DNA Transposons favour denovotranscript emergence through enrichment of transcription factor binding motifs

Abstract

AbstractDe novogenes emerge from non-coding regions of genomes via succession of mutations. Among others, such mutations activate transcription and create a new open reading frame (ORF). Although the mechanisms underlying ORFs emergence are well documented, relatively little is known about the mechanisms enabling new transcription events. Yet, in many species a continuum between absent and very prominent transcription has been reported for essentially all regions of the genome.In this study we searched forde novotranscripts by using newly assembled genomes and transcriptomes of seven inbred lines ofDrosophila melanogaster, originating from six European and one African population. This setup allowed us to detect line specificde novotranscripts, and compare them to their homologous non-transcribed regions in other lines, as well as genic and intergenic control sequences. We studied the association with transposable elements and the enrichment of transcription factor motifs upstream ofde novoemerged transcripts and compared them with regulatory elements.We found thatde novotranscripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with high CpG islands and regions of TEs activity. Moreover, upstream regions ofde novotranscripts are highly enriched with regulatory motifs. Such motifs abound in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstreamde novotranscripts than upstream their non-transcribed homologs. Overall, our study demonstrates that TEs insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.