Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome.

Details

Serval ID
serval:BIB_6BEA63E7DE51
Type
Article: article from journal or magazin.
Collection
Publications
Title
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome.
Journal
Genome Biology and Evolution
Author(s)
Young R.S., Marques A.C., Tibbit C., Haerty W., Bassett A.R., Liu J.L., Ponting C.P.
ISSN
1759-6653 (Electronic)
ISSN-L
1759-6653
Publication state
Published
Issued date
2012
Volume
4
Number
4
Pages
427-442
Language
english
Abstract
The functional repertoire of long intergenic noncoding RNA (lincRNA) molecules has begun to be elucidated in mammals. Determining the biological relevance and potential gene regulatory mechanisms of these enigmatic molecules would be expedited in a more tractable model organism, such as Drosophila melanogaster. To this end, we defined a set of 1,119 putative lincRNA genes in D. melanogaster using modENCODE whole transcriptome (RNA-seq) data. A large majority (1.1 of 1.3 Mb; 85%) of these bases were not previously reported by modENCODE as being transcribed. Significant selective constraint on the sequences of these loci predicts that virtually all have sustained functionality across the Drosophila clade. We observe biases in lincRNA genomic locations and expression profiles that are consistent with some of these lincRNAs being involved in the regulation of neighboring protein-coding genes with developmental functions. We identify lincRNAs that may be important in the developing nervous system and in male-specific organs, such as the testes. LincRNA loci were also identified whose positions, relative to nearby protein-coding loci, are equivalent between D. melanogaster and mouse. This study predicts that the genomes of not only vertebrates, such as mammals, but also an invertebrate (fruit fly) harbor large numbers of lincRNA loci. Our findings now permit exploitation of Drosophila genetics for the investigation of lincRNA mechanisms, including lincRNAs with potential functional analogues in mammals.
Keywords
Animals, Drosophila melanogaster/genetics, Evolution, Molecular, Female, Genome, Insect, Male, Mice, Molecular Sequence Annotation, RNA, Untranslated/genetics, RNA, Untranslated/isolation & purification
Pubmed
Web of science
Open Access
Yes
Create date
27/10/2014 14:46
Last modification date
20/08/2019 14:26
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