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HGNC Newsletter Summer 2009

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There are currently 28200 approved symbols

TOR signalling genes

We have recently completed a close collaborative effort with the MGNC in which we canvassed the opinions of over 100 researchers from the TOR signalling community about the name of MTOR.  This gene was approved as FRAP1 but the majority of researchers have published with the symbol mTOR for ‘mammalian target of rapamycin’. As the word mammalian is not transferable across all species it was agreed that the word 'mechanistic' is a suitable alternative.  Therefore, we have renamed this gene to MTOR, mechanistic target of rapamycin (serine/threonine kinase).

As a result of this extremely productive discussion, we have also approved symbols and names for several genes involved in TOR signalling.  RPTOR, (regulatory associated protein of MTOR, complex 1) has been popularly called raptor in the literature but the search term ‘raptor’ returns many papers about birds of prey.  It is intended that the unique gene symbol RPTOR should still be pronounced as ‘raptor’.  RICTOR matches the symbol that appears in the literature but the name has been adapted from ‘rapamycin-insensitive companion of TOR’ to ‘RPTOR independent companion of MTOR, complex 2’.  The gene MLST8 also matches the symbol used in the literature, but as with MTOR, the ‘m’ previously stood for mammalian as the LST8 symbol was derived from the yeast ortholog.  We have adapted the name of this gene to 'MTOR associated protein, LST8 homolog (S. cerevisiae)'.

LINE1 gene nomenclature

We have recently revisited the nomenclature of LINE1 transposable elements.  We have now standardized the rules so that to qualify for naming, each LINE1 element must be proved to be the progenitor of new insertions within the genome and therefore to be an active element.  The root symbol for these genes has been updated from LRE# to L1RE# for 'LINE1 retrotransposable element'. There are only four such elements identified so far; if you know of more, please contact us at hgnc@genenames.org.

HCOP update

The HCOP orthology search tool has been expanded with new orthology assertions from the OPTIC (orthologous and paralogous transcripts in clades) database.  Additionally, orthology assertions have been added between human and four new species: cow, C. elegans, S. cerevisiae and duck-billed platypu

Meetings Attended

It has been a busy few months for the HGNC team in terms of attending meetings.  Susan and Ruth attended the Third International Biocuration Conference in Berlin from 16th-19th April.  The HGNC poster was well attended and they enjoyed meeting curators from many different projects.  You can view their poster entitled “HGNC: the why and how of standardised gene nomenclature” at the Nature Precedings website, along with other presentations from this conference.

Matt was again invited to attend the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification NC-IUPHAR meeting in Paris, France on 24th-26th April. Following this meeting, we issued a joint HGNC/NC-IUPHAR letter to the editors of pharmacology journals. We hope this will encourage these editors to promote the use of approved gene and receptor nomenclature in their journals.

Matt also recently attended the 14th annual meeting of the RNA Society held in Madison, Wisconsin, USA, from 26th-30th May. He presented a poster detailing the excellent progress we've made in naming all of the known small classical non-coding RNA (ncRNA) genes and described our aim to also provide a name for each of the large ncRNA genes.

Michael attended the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB) in Stockholm, Sweden from June 27th to July 2nd, where he presented a poster entitled “HCOP: A one stop orthology shop”.  This poster generated a lot of interest and over 60 attendees took a handout copy away with them.  He then travelled straight back to Hinxton to attend the Quest for Orthologs conference at the Wellcome Trust Conference Centre from 3rd -5th July where he gave a well-received talk on HCOP.

Forthcoming meetings

Susan will be attending the 11th International Meeting on Human Genome Variation and Complex Genome Analysis (HGV2009) in Tallinn, Estonia from 11th-13th September. She will present a poster entitled "A nomenclature for copy number variable genes?".

Congratulations

Congratulations to our team member Ruth and her new husband Jonathan, who were married on June 13th.


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