Colin T. Waters, Stephen S. Gisselbrecht, Yuliya A. Sytnikova, Tiziana M. Cafarelli, David E. Hill et al.
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.
Colin T. Waters, Stephen S. Gisselbrecht, Yuliya A. Sytnikova, Tiziana M. Cafarelli, David E. Hill, Martha L. Bulyk. Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue. 2021-12-20. https://doi.org/10.1186/s13059-021-02574-x
A pooled library of wild-type and motif-mutated Drosophila enhancers was genomically integrated at a common landing site and assayed in stage 11–12 embryos crossed to a twi:CD2 driver. The CD2-positive whole-mesoderm fraction was quantified by targeted reporter RNA and DNA sequencing with UMI-tagged reporter molecules.
The same pooled genomically integrated enhancer-reporter library was assayed in stage 11–12 embryos crossed to a mef2[IE-D5]:CD2 driver. The CD2-negative, fusion-competent-myoblast-depleted fraction was quantified by targeted reporter RNA and DNA sequencing with UMI-tagged reporter molecules and combined across two collection series.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
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