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E-GEOD-32880 - Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution

Released on 22 December 2011, last updated on 4 May 2014
Danio rerio
Samples (16)
Protocols (10)
Thousands of large intervening non-coding 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. H3K4me3, H3K36me3 chromatin maps, 3P-Seq and RNA-Seq were used to identify lincRNAs in the zebrafish genome
Experiment types
ChIP-seq, RNA-seq of non coding RNA 
Alena Shkumatava, Calvin H Jan, David P Bartel, Hazel Sive, Igor Ulitsky
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-32880.idf.txt
Sample and data relationshipE-GEOD-32880.sdrf.txt
Processed data (13)Click to browse processed data