The first works of the lab are out in BioRxiv

After starting the laboratory during the pandemic in 2020, finally the projects that we've been working on start to see the light. Projects take time to mature, but here we have two exciting works on DNA methylation (what else!) that break new grounds.

In this study, Luke follows the rabbit hole of Amoebidium's genome, the major chunk of his PhD. What started as an evolutionary investigation into the origins of animal 5mC, ended up being a crazy story about giant viruses and other genomic oddities, lateral gene transfer in eukaryotes and epigenomic arm races. Have a look in BioRxiv here: https://www.biorxiv.org/content/10.1101/2024.01.08.574619v1.

A summarised "tweetorial" can be read here: https://x.com/deMendoza_Alex/status/1744633351036649884?s=20

Then, we are lucky to share department with the great Martin-Duran lab, so we joined forces to study annelid methylomes, a so far neglected phylum in 5mC research. Led by Kero Guynes, we found that methylation is all but stable across development in annelids, and that methylation erosion extends to ageing in these critters. Find the link to the preprint here: https://www.biorxiv.org/content/10.1101/2023.12.21.572802v1.full.

Chema wrote a nice tweetorial here: https://x.com/Chema_MD/status/1739740306344448329?s=20

Long life to non-model organisms!

The Transposable Elements Methods and Protocols Book is out

Together with our friend and collaborator from the QMUL Epigenetics Hub, Miguel Branco, we have edited a special number of the Methods in Molecular Biology Springer series. We aimed to cover both the bioinformatic and the molecular biology approaches to work with Transposable Elements. We tried to keep it broad and useful for anyone working on an eukaryotic system. Feel free to get in touch if you would like more information about any given chapter.

Link to the book: https://link.springer.com/book/10.1007/978-1-0716-2883-6

If you want to comment or congratulate us, feel free to drop a like or a message in this Twitter thread: https://twitter.com/BrancoLab/status/1598331922102493184

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