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Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

Sebastiaan van Heesch1, Maarten van Iterson1, Jetse Jacobi1, Sander Boymans1, Paul B Essers2, Ewart de Bruijn1, Wensi Hao1, Alyson W MacInnes2, Edwin Cuppen13* and Marieke Simonis1

Author Affiliations

1 Genome Biology Group, Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands

2 Ribosome Biogenesis and Disease Group, Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands

3 Department of Medical Genetics, University Medical Center Utrecht, 3584, CG Utrecht, The Netherlands

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Genome Biology 2014, 15:R6  doi:10.1186/gb-2014-15-1-r6

Published: 7 January 2014

Abstract

Background

Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensive understanding of the extent to which lncRNAs bind ribosomes, we performed systematic RNA sequencing on ribosome-associated RNA pools obtained through ribosomal fractionation and compared the RNA content with nuclear and (non-ribosome bound) cytosolic RNA pools.

Results

The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1.

Conclusions

Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes.