A standardised nomenclature for long non-coding RNAs

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.

Keywords: gene names; gene symbols; human genes; lncRNA; standardisation.

FIGURE 1

An example Symbol Report for the lncRNA gene XIST from genenames.org. HGNC Symbol Reports present the HGNC‐approved gene symbol, gene name, unique HGNC ID and other manually curated data in the top HGNC data section. The “Stable symbol” luggage tag is shown at the top of the report for approved symbols which are unlikely to ever be changed. Further down the report, links to many different biomedical resources are provided. Here, we have highlighted the resources that are particularly relevant to lncRNAs

FIGURE 2

The number of publications in PubMed for the top seven most highly published lncRNA genes. (a) For each of the seven highly published lncRNA genes, the number of publications has rapidly increased over the last 5 years. (b) For all of the most highly published lncRNA genes, the majority of publications use the current HGNC approved symbol. The first chart shows how over time the number of publications supporting the approved symbol MEG3 have increased compared to the previous symbol GTL2. The second chart shows NEAT1 and its published aliases (VINC, MENbeta, MENepsilon, TncRNA); the usage of NEAT1 far surpasses any of its aliases within the last decade. The third chart compares usage of the approved symbol MALAT1 and its published alias NEAT2; again MALAT1 is highly supported. The other four most highly published lncRNA symbols have negligible numbers of publications that do not use the approved symbol

FIGURE 3

The eight categories used by the HGNC to name lncRNA genes. For each category an example is given, along with a diagram that demonstrates, where applicable, how lncRNA genes within these categories are named relative to other genes. LncRNA genes are shown in pale orange, small RNAs are shown in green, and protein coding genes are shown in blue. Each category can be browsed from the HGNC gene group page “Long non‐coding RNAs” (https://www.genenames.org/data/genegroup/#!/group/788)