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

      Long Non-coding RNAs and Their Biological Roles in Plants

      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

          With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.

          Related collections

          Most cited references81

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

          Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

          Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana.

            To better understand the diversity of small silencing RNAs expressed in plants, we employed high-throughput pyrosequencing to obtain 887,000 reads corresponding to Arabidopsis thaliana small RNAs. They represented 340,000 unique sequences, a substantially greater diversity than previously obtained in any species. Most of the small RNAs had the properties of heterochromatic small interfering RNAs (siRNAs) associated with DNA silencing in that they were preferentially 24 nucleotides long and mapped to intergenic regions. Their density was greatest in the proximal and distal pericentromeric regions, with only a slightly preferential propensity to match repetitive elements. Also present were 38 newly identified microRNAs (miRNAs) and dozens of other plausible candidates. One miRNA mapped within an intron of DICER-LIKE 1 (DCL1), suggesting a second homeostatic autoregulatory mechanism for DCL1 expression; another defined the phase for siRNAs deriving from a newly identified trans-acting siRNA gene (TAS4); and two depended on DCL4 rather than DCL1 for their accumulation, indicating a second pathway for miRNA biogenesis in plants. More generally, our results revealed the existence of a layer of miRNA-based control beyond that found previously that is evolutionarily much more fluid, employing many newly emergent and diverse miRNAs, each expressed in specialized tissues or at low levels under standard growth conditions.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              The Arabidopsis Information Resource (TAIR): gene structure and function annotation

              The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release.
                Bookmark

                Author and article information

                Contributors
                Journal
                Genomics Proteomics Bioinformatics
                Genomics Proteomics Bioinformatics
                Genomics, Proteomics & Bioinformatics
                Elsevier
                1672-0229
                2210-3244
                30 April 2015
                June 2015
                30 April 2015
                : 13
                : 3
                : 137-147
                Affiliations
                [1 ]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
                [2 ]State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
                Author notes
                [#]

                Equal contribution.

                [a]

                ORCID: 0000-0002-2631-509X.

                [b]

                ORCID: 0000-0003-3432-7151.

                [c]

                ORCID: 0000-0003-1573-4747.

                [d]

                ORCID: 0000-0001-6871-9546.

                [e]

                ORCID: 0000-0003-3966-3111.

                Article
                S1672-0229(15)00042-X
                10.1016/j.gpb.2015.02.003
                4563214
                25936895
                f567f588-29ad-4817-b2c1-e5d7adfc342d
                © 2015 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 31 December 2014
                : 6 February 2015
                : 9 February 2015
                Categories
                Review

                long non-coding rna (lncrna),long non-coding natural antisense transcripts (lncnats),epigenetic,small rna,microrna,target mimicry

                Comments

                Comment on this article