OIST Marine Genomics Seminar Ser 32nd by Emma Farley

Variation in enhancer sequence underlies evolutionary diversity and predilection to
disease. Deciphering how enhancers mediate restricted transcription with base pair
resolution, and which sequence changes lead to novel expression patterns, is vital to
inform our understanding of evolution, development and disease states. Towards this
goal, we conducted the first high-throughput functional characterization of a
transcriptional enhancer in intact developing embryos, using the protovertebrate Ciona
intestinal is.
The Otx-a enhancer mediates expression in the presumptive neural plate upon
activation by FGF signaling and the tissue determinant GATA. We created millions of
synthetic Otx-a enhancer sequence variants and electroplated these into thousands of
embryos. We identified over 20,000 active enhancers, providing an unprecedented
opportunity to determine the causal relationships between enhancer DNA sequences
and tissue-specific gene activities.
We identified short nucleotide sequences flanking core GATA and ETS (FGF
signaling) transcription factor binding sites as the key determinants of enhancer
function. Subtle manipulation of gene activity. We therefore suggest that enhancers
responding to pleiotropic cell signaling pathways can readily evolve to drive novel
patterns of gene expression. Bioinformatic analysis of our high-throughput screen
enabled prediction of expression patterns based on sequence alone. We rigorously
tested these enhancer sequence rules by creation of synthetic minimal enhancers,
including an 18bp regulatory element that functions like the wild-type neural enhancer.
In addition to describing how sequence aviation affects expression patterns, we discuss
our findings regarding enhancer grammar and implications for evolution.