Literature DB >> 27937535

The emerging biology of RNA post-transcriptional modifications.

Sigrid Nachtergaele1, Chuan He1.   

Abstract

RNA modifications have long been known to be central in the proper function of tRNA and rRNA. While chemical modifications in mRNA were discovered decades ago, their function has remained largely mysterious until recently. Using enrichment strategies coupled to next generation sequencing, multiple modifications have now been mapped on a transcriptome-wide scale in a variety of contexts. We now know that RNA modifications influence cell biology by many different mechanisms - by influencing RNA structure, by tuning interactions within the ribosome, and by recruiting specific binding proteins that intersect with other signaling pathways. They are also dynamic, changing in distribution or level in response to stresses such as heat shock and nutrient deprivation. Here, we provide an overview of recent themes that have emerged from the substantial progress that has been made in our understanding of chemical modifications across many major RNA classes in eukaryotes.

Entities:  

Keywords:  Epitranscriptome; RNA modification; gene expression; post-transcriptional regulation; protein translation

Mesh:

Substances:

Year:  2016        PMID: 27937535      PMCID: PMC5324755          DOI: 10.1080/15476286.2016.1267096

Source DB:  PubMed          Journal:  RNA Biol        ISSN: 1547-6286            Impact factor:   4.652


  81 in total

1.  N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency.

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Journal:  Cell       Date:  2015-06-04       Impact factor: 41.582

Review 2.  RNA nucleotide methylation.

Authors:  Yuri Motorin; Mark Helm
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-03-23       Impact factor: 9.957

3.  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

4.  Impaired control of IRES-mediated translation in X-linked dyskeratosis congenita.

Authors:  Andrew Yoon; Guang Peng; Yves Brandenburger; Yves Brandenburg; Ornella Zollo; Wei Xu; Eduardo Rego; Davide Ruggero
Journal:  Science       Date:  2006-05-12       Impact factor: 47.728

5.  rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells.

Authors:  Karen Jack; Cristian Bellodi; Dori M Landry; Rachel O Niederer; Arturas Meskauskas; Sharmishtha Musalgaonkar; Noam Kopmar; Olya Krasnykh; Alison M Dean; Sunnie R Thompson; Davide Ruggero; Jonathan D Dinman
Journal:  Mol Cell       Date:  2011-11-18       Impact factor: 17.970

6.  Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.

Authors:  Irina Chernyakov; Joseph M Whipple; Lakmal Kotelawala; Elizabeth J Grayhack; Eric M Phizicky
Journal:  Genes Dev       Date:  2008-04-28       Impact factor: 11.361

7.  Sequence specificity of internal methylation in B77 avian sarcoma virus RNA subunits.

Authors:  K Dimock; C M Stoltzfus
Journal:  Biochemistry       Date:  1977-02-08       Impact factor: 3.162

8.  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

9.  The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis.

Authors:  Christiane Zorbas; Emilien Nicolas; Ludivine Wacheul; Emmeline Huvelle; Valérie Heurgué-Hamard; Denis L J Lafontaine
Journal:  Mol Biol Cell       Date:  2015-04-07       Impact factor: 4.138

10.  m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.

Authors:  Huiqing Zhou; Isaac J Kimsey; Evgenia N Nikolova; Bharathwaj Sathyamoorthy; Gianmarc Grazioli; James McSally; Tianyu Bai; Christoph H Wunderlich; Christoph Kreutz; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Nat Struct Mol Biol       Date:  2016-08-01       Impact factor: 15.369

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  69 in total

Review 1.  The Untranslated Regions of mRNAs in Cancer.

Authors:  Samantha L Schuster; Andrew C Hsieh
Journal:  Trends Cancer       Date:  2019-03-22

2.  MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database.

Authors:  Pietro Boccaletto; Błażej Bagiński
Journal:  Methods Mol Biol       Date:  2021

3.  Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.

Authors:  Wen Hu; Liu Qin; Menglong Li; Xuemei Pu; Yanzhi Guo
Journal:  J Comput Aided Mol Des       Date:  2018-11-26       Impact factor: 3.686

4.  Detection and Quantification of RNA Phosphorothioate Modifications Using Mass Spectrometry.

Authors:  Ying Wu; Ya Ying Zheng; Qishan Lin; Jia Sheng
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2020-09

Review 5.  A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications.

Authors:  Joshua D Jones; Jeremy Monroe; Kristin S Koutmou
Journal:  Wiley Interdiscip Rev RNA       Date:  2020-01-21       Impact factor: 9.957

6.  Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs.

Authors:  Yasutoshi Akiyama; Prakash Kharel; Takaaki Abe; Paul Anderson; Pavel Ivanov
Journal:  RNA Biol       Date:  2020-03-01       Impact factor: 4.652

7.  The PARP inhibitor olaparib exerts beneficial effects in mice subjected to cecal ligature and puncture and in cells subjected to oxidative stress without impairing DNA integrity: A potential opportunity for repurposing a clinically used oncological drug for the experimental therapy of sepsis.

Authors:  Akbar Ahmad; Juliana de Camargo Vieira; Aline Haas de Mello; Thais Martins de Lima; Suely Kubo Ariga; Denise Frediani Barbeiro; Hermes Vieira Barbeiro; Bartosz Szczesny; Gábor Törö; Nadiya Druzhyna; Elisa B Randi; Michela Marcatti; Tracy Toliver-Kinsky; András Kiss; Lucas Liaudet; Reinaldo Salomao; Francisco Garcia Soriano; Csaba Szabo
Journal:  Pharmacol Res       Date:  2019-05-06       Impact factor: 7.658

8.  Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs.

Authors:  Mehmet Tardu; Joshua D Jones; Robert T Kennedy; Qishan Lin; Kristin S Koutmou
Journal:  ACS Chem Biol       Date:  2019-06-25       Impact factor: 5.100

9.  Role of m5C-related regulatory genes in the diagnosis and prognosis of hepatocellular carcinoma.

Authors:  Yuting He; Xiao Yu; Jie Li; Qiyao Zhang; Qingyuan Zheng; Wenzhi Guo
Journal:  Am J Transl Res       Date:  2020-03-15       Impact factor: 4.060

Review 10.  Molecular characteristics and functional differences of anti-PM/Scl autoantibodies and two other distinct and unique supramolecular structures known as "EXOSOMES".

Authors:  Peter J Wermuth; Sergio A Jimenez
Journal:  Autoimmun Rev       Date:  2020-08-12       Impact factor: 9.754

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