A short guide to long non-coding RNA gene nomenclature
© Wright; licensee BioMed Central Ltd. 2014
Received: 18 February 2014
Accepted: 29 March 2014
Published: 9 April 2014
The HUGO Gene Nomenclature Committee (HGNC) is the only organisation authorised to assign standardised nomenclature to human genes. Of the 38,000 approved gene symbols in our database (http://www.genenames.org), the majority represent protein-coding (pc) genes; however, we also name pseudogenes, phenotypic loci, some genomic features, and to date have named more than 8,500 human non-protein coding RNA (ncRNA) genes and ncRNA pseudogenes. We have already established unique names for most of the small ncRNA genes by working with experts for each class. Small ncRNAs can be defined into their respective classes by their shared homology and common function. In contrast, long non-coding RNA (lncRNA) genes represent a disparate set of loci related only by their size, more than 200 bases in length, share no conserved sequence homology, and have variable functions. As with pc genes, wherever possible, lncRNAs are named based on the known function of their product; a short guide is presented herein to help authors when developing novel gene symbols for lncRNAs with characterised function. Researchers must contact the HGNC with their suggestions prior to publication, to check whether the proposed gene symbol can be approved. Although thousands of lncRNAs have been predicted in the human genome, for the vast majority their function remains unresolved. lncRNA genes with no known function are named based on their genomic context. Working with lncRNA researchers, the HGNC aims to provide unique and, wherever possible, meaningful gene symbols to all lncRNA genes.
KeywordsLong non-coding RNA Nomenclature ncRNA lncRNA
Since its inception in the 1970s, the HUGO Gene Nomenclature Committee (HGNC)  has kept apace with the discovery and characterisation of new human genes, providing each gene with a unique symbol and name and thus aiding effective scientific communication. By the time the initial sequence of the Human Genome was published in 2001 , the HGNC database (http://www.genenames.org)  contained more than 13,000 approved gene names, mostly for protein-coding genes with only around 200 non-coding RNA (ncRNA) gene names. With the burgeoning research and interest in ncRNAs over the last decade, the number of ncRNA loci with gene names has vastly expanded to more than 8,500 currently; about 2,000 of these represent long non-coding RNA (lncRNA) genes. Whereas classes of small ncRNAs can be defined by their shared homology and common function , in contrast, lncRNA genes are a disparate set of loci related only by their size (more than 200 bases in length), are non-homologous, and have variable functions . Their discovery has been further complicated because they are expressed at very low levels, sometimes only at specific developmental stages, and in specific tissues . Large-scale transcriptomic analyses, such as RNA-Seq, have now revealed thousands of putative long non-coding RNAs ; these present unique nomenclature challenges, especially because for the vast majority, the function of the resultant transcript(s) remains unknown. Below, we present a brief guide to the nomenclature of lncRNA genes and provide examples of some of the genes named to date.
lncRNA gene naming guidelines
The HGNC endeavours to approve symbols and names that have been used in publications, but this is not always possible. To ensure their symbol can be approved authors must contact the HGNC prior to publication to agree the nomenclature for each novel lncRNA gene. When creating a new lncRNA gene name, there are a number of factors that should be taken into account:
Each approved gene symbol must be unique
This is the paramount nomenclature rule and cannot be broken. Uniqueness enables unambiguous communication and this utility of approved gene nomenclature ensures that everyone knows they are speaking about the same gene. If an author publishes a lncRNA name that is already in use for another locus, then the HGNC will have to assign an alternative symbol. For instance, a novel lncRNA required to keep epidermal cells in an undifferentiated state was published as ANCR but this could not be approved since this was already in use for the ‘Angelman syndrome chromosome region’; so, in agreement with the authors, it was approved as DANCR for ‘differentiation antagonizing non-protein coding RNA’.
Symbols are short-form representations of the descriptive gene name
Each lncRNA is assigned a gene symbol that is an abbreviation or acronym of a descriptive name. For example, the symbol BANCR is an abbreviation of the full name ‘BRAF-activated non-protein coding RNA’. Gene symbols are the primary descriptors used in communications about genes and their brevity makes them user friendly.
Symbols should only contain Latin letters and Arabic numerals
Gene symbols should only contain Latin letters and Arabic numerals, e.g. NEAT1 (nuclear paraspeckle assembly transcript 1). Punctuation is not used and will generally be removed or replaced by a letter or number. The use of hyphens is limited to specific exceptions, such as genes named as antisense to protein-coding genes (discussed later), e.g. BACE1-AS (BACE1 antisense RNA).
Human gene symbols are all uppercase
By long-established convention, all human gene symbols are written in uppercase letters. This distinguishes them from rodent genes where only the first letter is uppercase and the rest lowercase. For instance the mouse gene Hotair is the ortholog of the human HOTAIR (HOX transcript antisense RNA) gene.
Symbols should not contain any reference to species
Symbols should not contain any reference to species, for example ‘H/h’ for human. The use of ‘human’ in gene names should also be avoided because approved human gene names are transferred across to homologous genes in other species, where ‘human’ would be potentially confusing and misleading.
Symbols should not spell out commonly used words
Whilst authors might be tempted to use commonly used words for gene symbols because they are easily recognized and pronounced, they should be avoided because they generate unnecessary confusion and make searching for information about a gene much more difficult. A good example of this is AIRN, which was first published as AIR . A search with ‘AIR’ in PubMed returns more than 220,000 unrelated hits, whereas a search with the approved symbol ‘AIRN’ returns only the 10 publications specific to this gene. Other examples include EGO , since approved as EGOT (eosinophil granule ontogeny transcript), and PANDA  now PANDAR (promoter of CDKN1A antisense DNA damage activated RNA).
If possible, names should be based on function
Genes are preferentially named based on the function of the gene product. Examples include the well-known 'XIST' which is short for 'X (inactive)-specific transcript' because the transcript is involved in transcriptionally silencing one of the pair of X chromosomes, and more recently ‘TINCR’  which stands for ‘tissue differentiation-inducing non-protein coding RNA’ because the product is required for epidermal tissue differentiation. If possible, the name of a gene should be based on the normal function of the gene product and not a mutant phenotype. Gene names should be concise and not attempt to represent all known information about a gene. The following are a few other things to consider in gene symbols and names:
Must not be offensive or pejorative
Must not be used to acknowledge individuals or places
Should not reference names of mythical, fictional, or historical figures
Should not be whimsical or impart no meaningful information about the gene
Functional transcribed pseudogenes should retain their pseudogene name
A small number of transcribed pseudogenes have now been shown to be functional, e.g. PTENP1 regulates levels of PTEN by binding to PTEN-targeting miRNA . Transcribed pseudogenes with published function will retain their pseudogene nomenclature and not be renamed based on function; however, ‘(functional)’ is added to the end of the gene name so that these genes can be found in a search, e.g. the full name of PTENP1 is ‘phosphatase and tensin homolog pseudogene 1 (functional)’.
Naming genes with no known function
Working together with the lncRNA community, the HGNC aims to provide informative names for all lncRNA genes in the human genome. The simple guidelines stated in this paper are intended to guide researchers, but the only way to approve a new lncRNA gene symbol is to contact the HGNC. For further information on lncRNA nomenclature please see the HGNC lncRNA webpage: http://www.genenames.org/rna/LNCRNA and email us at email@example.com.
Thank you to the lncRNA research community for their invaluable input over the years. Special thanks to fellow HGNC team members Dr Elspeth Bruford and Dr Ruth Seal for their helpful discussions and continuing camaraderie. This work was supported by the Wellcome Trust (099129/Z/12/Z) and the National Human Genome Research Institute (P41 HG03345).
- Povey S, Lovering R, Bruford E, Wright M, Lush M, Wain H: The HUGO Gene Nomenclature Committee (HGNC). Hum Genet. 2001, 109 (6): 678-680. 10.1007/s00439-001-0615-0.View ArticlePubMed
- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409 (6822): 860-921. 10.1038/35057062.View ArticlePubMed
- Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA: Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 2013, 41 (Database issue): D545-D552.PubMed CentralView ArticlePubMed
- Wright MW, Bruford EA: Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature. Hum Genom. 2011, 5 (2): 90-98. 10.1186/1479-7364-5-2-90.View Article
- Kung JT, Colognori D, Lee JT: Long noncoding RNAs: past, present, and future. Genetics. 2013, 193 (3): 651-669. 10.1534/genetics.112.146704.PubMed CentralView ArticlePubMed
- Clark MB, Mattick JS: Long noncoding RNAs in cell biology. Semin Cell Dev Biol. 2011, 22 (4): 366-376. 10.1016/j.semcdb.2011.01.001.View ArticlePubMed
- Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R: The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22 (9): 1775-1789. 10.1101/gr.132159.111.PubMed CentralView ArticlePubMed
- Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA: Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev. 2012, 26 (4): 338-343. 10.1101/gad.182121.111.PubMed CentralView ArticlePubMed
- Lyle R, Watanabe D, Te Vruchte D, Lerchner W, Smrzka OW, Wutz A, Schageman J, Hahner L, Davies C, Barlow DP: The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat Genet. 2000, 25 (1): 19-21. 10.1038/75546.View ArticlePubMed
- Wagner LA, Christensen CJ, Dunn DM, Spangrude GJ, Georgelas A, Kelley L, Esplin MS, Weiss RB, Gleich GJ: EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood. 2007, 109 (12): 5191-5198. 10.1182/blood-2006-06-027987.PubMed CentralView ArticlePubMed
- Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, Langerod A, Borresen-Dale AL, Kim SK, van de Vijver M, Sukumar S, Whitfield ML, Kellis M, Xiong Y, Chang HY: Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 2011, 43 (7): 621-629. 10.1038/ng.848.PubMed CentralView ArticlePubMed
- Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA: Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013, 493 (7431): 231-235.PubMed CentralView ArticlePubMed
- Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP: A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010, 465 (7301): 1033-1038. 10.1038/nature09144.PubMed CentralView ArticlePubMed
- Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, et al: GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22 (9): 1760-1774. 10.1101/gr.135350.111.PubMed CentralView ArticlePubMed
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