Comparative transcriptomics of long intergenic noncoding RNAs in Drosophila

Unequal distributions of sex-biased lincRNAs on the X chromosome and autosomes are consistent with selection-based models of gene trafficking on or off the X chromosome, implying function for some of these lincRNAs. Finally, reciprocal blast searches between annotated lincRNAs in the D. pseudoobscura and D. melanogaster transcriptomes identify 80 conserved lincRNAs. Interestingly, direct coordinate conversions between the two genomes reveal another 54 D. pseudoobscura lincRNAs that are expressed in the same position as a D. melanogaster lincRNA but have low enough sequence conservation to preclude alignment via blast.

Whether these positionally equivalent lincRNAs are true homologs with similar functions in both genomes is unclear, but we look at other transcript features, such as transcript orientation, gene structure, and developmental expression profiles to explore this possibility. We find 22 high-confidence lincRNA homologs with conservation of multiple transcript-level features, and we designate these as high-confidence homologs that warrant further biological investigation.

This work represents the first comparative transcriptomic analyses of lincRNAs in Drosophila.