Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5'-biased patches of sequence conservation nested in exonic architectures…

• HH
  Howard Hughes Medical Institute
• MF
  Minerva Foundation
• IS
  Israel Science Foundation

  Awards: 1242/14, 1242/14 and 1984/14, 1984/14, 1796/12
• NI
  National Institutes of Health

  Award: GM067031
• IC
  Israeli Centers for Research Excellence

  Award: 1796/12
• PA
  Planning and Budgeting Committee of the Council for Higher Education of Israel