@article{TEXTUAL,
      recid = {10459},
      author = {Kapusta, Aurélie and Kronenberg, Zev and Lynch, Vincent J.  and Zhuo, Xiaoyu and Ramsay, LeeAnn and Bourque, Guillaume  and Yandell, Mark and Feschotte, Cédric},
      title = {Transposable Elements Are Major Contributors to the  Origin, Diversification, and Regulation of Vertebrate Long  Noncoding RNAs},
      journal = {PLOS Genetics},
      address = {2013-04-25},
      number = {TEXTUAL},
      abstract = {&lt;p&gt;Advances in vertebrate genomics have uncovered  thousands of loci encoding long noncoding RNAs (lncRNAs).  While progress has been made in elucidating the regulatory  functions of lncRNAs, little is known about their origins  and evolution. Here we explore the contribution of  transposable elements (TEs) to the makeup and regulation of  lncRNAs in human, mouse, and zebrafish. Surprisingly, TEs  occur in more than two thirds of mature lncRNA transcripts  and account for a substantial portion of total lncRNA  sequence (∼30% in human), whereas they seldom occur in  protein-coding transcripts. While TEs contribute less to  lncRNA exons than expected, several TE families are  strongly enriched in lncRNAs. There is also substantial  interspecific variation in the coverage and types of TEs  embedded in lncRNAs, partially reflecting differences in  the TE landscapes of the genomes surveyed. In human, TE  sequences in lncRNAs evolve under greater evolutionary  constraint than their non–TE sequences, than their intronic  TEs, or than random DNA. Consistent with functional  constraint, we found that TEs contribute signals essential  for the biogenesis of many lncRNAs, including ∼30,000  unique sites for transcription initiation, splicing, or  polyadenylation in human. In addition, we identified  ∼35,000 TEs marked as open chromatin located within 10 kb  upstream of lncRNA genes. The density of these marks in one  cell type correlate with elevated expression of the  downstream lncRNA in the same cell type, suggesting that  these TEs contribute to &lt;em&gt;cis&lt;/em&gt;-regulation. These  global trends are recapitulated in several lncRNAs with  established functions. Finally a subset of TEs embedded in  lncRNAs are subject to RNA editing and predicted to form  secondary structures likely important for function. In  conclusion, TEs are nearly ubiquitous in lncRNAs and have  played an important role in the lineage-specific  diversification of vertebrate lncRNA repertoires.&lt;/p&gt;},
      url = {http://knowledge.uchicago.edu/record/10459},
}