New website coming soon!
Many thanks to all who tested and sent feedback on the beta version of the new site, https://beta.genenames.org/. We are delighted to announce that we plan to release the new website in mid November. As our regular newsletter readers may remember, the main reasons for the launch of a new version of genenames.org are to make the site fully cmopatible with mobile devices, to improve our search application and to give the site a more modern appearance. Based on valuable feedback, we have changed the format of the Symbol Reports so that the HGNC data in the top box is always in a single column, and we have reduced white space on the page to reduce the amount of scrolling needed when interacting with the page. Please make sure that you are following our Twitter account, @genenames, to ensure that you receive instant notification of when the new site is released. We hope that you will enjoy the improvements!
New Gene Family Resources
This is the last time that you will see the heading ‘New Gene Family Resources’ in our newsletter as, with the release of the new website, our gene families will be known as gene groups. This change is to reflect the diverse types of gene ‘group’ that we include, such as protein complexes and enzyme groups based on shared function, rather than only gene families that share homology. The following gene families/groups were recently added:
Cysteine rich transmembrane BMP regulators
Glutamyl-tRNA amidotransferase subunits
Flavin containing monooxygenases
Myosin light chain kinase family
We have also added groups that include a hierarchical structure, such as Glycoside hydrolases, which has the following new subgroups: Hexosaminidases, Amylases alpha, Neuraminidases, Heparanases, Glycoside hydrolase family 1, Alpha-L-fucosidases, Galactosidases beta and Galactosidases alpha, and has also become a parent group for the following pre-existing groups: Glycoside hydrolase family 31, Chitinases, Hyaluronidases, Lysozymes and Mannosidases. The Adaptor related protein complexes group is at the top of its hierarchy and has the subgroups: Adaptor related protein complex 1, Adaptor related protein complex 2, Adaptor related protein complex 3, Adaptor related protein complex 4 and Adaptor related protein complex 5.
Spotlight on a new gene family/group:
One of our specialist advisors for kinases informed us that the ‘FAM20’ genes, with the original full name ‘family with sequence similarity 20’, are related to the golgi associated kinase genes, GASK1A and GASK1B. Based on this information we contacted the community that publish on the FAM20 genes to see if it would be possible to rename these genes based on their encoded function(s). The community told us that since the FAM20 symbols are unique and well supported, they wanted to retain these as the approved symbols but that they supported informative updates to the gene names as follows: FAM20A, full name: FAM20A, golgi associated secretory pathway pseudokinase; FAM20B, full name: FAM20B, glycosaminoglycan xylosylkinase; and FAM20C, full name: FAM20C, golgi associated secretory pathway kinase. As well as updating the gene names we have created the page Golgi associated kinase family to group these three genes together with GASK1A, GASK1B and FJX1.
Gene Symbols in the News
In this edition, we bring news of two studies on animals which provide hope for future applications to human health. First, scientists have successfully used gene editing to correct the faulty DMD gene in dogs that carry the DMD mutation mostly commonly found in humans with Duchenne muscular dystrophy, bringing hope that similar therapy will be successful for humans in the future. Second, a study on antler regeneration in red deer implicated the UHRF1 and S100A10 genes in the process, leading to hope that futher studies on these genes may one day pave the way for bone regeneration therapies for humans.
Meeting News
Autumn has been a busy season in terms of HGNC meeting attendance. Bryony and Elspeth went to the Genome Informatics meeting in Hinxton from 17th-20th September, where Bryony presented a poster entitled ‘Standardizing gene names in key vertebrate species’. Tamsin and Beth attended the Livestock Genomics Meeting also in Hinxton on the 21st and 22nd September at which Tamsin presented a talk on ‘The importance of manual curation in vertebrate gene naming’. Ruth travelled to Heidelberg in Germany to attend The Complex Life of RNA from 3rd-6th October where she presented a poster that gave an overview of how the HGNC names non-coding RNA genes, and Paul travelled to San Diego, USA to attend ASHG 2018 from 16th-20th October where he presented a poster with the title ‘A balancing act: aiming for stability in human gene nomenclature’. The new year will see Tamsin attend the Plant and Animal Genome (PAG) XXVII conference in San Diego, USA from 12th-16th January.
Publications
Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, Yates B, Bruford E. Genenames.org: the HGNC and VGNC resources in 2019. Nucleic Acids Res. Epub 2018 Oct 10. PMID: 30304474 DOI:10.1093/nar/gky930
The RNAcentral Consortium (inc. Bruford, E and Seal, R). RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. Epub 2018 Nov 5. PMID:30395267 DOI:10.1093/nar/gky1034
Perbal B, Tweedie S, Bruford E. The official unified nomenclature adopted by the HGNC calls for the use of the acronyms, CCN1-6, and discontinuation in the use of CYR61, CTGF, NOV and WISP 1-3 respectively. J Cell Commun Signal. 2018 Nov 5. PMID: 30393824 DOI:10.1007/s12079-018-0491-1