The role of chromatin and DNA sequence changes in de novo gene origin
Authors: Logan Blair; Julie Cridland ; David Begun; Artyom Kopp
Affiliation: UC Davis
Keywords: d. evolution of gene expression; b. population variation
Although it’s clear that some genes originate de novo from nongenic sequence, the molecular mechanisms through which they first gain expression remain unclear. One hypothesis is that novel transcripts evolve more easily in regions with ancestrally permissive chromatin structure. Alternatively, de novo genes may evolve from ancestrally inaccessible regions and the transition to open chromatin is critical to de novo gene origin. To distinguish between these models, I used ATAC-seq to examine chromatin accessibility around recently evolved de novo transcripts. I compared chromatin states of accessory gland tissue between five Drosophila melanogaster strains polymorphic for de novo transcript expression, as well as two closely-related species in which orthologous DNA sequences are not expressed. I found that open chromatin in de novo transcript promoters was frequently not exclusive to genotypes in which the de novo transcript was expressed. However, the magnitude of chromatin accessibility was greater in lines expressing de novo transcript, and much greater than that of orthologous regions in related species. Next, to determine the location of cis-regulatory variants associated with de novo transcript expression, I generated RNA-seq libraries from accessory gland tissue in 29 D. melanogaster strains. I found that SNPs associated with de novo transcript expression frequently occur outside the regions of ATAC-seq peaks. Together these results paint a complex picture of de novo gene origin in which an increase in chromatin accessibility is required but frequently occurs in ancestrally open regions.