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      lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

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          Abstract

          The advent of high-throughput genome scale technologies has enabled us to unravel a large amount of the previously unknown transcriptionally active regions of the genome. Recent genome-wide studies have provided annotations of a large repertoire of various classes of noncoding transcripts. Long noncoding RNAs (lncRNAs) form a major proportion of these novel annotated noncoding transcripts, and presently known to be involved in a number of functionally distinct biological processes. Over 18 000 transcripts are presently annotated as lncRNA, and encompass previously annotated classes of noncoding transcripts including large intergenic noncoding RNA, antisense RNA and processed pseudogenes. There is a significant gap in the resources providing a stable annotation, cross-referencing and biologically relevant information. lncRNome has been envisioned with the aim of filling this gap by integrating annotations on a wide variety of biologically significant information into a comprehensive knowledgebase. To the best of our knowledge, lncRNome is one of the largest and most comprehensive resources for lncRNAs.

          Database URL: http://genome.igib.res.in/lncRNome

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          Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.

          Andrea Pauli, Eivind Valen, Michael Lin … (2012)
          Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time-series of RNA-seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1133 noncoding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to that of introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than are protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies.
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            miRDB: a microRNA target prediction and functional annotation database with a wiki interface.

            Xiaowei Wang (2008)
            MicroRNAs (miRNAs) are short noncoding RNAs that are involved in the regulation of thousands of gene targets. Recent studies indicate that miRNAs are likely to be master regulators of many important biological processes. Due to their functional importance, miRNAs are under intense study at present, and many studies have been published in recent years on miRNA functional characterization. The rapid accumulation of miRNA knowledge makes it challenging to properly organize and present miRNA function data. Although several miRNA functional databases have been developed recently, this remains a major bioinformatics challenge to miRNA research community. Here, we describe a new online database system, miRDB, on miRNA target prediction and functional annotation. Flexible web search interface was developed for the retrieval of target prediction results, which were generated with a new bioinformatics algorithm we developed recently. Unlike most other miRNA databases, miRNA functional annotations in miRDB are presented with a primary focus on mature miRNAs, which are the functional carriers of miRNA-mediated gene expression regulation. In addition, a wiki editing interface was established to allow anyone with Internet access to make contributions on miRNA functional annotation. This is a new attempt to develop an interactive community-annotated miRNA functional catalog. All data stored in miRDB are freely accessible at http://mirdb.org.
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              Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

              Victoria Moran, Ranjan Perera, Ahmad Khalil (2012)
              The recent discovery that the human and other mammalian genomes produce thousands of long non-coding RNAs (lncRNAs) raises many fascinating questions. These mRNA-like molecules, which lack significant protein-coding capacity, have been implicated in a wide range of biological functions through diverse and as yet poorly understood molecular mechanisms. Despite some recent insights into how lncRNAs function in such diverse cellular processes as regulation of gene expression and assembly of cellular structures, by and large, the key questions regarding lncRNA mechanisms remain to be answered. In this review, we discuss recent advances in understanding the biology of lncRNAs and propose avenues of investigation that may lead to fundamental new insights into their functions and mechanisms of action. Finally, as numerous lncRNAs are dysregulated in human diseases and disorders, we also discuss potential roles for these molecules in human health.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Database (Oxford)
                Journal ID (iso-abbrev): Database (Oxford)
                Journal ID (publisher-id): database
                Journal ID (hwp): databa
                Title: Database: The Journal of Biological Databases and Curation
                Publisher: Oxford University Press
                ISSN (Electronic): 1758-0463
                Publication date Collection: 2013
                Publication date (Electronic): 11 July 2013
                Publication date PMC-release: 11 July 2013
                Volume: 2013
                Electronic Location Identifier: bat034
                Affiliations
                1GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India, 2CSIR Open Source Drug Discovery Unit, Council of Scientific and Industrial Research, Anusandhan Bhavan, Delhi 110001, India, 3Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and 4Bioinformatics Centre, CSIR Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
                Author notes
                *Corresponding author: Tel: +91 9650466002; Fax: +91 11 27667471; Email: vinods@ 123456igib.in

                †These authors contributed equally to this work.

                Citation details: Bhartiya,D., Pal,K., Ghosh,S., et al. lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (2013) Vol. 2013: article ID bat034; doi:10.1093/database/bat034.

                Article
                Publisher ID: bat034
                DOI: 10.1093/database/bat034
                PMC ID: 3708617
                PubMed ID: 23846593
                SO-VID: 86bff8c3-c36d-4a39-9f0c-372d929d5d06
                Copyright © © The Author(s) 2013. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 17 October 2012
                Date revision received : 8 April 2013
                Date accepted : 11 April 2013
                Page count
                Pages: 6
                Categories
                Subject: Original Article

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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