Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

Abstract

Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. We find that the functions of a large fraction of D. melanogaster enhancers are conserved for their orthologous sequences owing to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogaster–Drosophila yakuba split about 11 million years ago without apparent adaptive selection and can contribute to changes in gene expression in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides functional insights into regulatory evolution.

Evolution of transcript modification by N6-methyladenosine in primates

“…The majority of effort in deciphering the basis for gene expression evolution has focused on identification of cis-acting genomic regulatory elements and transacting regulatory factors that drive differences between species and populations (Schmidt et al 2010;Zheng et al 2010;He et al 2011;Ni et al 2012;McVicker et al 2013;Arnold et al 2014;Villar et al 2015). Largely unexplored is whether gene regulation has also differentiated at the post-transcriptional level during evolution and what impact if any that may have on gene expression.…”

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

“…New innovative, massively parallel approaches provide ways to perform large-scale quantitative studies of enhancer activities (reviewed in [6,36]). Even if they remained difficult to apply in vivo, these approaches offer a very useful, functional and quantitative, measurement of the regulatory activity of these elements, enabling not only to map endogenous enhancers in different genomes [37] but also to dissect their internal logic [36].…”

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

“…Besides, previous studies have focused their efforts on the isolation of enhancers using high-throughput gene reporter assays coupled to cell sorting 2,3 or tags sequencing 4 , providing limited quantitative information. Recently, a technique named Starr-seq enabling genome-wide quantification of enhancer activity in Drosophila cell lines has been developed [5][6][7] . Although Starr-seq was also applied to human cells using selected BACs 5 , one major limitation for its implementation to mammalian systems resides in their genome size and complexity, rendering challenging the preparation of representative libraries and requiring very high sequencing depth.…”