33
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels

      review-article

      Read this article at

      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

          Long non-coding (lnc) RNAs are non-coding RNAs longer than 200 nt. lncRNAs primarily interact with mRNA, DNA, protein, and miRNA and consequently regulate gene expression at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels in a variety of ways. They play important roles in biological processes such as chromatin remodeling, transcriptional activation, transcriptional interference, RNA processing, and mRNA translation. lncRNAs have important functions in plant growth and development; biotic and abiotic stress responses; and in regulation of cell differentiation, the cell cycle, and the occurrence of many diseases in humans and animals. In this review, we summarize the functions and mechanisms of lncRNAs in plants, humans, and animals at different regulatory levels.

          Related collections

          Most cited references126

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

          Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs) (e.g. lncRNAs, pseudogenes and circRNAs) and competing endogenous RNAs (ceRNAs) have been implicated in cell-fate determination and in various human diseases, surprisingly little is known about the regulatory interaction networks among the multiple classes of RNAs. In this study, we developed starBase v2.0 (http://starbase.sysu.edu.cn/) to systematically identify the RNA–RNA and protein–RNA interaction networks from 108 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) data sets generated by 37 independent studies. By analyzing millions of RNA-binding protein binding sites, we identified ∼9000 miRNA-circRNA, 16 000 miRNA-pseudogene and 285 000 protein–RNA regulatory relationships. Moreover, starBase v2.0 has been updated to provide the most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and miRNA-lncRNA interaction networks to date. We identified ∼10 000 ceRNA pairs from CLIP-supported miRNA target sites. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from the miRNA-mediated regulatory networks. Finally, we developed interactive web implementations to provide visualization, analysis and downloading of the aforementioned large-scale data sets. This study will greatly expand our understanding of ncRNA functions and their coordinated regulatory networks.
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            MicroRNAs

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

              Functional Classification and Experimental Dissection of Long Noncoding RNAs

              Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bidirectional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncRNA field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncRNA function. We categorize lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans , and propose an experimental approach to dissect lncRNA activity based on these classifications. These strategies to further understand lncRNAs promise to reveal new and unanticipated biology, with great potential to advance our understanding of normal physiology and disease.
                Bookmark

                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                08 November 2019
                November 2019
                : 20
                : 22
                : 5573
                Affiliations
                [1 ]State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an 271018, Shandong, China; xpzhang@ 123456sdau.edu.cn (X.Z.); weiwang@ 123456sdau.edu.cn (W.W.); 2018110136@ 123456sdau.edu.cn (J.D.); 2017110205@ 123456sdau.edu.cn (Y.C.)
                [2 ]State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences Cotton Research Institute, Key Laboratory for Cotton Genetic Improvement, Anyang 45500, Henan, China; zwdd1005@ 123456gmail.com
                Author notes
                [* ]Correspondence: yinzujun@ 123456caas.cn (Z.Y.); cotton1@ 123456sdau.edu.cn (F.S.); Tel.: +86-372-256-2219 (Z.Y.); +86-538-824-6011 (F.S.); Fax: +86-372-256-2311 (Z.Y.); +86-538-824-2226 (F.S.)
                Author information
                https://orcid.org/0000-0002-5705-8591
                https://orcid.org/0000-0003-1977-8712
                Article
                ijms-20-05573
                10.3390/ijms20225573
                6888083
                31717266
                c8f5b2b9-c6b7-4ab6-b1ab-bd905fbbaa55
                © 2019 by the authors.

                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
                : 20 September 2019
                : 06 November 2019
                Categories
                Review

                Molecular biology
                lncrna,epigenetic,transcriptional,post-transcriptional,translation,post-translational modification

                Comments

                Comment on this article