Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom.
Genome Biology and Evolution (Impact Factor: 4.23). 03/2012; 4(4):427-42. DOI: 10.1093/gbe/evs020
Source: PubMed


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.

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