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Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysis

By Yann Le Poul, Yaqun Xin, Liucong Ling, Bettina Mühling, Rita Jaenichen, David Hörl, David Bunk, Hartmann Harz, Heinrich Leonhardt, Yingfei Wang, Elena Osipova, Mariam Museridze, Deepak Dharmadhikari, Eamonn Murphy, Remo Rohs, Stephan Preibisch, Benjamin Prud’Homme, Nicolas Gompel

Posted 25 Jun 2020
bioRxiv DOI: 10.1101/2020.06.24.169748

Transcriptional enhancers are short DNA sequences controlling the spatial activity, timing and levels of eukaryotic gene transcription. Their quantitative transcriptional output is thought to result from the number and organization of transcription factor binding sites (TFBSs). Yet, how the various aspects of regulatory information are encoded in enhancer sequences remains elusive. We addressed this question by quantifying the spatial activity of the yellow spot enhancer active in developing Drosophila wings. To identify which enhancer DNA sequence contributes to enhancer activity, we introduced systematic mutations along the enhancer. We developed an analytic framework that uses comprehensive descriptors to quantify reporter assay in transgenic flies and measure spatial variations in activity levels across the wing. Our analysis highlights an unexpected density of regulatory information in the spot enhancer sequence. Furthermore, it reveals an unanticipated regulatory logic underlying the activity of this enhancer, and how it reads the wing trans-regulatory landscape to encode a spatial pattern. ### Competing Interest Statement The authors have declared no competing interest.

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