Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

• Main Authors: Ulitsky, Igor (Contributor), Shkumatava, Alena (Contributor), Jan, Calvin H. (Contributor), Sive, Hazel L. (Contributor), Bartel, David (Contributor)
• Other Authors: Massachusetts Institute of Technology. Department of Biology (Contributor), Whitehead Institute for Biomedical Research (Contributor)
• Format: Article
• Language: English
• Published: Elsevier B.V., 2014-02-07T17:54:02Z.
• Subjects: Article
• Online Access: Get fulltext

Thousands of long intervening noncoding RNAs (lincRNAs) have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, poly(A)-site mapping and RNA-Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs, only 29 had detectable sequence similarity with putative mammalian orthologs, typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without detectable sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation.
National Institutes of Health (U.S.) (grant GM067031)
European Molecular Biology Organization (long-term fellowship)
National Science Foundation (U.S.) (Predoctoral fellowship)
Human Frontier Science Program (Strasbourg, France) (Long-term Fellowship)