Tag Archives: lncRNA

RNAcentral v1.0 is launched

RNAcentral 1.0 provides a single access point to non-coding RNA data, vastly improving research into gene products.

RNAcentral, the first unified resource for all types of non-coding RNA data, has been launched today by the RNAcentral Consortium. It aggregates information from a federation of expert databases, and provides tools for easy browsing. The initial release of RNAcentral contains approximately 8 million sequences.

Since the 1950s, scientists have thought of RNA as an intermediate molecule that provides a link between stable DNA and proteins. However, over the past decade it has become clear that RNA plays a much wider range of roles in living organisms. Researchers have discovered a lot about different types of RNA, but until now these data have not been put in one place.

Before RNAcentral, finding the RNAs encoded by a specific genome required fetching information from several independent resources, for example miRBase for microRNAs and HAVANA for lncRNAs.

“There is plenty of published data on non-coding RNAs, but each subtype is maintained separately,” explains Alex Bateman, head of Protein Sequence Resources at EMBL-EBI. “This is the first time we have a central place where you can find it all: piRNAs, ribosomal RNAs, everything. A lot of that information has typically been locked up in supplementary materials, or referred to only by a non-standard gene name. RNAcentral is a big step towards making RNA sequence as easy to access for research as protein sequence.”

RNAcentral 1.0 offers access to data from ten different expert databases and provides stable accession numbers that can be used consistently in the literature, other molecular databases and search engines. The RNAcentral website features a faceted search, which lets users explore different RNA sequences according to source, species and molecular function. Further expert databases are expected to be included in future releases.

The RNAcentral consortium has its roots in a workshop held on the Wellcome Genome Campus in 2010, where members of the RNA community came together to discuss the lack of centralised access to RNA data.

“It is really satisfying to see this project come to fruition,” explains Sam Griffiths-Jones of The University of Manchester. “When the consortium first met in 2010, we were seeing very rapid growth in ncRNA sequence and functional information and that trend has continued. New types of RNAs continue to be reported and there has never been a greater demand for a universal resource for these data.”

Thanks to funding from the UK’s Biotechnology and Biological Sciences Research Council (BBSRC), partner institutes throughout the world were able to come together and build a practical solution to a shared problem.

BBSRC Chief Executive Professor Jackie Hunter said: “Fundamental research into non-coding RNAs has many potential applications, including disease diagnostics, new therapies and biotechnology. With the abundance of data now available due to next generation DNA sequencing, there is an urgent need for informatics tools to decipher it. RNAcentral is vital resource that will aggregate and integrate information to unify the data landscape and improve the discoverability and use of data by researchers worldwide.”

The resource uses EMBL-EBI infrastructure, notably data-submission and cross-reference services provided by the European Nucleotide Archive (ENA). It takes advantage of the nightly, global synchronisation of data from the International Nucleotide Sequence Database Collaboration (INSDC).

Future versions of RNAcentral will include additional data types and information about RNA structure, modifications, molecular interactions and function. A paper describing RNAcentral tools and features in detail has been accepted for publication in the journal Nucleic Acids Research.

 

RNAcentral expert databases

The RNAcentral consortium currently includes 24 RNA database resources. Ten of these are present in the first release: European Nucleotide Archive; Rfam; RefSeq; VEGA; gtRNAdb, RDP; miRBase, tmRNA Website, SRPDB and lncRNAdb, with the many others planned for coming releases. See http://rnacentral.org/expert-databases for an up-to-date list.

 

RNAcentral partners

European Bioinformatics Institute (EMBL-EBI), UK; University of Manchester, UK; Wellcome Trust Sanger Institute, UK; University of California Santa Cruz, US; University of Texas, US; Auburn University, US; Sandia National Laboratory, US; University of Oxford, UK; Garvan Institute of Medical Research, Australia; International Institute of Molecular and Cell Biology Warsaw and Adam Mickiewicz University, Poland; Rockefeller University, US; Chinese Academy of Sciences, China; Peking Union Medical College and Taicang Institute of Life Sciences Information, China; Michigan State University, US; National Chiao Tung University, China; Stanford University, US; University of Thessaly, Greece; National Center for Biotechnology Information (NCBI), US.

Source article

RNAcentral Consortium. (2014). RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res. (In revision).

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Functional annotation of your long non-coding RNA

So you have performed some differential gene expression experiments and have discovered a (few) non-coding RNAs that are of conspicuous interest… What now? Unless you are lucky and someone else has already characterised your needle in a haystack, odds are little is known about this transcript. You might be tempted to paste that .fasta file into mfold and say: “Look! It folds into an RNA secondary structure!” yet this won’t tell you much, besides that your RNA might look like a Christmas tree in February. This video explains how you can find out which regions of your RNA transcript of interest might be responsible for its biological function.

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by | August 27, 2013 · 6:37 am

A novel role for Alu elements in epigenetic trans-regulation of gene networks

Screen Shot 2013-07-26 at 9.42.44 PMEver so often, you stumble across a magnificent work of science. This was the case for me a few weeks ago when this work popped up in my news feed. The authors investigate how a genomic locus that is the strongest risk factor for artherosclerosis produces a regulatory non-coding gene that regulates other genes associated to the disease.

They used stable over-expression and knock-down approaches to investigate the role of distinct ANRIL (a long non-coding RNA, aka lncRNA) isoforms in several key mechanisms of atherogenesis. They show that this gene guides epigenetic effector complexes to specific genomic loci.

Through what molecular mechanism you ask? None other than via endogenous transposable elements–ALUs specifically–that have been harnessed through evolution to perform regulation of gene expression in our genomes. FYI, repetitive elements compose ~46% of the human genome, 20% of which are ALUs.
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