Spring newsletter 2019Newsletters ·
Welcome to the new format newsletter
Welcome to the first HGNC newsletter published on our brand new HGNC and VGNC blog! The blog was launched on April 1st, 2019 and this forms our second ever post. Aside from publishing our newsletters, we will use this blog to highlight nomenclature issues, explain new developments within our project, publish ‘how-to’ guides for specific aspects of our websites, host guest posts from our collaborators, and highlight contents of talks and posters from conferences that we attend. The blog will also promote greater interaction with our community as it will be possible to post comments on each blog post. Such comments will be mediated by a member of our team prior to publication. We will tweet about every new blog post that we create, so please make sure that you are following our @genenames Twitter account!
New website released
Since our last newsletter, we have released a new version of our website, genenames.org. We hope you are enjoying the new clear format, particularly if you view our website on mobile devices. Highlights of the new version include:
- the addition of an ‘HCOP homology predictions’ tab to Symbol Reports
- a new ‘Orthologs from selected species’ section on Symbol Reports that includes, where applicable, the named VGNC orthologs for Bos taurus (cow), Equus caballus (horse), Pan troglodytes (chimp), Canis familiaris (dog) and Felis catus (cat) as well as named rat and mouse orthologs
- replacement of the term ‘gene families’ with the broader term ‘gene groups’ and improvement of the layout of our gene group pages
- optimization of the order of search results
- improvement of the presentation of search results, especially the new colour coding for each main type of result: Gene [orange], Group [dark blue] or Other [grey]
Cat now in VGNC!
We bring the exciting news that we have added cat gene symbols into our Vertebrate Gene Nomenclature Committee (VGNC) project! We already have a sizeable set of 9870 cat Symbol Reports, including MTOR and BRCA1, all of which display a lovely image of Cinnamon, the beautiful Abyssinian cat whose genome is the source of annotated cat genes. We are currently working hard on adding rhesus macaque to VGNC so watch this space for more news! As for the other four species already included in the VGNC project (chimp, horse, dog and cow), these two new species were chosen based on the quality of their sequenced genomes and their relevance to research. The rhesus macaque has a long scientific history, including giving its name to the Rh blood group, being the first cloned and the first transgenic primate, and being sent to space by those on both sides of the space race. The cat provides a model for HIV/AIDS research and also for certain inherited diseases such as hereditary retinal blindness. Standardised nomenclature is therefore important for both of these species.
Progress on replacing placeholder symbols
We are continuing to rename placeholder symbols to provide more informative nomenclature that is transferrable across species. Some examples of C#orf symbols that we have been able to replace recently, along with links to the new symbols approved for our VGNC species, are shown below:
- C19orf66 – SHFL, ‘shiftless antiviral inhibitor of ribosomal frameshifting’ – cow, dog, horse and chimp
- C8orf59 – RBIS, ‘ribosomal biogenesis factor’ – chimp and horse
- C6orf106 – ILRUN, ‘inflammation and lipid regulator with UBA-like and NBR1-like domains’ frameshifting’ – cow, dog, horse and chimp
- C16orf45 – BMERB1, bMERB domain containing 1 – chimp, cow, dog and horse
A special case is the C9orf72 gene, which is undergoing an incredibly high amount of research following the discovery in 2011 that hexanucleotide repeat expansions in this gene cause neurological disease. The C9orf72 gene symbol has now been used in over 1340 publications. We have contacted the community in the past to discuss the possibility of updating this gene symbol and have been informed that is now so famous, a rename would be unhelpful. Due to the overwhelming usage, this is the only C#orf symbol approved by the mouse genomic nomenclature committee for a mouse gene. Therefore, we have no current plans to change this symbol, but we have updated the gene name from ‘chromosome 9 open reading frame 72’ to ‘C9orf72-SMCR8 complex subunit’.
Our FAM# placeholder symbols are used to name paralogous genes together where there is no other available information at the time of naming. Wherever possible, the paralogs are renamed with the same new, informative root symbol, as shown in the examples below:
- FAM129A to NIBAN1, niban apoptosis regulator 1 – chimp, horse, cow and dog
- FAM129B to NIBAN2, niban apoptosis regulator 2 – chimp, horse, cow and dog
- FAM129C to NIBAN3, niban apoptosis regulator 3 – horse, cow and dog
- FAM208A to TASOR, transcription activation suppressor – chimp, horse, cow and dog
- FAM208B to TASOR2, transcription activation suppressor family member 2 – chimp, horse, cow and dog
- FAM84A to LRATD1, LRAT domain containing 1 – chimp, cow and dog
- FAM84B to LRATD2, LRAT domain containing 2 – chimp, cow and dog
New gene groups
HGNC curators continue to add new gene groups to our resource. Some highlights from the last few months include:
Deoxyribonucleoside kinases, SWC tripartite complex, Macro domain containing, LRAT domain containing family, Endoribunucleases, Subcortical maternal complex, TLE family, EMAP like, Wnt enhanceosome complex
The Adaptor related protein complexes is the top of a hierarchy that includes the following subgroups: Adaptor related protein complex 1, Adaptor related protein complex 2, Adaptor related protein complex 3, Adaptor related protein complex 4, Adaptor related protein complex 5
The Mitochondrial intermembrane space bridging complex has the following subgroups: Mitochondrial contact site and cristae organizing system subunits and Mitochondrial sorting and assembly machinery complex, which has the subgroup Metaxins
Gene Symbols in the News
Gene therapy has featured in the news recently – a team in Tennessee have developed a safer form of the therapy to treat children with mutations in the IL2RG gene that cause X-linked severe combined immunodeficiency. Some children given gene therapy for this condition in the past have gone on to develop leukaemia. In the new treatment strategy, a lentiviral vector was created with an “insulator sequence” at the end of the IL2RG sequence to prevent genes downstream from the inserted IL2RG gene from being switched on and possibly causing cancer in the future. Another news item covered the story of the successful treatment of choroideremia via injection of adeno-associated virus vectors carrying functional copies of the CHM gene into the back of the retina. Each patient had treatment in only one eye and the treated eye showed improved or maintained vision five years after treatment while sight in the untreated eye had deteriorated.
In other news, associations between variants in single genes such as SLC6A4 and likelihood of depression have been called into question. A new study used data from hundreds of thousands of people to analyse the probability of an individual developing depression who carries particular gene variants that have previously been reported to be major contributors to the likelihood of developing depression. The study found that single gene variants were unlikely to be indicators of depression on their own, but each likely contributed a small effect towards developing the condition.
Tamsin attended the International Plant & Animal Genome (PAG) XXVII (San Diego, USA) 12-16 January 2019 where she gave her talk entitled ‘The VGNC – Updates and Future Plans-‘ at both the Genome Annotation Resources EBI workshop and at the Swine workshop, and also presented a poster on ‘The value of manual curation in assigning gene nomenclature across vertebrates’!
Susan and Ruth attended the 12th International Biocuration Conference from 7-10 April 2019 where they enjoyed meeting many biocurator colleagues! Their poster, HGNC: promoting standardized gene names for 40 years, can be accessed below.
Tweedie S, Seal R, Braschi B et al. HGNC: promoting standardized gene names for 40 years [version 1; not peer reviewed]. F1000Research 2019, 8:449 (poster) (doi: 10.7490/f1000research.1116583.1)