Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Highly Accessed Research

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

David Kelley123 and John Rinn123*

Author Affiliations

1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

2 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA

3 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA

For all author emails, please log on.

Genome Biology 2012, 13:R107  doi:10.1186/gb-2012-13-11-r107

Published: 26 November 2012

Abstract

Background

Numerous studies over the past decade have elucidated a large set of long intergenic noncoding RNAs (lincRNAs) in the human genome. Research since has shown that lincRNAs constitute an important layer of genome regulation across a wide spectrum of species. However, the factors governing their evolution and origins remain relatively unexplored. One possible factor driving lincRNA evolution and biological function is transposable element (TE) insertions. Here, we comprehensively characterize the TE content of lincRNAs relative to genomic averages and protein coding transcripts.

Results

Our analysis of the TE composition of 9,241 human lincRNAs revealed that, in sharp contrast to protein coding genes, 83% of lincRNAs contain a TE, and TEs comprise 42% of lincRNA sequence. lincRNA TE composition varies significantly from genomic averages - L1 and Alu elements are depleted and broad classes of endogenous retroviruses are enriched. TEs occur in biased positions and orientations within lincRNAs, particularly at their transcription start sites, suggesting a role in lincRNA transcriptional regulation. Accordingly, we observed a dramatic example of HERVH transcriptional regulatory signals correlating strongly with stem cell-specific expression of lincRNAs. Conversely, lincRNAs devoid of TEs are expressed at greater levels than lincRNAs with TEs in all tissues and cell lines, particularly in the testis.

Conclusions

TEs pervade lincRNAs, dividing them into classes, and may have shaped lincRNA evolution and function by conferring tissue-specific expression from extant transcriptional regulatory signals.