Amphioxus functional genomics and the origins of vertebrate gene regulation 

This long-awaited study was published in Nature this week. The summary below was shamelessly copied from Manuel Irimias twitter feed. Our lab members, Ksenia Skvortsova and Ted Duckett participated in the study. Congrats!!

We generated a functional genomics resource for amphioxus (B. lanceolatum) comprising 96 datasets of RNA-seq, MethylC-seq, CAGE-seq, ChIP-seq and ATAC-seq. We found multiple conserved and vertebrate-specific features:

Conserved features:

1) We report the first case in non-vertebrates of transcriptional enhancers whose activation is associated with developmental DNA demethylation.
2) We uncover a chordate “phylotypic period” of highest transcriptomic similarity, which seems to occur earlier than the one reported for vertebrates (the pharyngula stage).
3) Conserved bodyplan and homology of adult tissues in chordates is mirrored by conserved transcriptomic and cis-regulatory

The most interesting bits – vertebrate-specific features:

1) We find a higher number of regulatory elements per gene in vertebrates, particularly distal elements in duplicates coming from the whole genome duplications (WGD).
2) Specialization, and not subfunctionalization, is the principal route of regulatory evolution following WGDs in vertebrates.
3) Strongly specialized copies (i.e. with the fewest number of remaining expression domains) have unexpectedly increased the number of regulatory elements in their regulatory landscapes.

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