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Series GSE43520 Query DataSets for GSE43520
Status Public on Jan 19, 2014
Title The evolution of lncRNA repertoires and expression patterns in tetrapods
Organisms Xenopus tropicalis; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Gorilla gorilla; Homo sapiens; Mus musculus; Monodelphis domestica
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. We identify ~11,000 primate- specific lncRNA families, which show evidence for selective constraint during recent evolution, and ~2,400 highly conserved lncRNAs (including ~400 genes that likely originated more than 300 million years ago). We find that lncRNAs, in particular ancient ones, are generally actively regulated and may predominantly function in embryonic development. lncRNA X-inactivation patterns reveal an extremely female-biased monotreme-specific lncRNA, which may partially compensate X-dosage in this lineage. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but global patterns like tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network, which surprisingly contains many lncRNA hubs, suggests potential functions for lncRNAs in fundamental processes like spermatogenesis or synaptic transmission, but also in more specific mechanisms such as placenta growth suppression through miRNA production.
Overall design [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis.
Contributor(s) Necsulea A, Soumillon M, Liechti A, Daish T, Zeller U, Baker J, Grutzner F, Kaessmann H, Warnefors M
Citation(s) 24463510
Submission date Jan 15, 2013
Last update date May 15, 2019
Contact name Anamaria Necsulea
Organization name CNRS, Université Claude Bernard Lyon 1
Department Laboratoire de Biométrie et Biologie Evolutive
Street address 43 Bd. du 11 Novembre 1918
City Lyon
ZIP/Postal code 69622
Country France
Platforms (15)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (55)
GSM1064822 hsa br M 2ss [batch1]
GSM1064824 hsa br M7 [batch1]
GSM1064826 hsa ts M3 [batch1]
BioProject PRJNA186646
SRA SRP017959

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Supplementary file Size Download File type/resource
GSE43520_RAW.tar 5.4 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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