Genetic variation between individuals affects promoter shape and strength during development

SCHOR IE*; DEGNER JF*; CANNAVÒ E; SHIM H; CASALE FP; BIRNEY E; STEPHENS M; STEGLE O; FURLONG EE

Paris

Simposio; EMBO François Jacob Symposium: Genetic Control of Development and Evolution; 2015

EMBO - Institut Pasteur

<!-- /* Font Definitions */@font-face{font-family:"ＭＳ 明朝";mso-font-charset:78;mso-generic-font-family:auto;mso-font-pitch:variable;mso-font-signature:-536870145 1791491579 18 0 131231 0;}@font-face{font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;mso-font-charset:0;mso-generic-font-family:auto;mso-font-pitch:variable;mso-font-signature:-536870145 1107305727 0 0 415 0;}@font-face{font-family:Cambria;panose-1:2 4 5 3 5 4 6 3 2 4;mso-font-charset:0;mso-generic-font-family:auto;mso-font-pitch:variable;mso-font-signature:-536870145 1073743103 0 0 415 0;} /* Style Definitions */p.MsoNormal, li.MsoNormal, div.MsoNormal{mso-style-unhide:no;mso-style-qformat:yes;mso-style-parent:"";margin:0cm;margin-bottom:.0001pt;mso-pagination:widow-orphan;font-size:12.0pt;font-family:Cambria;mso-ascii-font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"ＭＳ 明朝";mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:Cambria;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;}.MsoChpDefault{mso-style-type:export-only;mso-default-props:yes;font-family:Cambria;mso-ascii-font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"ＭＳ 明朝";mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:Cambria;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;}@page WordSection1{size:612.0pt 792.0pt;margin:72.0pt 90.0pt 72.0pt 90.0pt;mso-header-margin:36.0pt;mso-footer-margin:36.0pt;mso-paper-source:0;}div.WordSection1{page:WordSection1;}-->Transcription initiation is controlled bythe activity of promoter proximal and distal cis-regulatory elements, which ultimately modulate RNA pol IIactivity at transcriptional start sites (TSS). Moreover, different classes ofcore promoters can be regulated by different subsets of regulatory elements,showing the importance of promoter structure in the architecture ofgene-regulatory networks. While the location and shape of TSS clusters havebeen described at a genome-wide level, the features that define and modulatethe position, number and usage of TSSs remain unknown, and yet are essential tounderstand complex trait genetics and gene-regulatory evolution.Here, we performed a comprehensive study ofpopulation variation in TSSs during embryonic development using Cap-Analysis ofGene Expression (CAGE) and quantitative trait locus (QTL) mapping across a collectionof Drosophila melanogaster inbred wild-isolates.In a developmental time course, we identified thousands of genetic variantsaffecting the usage and/or distribution of TSSs. These include not only effectson average promoter strength, but also on the shape of TSS clusters, the relativeusage of specific TSSs within a cluster and the relative strand activity inbi-directional promoters.Surprisingly, analysis of the variation onCAGE signal at base-pair resolution shows the existence of two classes ofeffects: QTLs with a directional effect on promoter output and QTLs where aredistribution in TSS usage results in promoter shape changes, with minimaleffect on overall RNA levels. The genetic variants that cause adirectional effect on RNA levels detected by CAGE are located both in promoter-proximaland distal location, including the transcribed region. Actually, by comparingthe effects of variants on CAGE vs. RNAseq signal, we discover a class ofCAGE-only effects that most likely corresponds to variants affecting stabilityof the messenger.  In contrast, the genetic variants leadingto effects purely on redistribution of TSSs show a strong bias towards corepromoter regions. This shows for the first time that differences in promotershape do not only exist between different genes, but many natural polymorphismsare affecting shape for the same promoter in the population with minimaleffects on RNA levels.Therefore, the discovery and classificationof transcription start sites QTLs provides novel insights for understanding themechanistic details of transcriptional initiation and the evolution of promoterfunction.