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Series GSE32880 Query DataSets for GSE32880
Status Public on Dec 22, 2011
Title Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution
Organism Danio rerio
Experiment type Non-coding RNA profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design H3K4me3, H3K36me3 chromatin maps, 3P-Seq and RNA-Seq were used to identify lincRNAs in the zebrafish genome
Contributor(s) Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP
Citation(s) 22196729
Submission date Oct 11, 2011
Last update date May 15, 2019
Contact name Igor Ulitsky
Organization name Whitehead Institute for Biomedical Research
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02472
Country USA
Platforms (1)
GPL9319 Illumina Genome Analyzer II (Danio rerio)
Samples (16)
GSM813749 H3K4me3 IP 24 hpf
GSM813750 H3K4me3 IP 72 hpf
GSM813751 H3K4me3 IP Adult
BioProject PRJNA146609
SRA SRP008845

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Supplementary file Size Download File type/resource
GSE32880_RAW.tar 8.0 Gb (http)(custom) TAR (of BAM, BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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