Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

Colin T Waters,Tiziana M Cafarelli,David E Hill,Stephen S Gisselbrecht,Martha L Bulyk,Yuliya A Sytnikova

doi:10.1186/s13059-021-02574-x

Abstract

Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers. We measure quantitative changes in enhancer activity and discover a range of epistatic interactions among the motifs, both synergistic and alleviating. We find that understanding the regulatory consequences of TF binding motifs requires that they be investigated in combination across enhancer contexts.

Highlights

Identifying sequence features of cis-regulatory elements that are important for their activities is a key challenge in understanding how regulatory information is encoded in genomes
Here we have developed Quantitative enhancer-FACS-Seq (QeFS) technology, which provides an RNA-Seq-based readout of enhancer activity
Drosophila embryos, we developed quantitative enhancer-FACS-Seq (QeFS)

Summary

Introduction

Identifying sequence features of cis-regulatory elements that are important for their activities is a key challenge in understanding how regulatory information is encoded in genomes. Computational analysis of transcriptional enhancers with overlapping tissue and temporal expression patterns for enrichment of sequence matches to transcription factor (TF) DNA binding site motifs can aid in the identification of TFs that contribute to the enhancers’ activities [1, 2]. Combinatorial regulation by multiple TFs is required to specify an appropriate expression pattern, and the contribution of a given motif instance to transcriptional regulation is sensitive to context. This complicates the interpretation of motif enrichment. Experimental analysis of enhancers in which motif occurrences have been mutated in various combinations is Waters et al Genome Biology (2021) 22:348 needed to determine the contributions of the motifs to the activities of the enhancers and whether a motif exerts different effects depending on the enhancer context [7, 8]

Methods

Results

Discussion

Conclusion