For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
3
views
85
references
 Top references
cited by
11
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      302
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      On the Way to Understanding the Interplay between the RNA Structure and Functions in Cells: A Genome-Wide Perspective

      review-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          RNAs adopt specific structures in order to perform their biological activities. The structure of RNA is an important layer of gene expression regulation, and can impact a plethora of cellular processes, starting with transcription, RNA processing, and translation, and ending with RNA turnover. The development of high-throughput technologies has enabled a deeper insight into the sophisticated interplay between the structure of the cellular transcriptome and the living cells environment. In this review, we present the current view on the RNA structure in vivo resulting from the most recent transcriptome-wide studies in different organisms, including mammalians, yeast, plants, and bacteria. We focus on the relationship between the mRNA structure and translation, mRNA stability and degradation, protein binding, and RNA posttranscriptional modifications.

          Related collections

          Most cited references85

          • Record: found
          • Abstract: found
          • Article: not found

          Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.

          Dan Dominissini, Sharon Moshitch-Moshkovitz, Schraga Schwartz … (2012)
          An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. Here we present the human and mouse m(6)A modification landscape in a transcriptome-wide manner, using a novel approach, m(6)A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12,000 m(6)A sites characterized by a typical consensus in the transcripts of more than 7,000 human genes. Sites preferentially appear in two distinct landmarks--around stop codons and within long internal exons--and are highly conserved between human and mouse. Although most sites are well preserved across normal and cancerous tissues and in response to various stimuli, a subset of stimulus-dependent, dynamically modulated sites is identified. Silencing the m(6)A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. Our findings therefore suggest that RNA decoration by m(6)A has a fundamental role in regulation of gene expression.
          Article 0 comments Cited 1389 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

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

            Kate D Meyer, Yogesh Saletore, Paul Zumbo … (2012)
            Methylation of the N(6) position of adenosine (m(6)A) is a posttranscriptional modification of RNA with poorly understood prevalence and physiological relevance. The recent discovery that FTO, an obesity risk gene, encodes an m(6)A demethylase implicates m(6)A as an important regulator of physiological processes. Here, we present a method for transcriptome-wide m(6)A localization, which combines m(6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m(6)A, indicating that m(6)A is a common base modification of mRNA. The m(6)A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m(6)A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m(6)A residues and microRNA-binding sites within 3' UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome. Copyright © 2012 Elsevier Inc. All rights reserved.
            Article 0 comments Cited 1197 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions

              Nian Liu, Chao-Qing Dai, Guanqun Zheng … (2015)
              RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBM) 1-3 . However, RBMs can be buried within their local RNA structures 4-7 , thus inhibiting RNA-protein interactions. N 6-methyladenosine (m6A), the most abundant and dynamic internal modification in eukaryotic messenger RNA 8-19 , can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs 15 , but how m6A achieves wide-ranging physiological significance needs further exploration. Here we show that m6A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism “m6A-switch”. We found that m6A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (hnRNP C), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing 20-24 . Combining PAR-CLIP and m6A/MeRIP approaches enabled us to identify 39,060 m6A-switches among hnRNP C binding sites; and global m6A reduction decreased hnRNP C binding at 2,798 high confidence m6A-switches. We determined that these m6A-switch-regulated hnRNP C binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m6A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m6A-dependent RNA structural remodeling, and provide a new direction for investigating RNA-modification-coded cellular biology.
              Article 0 comments Cited 620 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: MDPI
                ISSN (Electronic): 1422-0067
                Publication date (Electronic): 15 September 2020
                Publication date Collection: September 2020
                Volume: 21
                Issue: 18
                Electronic Location Identifier: 6770
                Affiliations
                Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Structure and Function of Retrotransposons, Noskowskiego 12/14, 61-704 Poznan, Poland; aandrzejewska@ 123456ibch.poznan.pl (A.A.); mzawadzka@ 123456ibch.poznan.pl (M.Z.)
                Author notes
                [* ]Correspondence: kasiapw@ 123456ibch.poznan.pl ; Tel.: +48-618528503
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-6128-6343
                https://orcid.org/0000-0002-2667-9926
                https://orcid.org/0000-0002-5723-6204
                Article
                Publisher ID: ijms-21-06770
                DOI: 10.3390/ijms21186770
                PMC ID: 7554983
                PubMed ID: 32942713
                SO-VID: 236868fb-1895-4603-a426-ad07efa5aeb3
                Copyright © © 2020 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 06 August 2020
                Date accepted : 11 September 2020
                Categories
                Subject: Review

                ScienceOpen disciplines: Molecular biology
                Keywords: transcriptome-wide studies,rna structure in cells,structure-function relationship,translation,rna stability and degradation,rna binding proteome,rna modifications
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: transcriptome-wide studies, rna structure in cells, structure-function relationship, translation, rna stability and degradation, rna binding proteome, rna modifications

                Comments

                Comment on this article

                scite_

                Similar content302

                See all similar

                Cited by11

                See all cited by

                Most referenced authors1,640

                See all reference authors