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      A standardised nomenclature for long non‐coding RNAs

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          Abstract

          The HUGO Gene Nomenclature Committee (HGNC) is the sole group with the authority to approve symbols for human genes, including long non‐coding RNA (lncRNA) genes. Use of approved symbols ensures that publications and biomedical databases are easily searchable and reduces the risks of confusion that can be caused by using the same symbol to refer to different genes or using many different symbols for the same gene. Here, we describe how the HGNC names lncRNA genes and review the nomenclature of the seven lncRNA genes most mentioned in the scientific literature.

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          Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

          Nuala A. O'Leary, Mathew Wright, J. Rodney Brister … (2015)
          The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
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            The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.

            Gil Stelzer, Naomi Rosen, Inbar Plaschkes … (2016)
            GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc.
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              Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.

              John Rinn, Michael Kertesz, Jordon K. Wang … (2007)
              Noncoding RNAs (ncRNA) participate in epigenetic regulation but are poorly understood. Here we characterize the transcriptional landscape of the four human HOX loci at five base pair resolution in 11 anatomic sites and identify 231 HOX ncRNAs that extend known transcribed regions by more than 30 kilobases. HOX ncRNAs are spatially expressed along developmental axes and possess unique sequence motifs, and their expression demarcates broad chromosomal domains of differential histone methylation and RNA polymerase accessibility. We identified a 2.2 kilobase ncRNA residing in the HOXC locus, termed HOTAIR, which represses transcription in trans across 40 kilobases of the HOXD locus. HOTAIR interacts with Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states.
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                Author and article information

                Contributors
                Ruth L. Seal:
                ORCID: https://orcid.org/0000-0002-7545-6817
                rseal@ebi.ac.uk
                Journal
                Journal ID (nlm-ta): IUBMB Life
                Journal ID (iso-abbrev): IUBMB Life
                Journal ID (doi): 10.1002/(ISSN)1521-6551
                Journal ID (publisher-id): IUB
                Title: Iubmb Life
                Publisher: John Wiley & Sons, Inc. (Hoboken, USA )
                ISSN (Print): 1521-6543
                ISSN (Electronic): 1521-6551
                Publication date (Electronic): 26 July 2022
                Publication date (Print): May 2023
                Volume: 75
                Issue: 5 ( doiID: 10.1002/iub.v75.5 )
                Pages: 380-389
                Affiliations
                [ 1 ] HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Genome Campus Hinxton UK
                [ 2 ] Department of Haematology University of Cambridge School of Clinical Medicine Cambridge UK
                Author notes
                [*] [* ] Correspondence

                Ruth L. Seal, HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton CB10 1SD, UK.

                Email: rseal@ 123456ebi.ac.uk

                Author information
                https://orcid.org/0000-0002-7545-6817
                https://orcid.org/0000-0003-1818-8243
                https://orcid.org/0000-0002-8380-5247
                Article
                Publisher ID: IUB2663
                DOI: 10.1002/iub.2663
                PMC ID: 9877250
                PubMed ID: 35880706
                SO-VID: 6316e6f0-8a0f-4c28-a43e-4ec977f77a60
                Copyright © © 2022 The Authors. IUBMB Life published by Wiley Periodicals LLC on behalf of International Union of Biochemistry and Molecular Biology.
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 26 May 2022
                Date accepted : 08 July 2022
                Page count
                Figures: 3, Tables: 0, Pages: 10, Words: 6743
                Funding
                Funded by: National Human Genome Research Institute , doi 10.13039/100000051;
                Award ID: U24HG003345
                Funded by: Wellcome Trust , doi 10.13039/100010269;
                Award ID: 208349/Z/17/Z
                Categories
                Subject: Special Issue
                Subject: Special Issue
                Custom metadata
                source-schema-version-number 2.0
                cover-date May 2023
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.9 mode:remove_FC converted:20.03.2024

                Keywords: gene names,gene symbols,human genes,lncrna,standardisation
                Data availability:
                Keywords: gene names, gene symbols, human genes, lncrna, standardisation

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