We are very excited to see the last chapter of Sam Ross’ PhD thesis finally in press in Nucleic Acids Research. Here, we investigated the evolutionary conservation and divergence of DNA methylation remodelling in teleosts by generating base resolution DNA methylome datasets of developing medaka and medaka-zebrafish hybrid embryos. In contrast to previous reports, we show that medaka display comparable DNA methylome dynamics to zebrafish with high gametic mCG levels (sperm: ∼90%; egg: ∼75%), and adoption of a paternal-like methylome during early embryogenesis, with no signs of prior DNA methylation erasure. We also demonstrate that non-canonical DNA methylation (mCH) reprogramming at TGCT tandem repeats is a conserved feature of teleost embryogenesis. Lastly, we find remarkable evolutionary conservation of DNA methylation remodelling patterns in medaka-zebrafish hybrids, indicative of compatible DNA methylation maintenance machinery in far-related teleost species. Overall, these results suggest strong evolutionary conservation of DNA methylation remodelling pathways in teleosts, which is distinct from the global DNA methylome erasure and reestablishment observed in mammals.

Our latest research lead by Ksenia Skvortsova is out in Science Advances. Check out this fun collaborative effort where we unravel the usage of active DNA demethylation pathways in non-vertebrate lineages. We find that invertebrate deuterostomes such as lancelet and se a urchin use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes and show that the complement of identified 5hmC-regulated genes is conserved to vertebrates. This work demonstrates that active 5mC removal from regulatory regions is a common feature of deuterostome embryogenesis suggestive of an unexpected deep conservation of a major gene-regulatory module.

The lab has recently relocated from the Garvan Institute / UNSW (Sydney, Australia) to the Andalusian Centre for Developmental Biology – CABD (Seville, Spain). We will soon be hiring at all levels. In the meantime please direct any informal inquiries to Ozren Bogdanovic (obog@upo.es).

In our latest work, Sam Ross provides a detailed protocol for the generation of triple TET zebrafish CRISPants (F0 CRISPR/Cas9 KOs) and their subsequent molecular analyses by reduced representation bisulfite sequencing (RRBS). The full protocol can be accessed here, while the entire book (TET proteins and DNA demethylation, Methods and Protocols) can be obtained through the Springer website.

Check out the latest book on protocols in the field of TET proteins and DNA demethylation coedited by Michiel Vermeulen (Radboud University) and myself. The book is divided in five parts. Part One describes technologies aimed at detecting and quantifying DNA methylation turnover using massively parallel sequencing, ELISA, and mass spectrometry approaches. Part Two looks at data analyses protocols for distinguishing acting versus passive DNA demethylation and estimation of 5mC and 5hmC levels. Part Three deals with a new topic that takes advantage of modified CRISPR/Cas9 genome editing systems to target DNA demethylation activity to genomic loci of interest. Part Four discusses protocols that detail how to purify TET proteins and unravel their protein interactions, and Part Five looks at the assessment of TET protein function and activity in vivo and in vitro. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Our latest is out in Frontiers in Cell and Developmental Biology. Here we demonstrate that zebrafish, just like mammals, accumulate non-canonical DNA methylation (mCH) during brain development. Moreover, we identify accumulation of mCH at transposons from the Tc1-mariner superfamily.  Overall, this work demonstrates the evolutionary conservation of developmental mCH dynamics and highlights the potential of zebrafish as a model to study mCH regulation and function during normal and perturbed development (i.e Rett syndrome).

The latest from our lab is out in Nucleic Acids Research. This exciting project was led by the very talented Sam Ross who uncovered a novel non-CG DNA (mCH) methylation signature that is highly abundant at zebrafish MOsaic SATellite repeats (MOSAT). MOSAT mCH is high in gonads, decreases during cleavage stages, and reaches its lowest point at ZGA. Unlike mammalian mCH – that is mostly present in oocytes and in the nervous system – MOSAT mCH increases during gastrulation and is deposited in tissues originating from all embryonic layers. Also, in contrast to mammals, this mCH type positively correlates with heterochromatin (H3K9me3). We uncovered the actinopterygian-specific Dnmt3ba as the principal MOSAT mCH DNA methyltransferase and fully resolved its phylogenetic origin. This work thus provides proof for yet another “love story” between repetitive elements and DNMTs in the animal kingdom.

Our lab has participated in the special issue of the Journal of Molecular Biology: “Reading DNA modifications”. We contributed with a review: “Evolution of DNA methylome diversity in eukaryotes”. In this piece, we summarise a decade worth of insights obtained from whole genome bisulfite sequencing studies across eukaryotes. We speculate on the origins and functions of diverse DNA methylation patterns observed in different organisms and propose how such patterns might have evolved. This work expands our knowledge on the function and evolutionary origins of DNA methylation in plants, animals and fungi. The bonus was that our artwork (designed by Scot Nicholls) was selected for the cover of this special issue.

Evolutionary conservation of DNA methylation loss during chordate development. Hourglass represents the developmental morphological divergence across species, where the mid-developmental phylotypic stage shows similar morphologies across distant taxa whereas early and late development are more prone to lineage specific forms.

In mammals, DNA methylation undergoes two rounds of developmental remodelling; in primordial germ cells and in the pre-implantation embryo. However, it is currently unclear whether such DNA methylome reprogramming is more broadly conserved among vertebrates. This work led by Ksenia Skvortsova from our lab, published today in Nature Communications, demonstrates inheritance of the paternal methylation pattern in developing germ cells and absence of genome-wide reprogramming events. This study was published back to back with a similar study from the Hore lab (University of Otago).