Promoter shape varies across populations and affects promoter evolution and expression noise

Abstract

Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

“…S2; Supplemental Table S2). This was complemented by our previously published CAGE data (Schor et al 2017), performed on 81 wild-type inbred lines from the same population at the same two stages of embryogenesis (Materials and Methods). As differences in gene expression are higher between developmental time points than between individuals at a given time point , we combined CAGE reads from all samples at equivalent time points, providing information on transcriptional initiation events at unprecedented depth (1045 million mapped reads) at these two stages of embryogenesis (Supplemental Tables S3, S4).…”

“…To investigate this further, we ranked all intergenic non-TSS DHS (Schor et al 2017) signal from embryos at 6-8 h at enhancers that are active at 6-8 h in any embryonic tissue or inactive at 6-8 h but active at other time points in any tissue. (C) CAGE signal from mesodermal cells (CAGE mesoderm) at 6-8 h at enhancers active in mesoderm at 6-8 h or inactive in mesoderm at 6-8 h but active in other tissues at the same time.…”

“…To obtain mesoderm-specific CAGE libraries, mesodermal cells were FACS-purified from unfixed 6-to 8-h staged embryos expressing an EGFP under the control of an early mesodermal enhancer from the twist gene (Bonn et al 2012b), and CAGE libraries were prepared as described in Schor et al (2017). Biological replicates for both PRO-cap and CAGE came from independent embryo collections and RNA isolations.…”

“…Despite sharing some features such as transcription factor (TF)-binding sites, promoters and enhancers have historically been considered as two distinct classes of regulatory elements. The term "promoter" implies the ability to recruit RNA polymerase II (Pol II) and initiate gene expression either at focused transcriptional start sites (TSSs; often called narrow promoters) or through more dispersed regions (broad promoters) (Lenhard et al 2012;Roy and Singer 2015;Schor et al 2017;Vo Ngoc et al 2017). In contrast, enhancers are defined by their ability to activate transcription remotely using a promoter at another distal site and to function in an orientationindependent manner.…”

Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression

“…Variation in the amino-acid sequence of the TFs has recently been shown to be more common than previously assumed, and can have a significant impact on DNA binding specificity [42]. More subtle regulatory traits such as the degree to which transcriptional initiation is spread over multiple positions within a particular promoter have also been shown to have a genetic component [43]. In the second view, trans -acting loci exert their effect along a causal path that begins at the polymorphism, continues via signal transduction pathways upstream of the TF, affects the protein-level activity of the TF, and finally proceeds downstream to affect the transcript abundance of target genes.…”