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May 2016

Editor - Ruth Lovering

Gene annotation

Based on the EBI statistics, 9th April 2016, the cardiovascular gene annotation team has associated 37,000 GO annotations with 5,000 proteins, 25,597 of which are to 2,802 human proteins. In addition, we have annotated 189 RNAs, creating 1791 GO annotations.

As a part of our on-going effort to describe the biological roles of microRNAs (miRs), we are currently focusing on curating miRs reported to have a role in cardiac regeneration. MiRs have emerged as potentially important therapeutic tools for cardiac repair, due to their key roles in cardiovascular development; making the functional information about these miRs easily accessible to researchers will enable faster progress in this area. As part of this project, we have recently completed our annotation of six miRs encoded by the miR-17~92 cluster (miR-17, -18a, -19a, -19b, -20a, -92a), focusing on their contribution to cardiac regeneration processes. This has led to the generation of 342 annotations, 205 of which are associated with human miRs. Many known miRs, such as the six members of the miR-17~92 cluster, are encoded within strongly conserved polycistronic DNA regions, transcribed as one RNA, following which they undergo individual processing. The annotations we have created demonstrate the requirement of the whole miR-17~92 cluster for normal cardiac development, in fact this was the first miR cluster linked to developmental abnormalities. Furthermore, in addition to gene silencing by binding to mRNA targets (e.g. angiotensin II), individual members of this cluster have a role in several cardiovascular-relevant processes, including regulating inflammatory response in blood vessels, cell adhesion, cell migration, sprouting angiogenesis, Stat3 phosphorylation, coagulation, cholesterol efflux, cytokine production and nitric oxide biosynthesis.

Community engagement

Registration to our ninth 2-day Introduction to Bioinformatic resources and GO Workshop (14-15 July) is now open. This 2-day course provides hands-on training in the use of GO, as well as other bioinformatics resources, such as UniProt, Ensembl, Biomart, IntAct and Cytoscape. As always this workshop is freely available to all biological or biomedical Ph.D. and Post-Doc research scientists. If you wish to attend, please register online.

Forthcoming meetings

In June, Ruth will be presenting our miRNA annotation progress at the BAS/BSCR Spring Meeting, in Manchester.

Meetings attended

In April, Ruth presented two posters entitled Functional annotation of cardiovascular microRNAs with GO and Exploring Autophagy with Gene Ontology at the International Biocuration Conference in Geneva. Ruth also attended the associated GO Consortium meeting, where she gave a presentation entitled ‘GOC community annotation webpages’. The suggestions she presented here have already led to the simplification of these webpages. However, the GO Consortium is continuing to discuss how to make it easier for experts to submit data and suggest improvements.

Publications

Guidelines for the functional annotation of microRNAs using the Gene Ontology. Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. RNA. 2016 May;22(5):667-76. PMID: 26917558

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