bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage

Natural Antisense Transcripts (NATs) are long non-coding RNAs (lncRNAs) that overlap coding genes in the opposite strand. NATs roles have been related to gene regulation through different mechanisms, including post-transcriptional RNA processing. With the aim to identify NATs with potential regulatory function during fly development, we generated RNA-Seq data in Drosophila developing tissues and found bsAS, one of the most highly expressed lncRNAs in the fly wing. bsAS is antisense to bs/DSRF, a gene involved in wing development and neural processes. bsAS plays a crucial role in the tissue specific regulation of the expression of the bs/DSRF isoforms. This regulation is essential for the correct determination of cell fate during Drosophila development, as bsAS knockouts show highly aberrant phenotypes. Regulation of bs isoform usage by bsAS is mediated by specific physical interactions between the promoters of these two genes, which suggests a regulatory mechanism involving the collision of RNA polymerases transcribing in opposite directions. Evolutionary analysis suggests that bsAS NAT emerged simultaneously to the long-short isoform structure of bs, preceding the emergence of wings in insects. Author summary Long non-coding RNAs (lncRNAs) are transcribed regions of the genome that, unlike coding genes, are not translated to proteins. Mostly undetected until the recent development of advanced sequencing methods to profile the RNA content (the transcriptome) of the cells, we know now that in many species they rival in number protein coding genes. In the fly genome, there are more than two thousand lncRNAs, most of which of unknown function. Here we characterize the function of bsAS, one of the most abundant lncRNAs encoded in this genome. We show that bsAS is essential for the correct development of the fly wings, since these become very aberrant and ill-formed in mutants in which we delete this gene. We also show that the function of bsAS in the development of fly wings is mediated by the regulation of the expression of the blistered gene, a protein coding gene that overlaps in the fly genome with bsAS.