The last few months in the lab were pretty busy: Sam Ross  and Allegra Angeloni published reviews on how DNA methylation participates in enhancer function and how TET proteins regulate embryonic development , while Ksenia Skvortsova ‘s story on the DNA methylome of zebrafish germ cells also finally saw the light of day. This work, published in Nature Communications provides insight into how zebrafish primordial germ cells (PGCs) remodel their DNA methylomes and their transcriptomes while making their way to the site of the prospective gonad.

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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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Review on epigenetic inheritance published in Nat Rev Mol Cell Biol

Check out our review on inter- and transgenerational epigenetic inheritance in animals just published by Nature Reviews Molecular Cell Biology. This is our take on trying to summarise a highly complex and polemic field on a few pages of text. This effort was led by Ksenia Skvortsova and our long term collaborator Nicola Iovino from the Max Planck Institute of Immunobiology and Epigenetics. For those who don’t feel like reading the whole piece, this is a two-sentence summary of the review: Briefly, epigenetic inheritance (EI) across generations is widespread in animals. There are excellent examples in flies and worms. In mammals EI that spans multiple generations is a rare event. Anamniotes that lack embryonic epigenome reprogramming might be useful models for EI.

Welcome Michael!

Michael Geng is joining the Garvan Institute this week to undertake his postdoctoral training at the Bogdanovic lab. Michael has a long standing interest in zebrafish (epi)genomics and embryonic gene regulation. Welcome onboard Michael!