LncATLAS – a database for subcellular localisation of long noncoding RNAs

The subcellular localisation of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localisation of newly-discovered lncRNAs involves time-consuming and costly experimental methods.

Researchers from the Centre for Genomic Regulation and the University of Bern have created “LncATLAS”, a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. The researchers introduce “Relative concentration index” (RCI) as a useful measure of localisation derived from ensemble RNAseq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localisation is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire dataset is also available to download.

Overview of lncATLAS data


A) Cell lines available in lncATLAS, indicating their approximate origin. B) Cellular compartments available. * Compartments with only total RNA samples available. C) The relative concentration index (RCI), in this case calculated for the cytoplasm and nucleus (CN-RCI). The RCI can be thought of as the log-ratio, between two compartments, of the concentration of a given RNA molecule per unit mass of RNA.

LncATLAS makes lncRNA subcellular localisation data available to the widest possible number of researchers.

Availability –  http://lncatlas.crg.eu/

David Mas-Ponte D, Joana Carlevaro-Fita C, Emilio Palumbo E, Toni Hermoso T, Roderic Guigo R, Rory Johnson R. (2017) LncATLAS database for subcellular localisation of long noncoding RNAs. bioRXiv [Epub ahead of print]. [abstract]

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