; Mark Helm
Journal:  RNA Biol       Date:  2014       Impact factor: 4.652

7.  Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae.

Authors:  Alexander F Lovejoy; Daniel P Riordan; Patrick O Brown
Journal:  PLoS One       Date:  2014-10-29       Impact factor: 3.240

8.  N6-methyladenosine-dependent regulation of messenger RNA stability.

Authors:  Xiao Wang; Zhike Lu; Adrian Gomez; Gary C Hon; Yanan Yue; Dali Han; Ye Fu; Marc Parisien; Qing Dai; Guifang Jia; Bing Ren; Tao Pan; Chuan He
Journal:  Nature       Date:  2013-11-27       Impact factor: 49.962

9.  Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.

Authors:  Shivendra Kishore; Andreas R Gruber; Dominik J Jedlinski; Afzal P Syed; Hadi Jorjani; Mihaela Zavolan
Journal:  Genome Biol       Date:  2013-05-26       Impact factor: 13.583

10.  A role for H/ACA and C/D small nucleolar RNAs in viral replication.

Authors:  James L Murray; Jinsong Sheng; Donald H Rubin
Journal:  Mol Biotechnol       Date:  2014-05       Impact factor: 2.695

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  48 in total

Review 1.  RNA modifications and structures cooperate to guide RNA-protein interactions.

Authors:  Cole J T Lewis; Tao Pan; Auinash Kalsotra
Journal:  Nat Rev Mol Cell Biol       Date:  2017-02-01       Impact factor: 94.444

2.  Pseudouridine-Free Escherichia coli Ribosomes.

Authors:  Michael O'Connor; Margus Leppik; Jaanus Remme
Journal:  J Bacteriol       Date:  2018-01-24       Impact factor: 3.490

Review 3.  Specific genomic cues regulate Cajal body assembly.

Authors:  Iain A Sawyer; Gordon L Hager; Miroslav Dundr
Journal:  RNA Biol       Date:  2016-10-07       Impact factor: 4.652

4.  Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV-1 transcription and escape from latency.

Authors:  Yang Zhao; John Karijolich; Britt Glaunsinger; Qiang Zhou
Journal:  EMBO Rep       Date:  2016-08-24       Impact factor: 8.807

5.  Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.

Authors:  Katherine I Zhou; Wesley C Clark; David W Pan; Matthew J Eckwahl; Qing Dai; Tao Pan
Journal:  RNA Biol       Date:  2018-05-11       Impact factor: 4.652

6.  Detection and quantification of RNA 2'-O-methylation and pseudouridylation.

Authors:  Chao Huang; John Karijolich; Yi-Tao Yu
Journal:  Methods       Date:  2016-02-04       Impact factor: 3.608

7.  Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation.

Authors:  Jinghui Song; Yuan Zhuang; Chenxu Zhu; Haowei Meng; Bo Lu; Bingteng Xie; Jinying Peng; Mo Li; Chengqi Yi
Journal:  Nat Chem Biol       Date:  2019-12-09       Impact factor: 15.040

Review 8.  Epitranscriptome sequencing technologies: decoding RNA modifications.

Authors:  Xiaoyu Li; Xushen Xiong; Chengqi Yi
Journal:  Nat Methods       Date:  2016-12-29       Impact factor: 28.547

Review 9.  How to benchmark RNA secondary structure prediction accuracy.

Authors:  David H Mathews
Journal:  Methods       Date:  2019-04-02       Impact factor: 3.608

Review 10.  RNA-modifying proteins as anticancer drug targets.

Authors:  P Ann Boriack-Sjodin; Scott Ribich; Robert A Copeland
Journal:  Nat Rev Drug Discov       Date:  2018-05-18       Impact factor: 84.694

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