Diverse logics and grammar encode notochord enhancers

The notochord is a defining feature of all chordates. The transcription factors Zic and ETS regulate enhancer activity within the notochord. We conduct high-throughput screens of genomic elements within developing Ciona embryos to understand how Zic and ETS sites encode notochord activity. Our screen discovers an enhancer located near Lama, a gene critical for notochord development. Reversing the orientation of an ETS site within this enhancer abolishes expression, indicating that enhancer grammar is critical for notochord activity. Similarly organized clusters of Zic and ETS sites occur within mouse and human Lama1 introns. Within a Brachyury (Bra) enhancer, FoxA and Bra, in combination with Zic and ETS binding sites, are neces-sary and sufficient for notochord expression. This binding site logic also occurs within other Ciona and vertebrate Bra enhancers. Collectively, this study uncovers the importance of grammar within notochord enhancers and discovers signatures of enhancer logic and grammar conserved across chordates.

Automated summary

By conducting high-throughput screens on genomic elements in developing Ciona embryos, this study identifies an enhancer near Lama gene that is critical for notochord development. Transcription factors Zic and ETS regulate enhancer activity and their binding sites are conserved in Lama1 introns in mouse and human. Furthermore, a similar binding site logic is observed in other Ciona and vertebrate Bra enhancers. The study uncovers the importance of enhancer grammar and discovers conserved signatures of enhancer logic and grammar in chordates.