A Long Journey into Epigenome engineering comes to an end

Not all projects need to be about evolution! This would be the first project in which no phylogenetic trees were used at any stage, as it focuses on human cell lines and epigenome engineering approaches. We generated an artificial zinc finger fused to DNMT3A to methylate thousands of promoters in the human genome. This revealed some surprising transcriptional responses, showing that not all genes got silenced, and we used several epigenomic profiling techniques to understand the potential differences across these promoters. Also, we found that methylation did not last long in either promoters or enhancers, driven by Transcription Factor binding. This project took some years to finish, yet was a nice collaboration with the Lister Lab.

To read more, have a look at the paper here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02728-5.

For a "tweetorial" about the main findings, check this: https://twitter.com/deMendoza_Alex/status/1551917337128886272?s=20&t=ZeyNylC5jlNMIN008u_Bmg

The birth of a novel epigenomic regulatory layer

This week we have published a story about non-CpG methylation evolution in the brain in vertebrates and beyond. A link to the open access to the manuscript can be found here:

https://rdcu.be/cdMk8

And also a blogpost comment on how this project started and developed thanks to a great network of collaborators:

https://natureecoevocommunity.nature.com/posts/a-brain-zoo-reveals-how-a-non-canonical-form-of-dna-methylation-emerged

Two new publications with long-term collaborators

This week we've been lucky to have two publications coming out.

Together with Iñaki Ruiz-Trillo we have written a brief review about of animal multicellularity and the origins of embryonic development, focusing on processes observed in unicellular holozoans. See it here (Open Access): https://dev.biologists.org/content/147/23/dev192575

With Ozren Bogdanovic and his team, we have discovered how an actinopterygian-specific Dnmt3b duplicate (Dnmt3ba) has a specific role in maintaining a non-canonical form of cytosine DNA methylation in zebrafish. This is another interesting example on how DNA methyltransferases specialise in transposable element silencing. Open access link here: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa1135/6017363.

Evolution of Dnmt3b gene family in actinopterygians.

The Garvan Institute of Medical Research has made a brief press release where Ozren explains some of the findings: https://www.garvan.org.au/news-events/news/new-dna-modification-2018signature2019-discovered-in-zebrafish