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Dark matter RNA illuminates the puzzle of genome-wide association studies

Georges St. Laurent1, Yuri Vyatkin12 and Philipp Kapranov1*

Author Affiliations

1 St. Laurent Institute, 317 New Boston St, Suite 201, Woburn, MA 01801, USA

2 AcademGene Ltd., 6, Acad. Lavrentyev ave., Novosibirsk 630090, Russia

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BMC Medicine 2014, 12:97  doi:10.1186/1741-7015-12-97

Published: 12 June 2014

Abstract

In the past decade, numerous studies have made connections between sequence variants in human genomes and predisposition to complex diseases. However, most of these variants lie outside of the charted regions of the human genome whose function we understand; that is, the sequences that encode proteins. Consequently, the general concept of a mechanism that translates these variants into predisposition to diseases has been lacking, potentially calling into question the validity of these studies. Here we make a connection between the growing class of apparently functional RNAs that do not encode proteins and whose function we do not yet understand (the so-called ‘dark matter’ RNAs) and the disease-associated variants. We review advances made in a different genomic mapping effort – unbiased profiling of all RNA transcribed from the human genome – and provide arguments that the disease-associated variants exert their effects via perturbation of regulatory properties of non-coding RNAs existing in mammalian cells.

Keywords:
Genome-wide association study; Non-coding RNA; vlincRNA; Intronic RNA; lncRNA; RNA scaffold; LincRNA; Long Non-coding RNA; Long intergenic non-coding RNA; Very long intergenic non-coding RNA