The humble origins of Sox/POU

In this fantastic collaboration with the group of Ralf Jauch in Hong Kong University, we found out that Sox and POU genes, famous for their roles in stem cells, are older than previously thought. Not only that, but choanoflagellate Sox genes can substitute Sox2 when making mice induced pluripotent stem cells (iPSC). These, in turn, can contribute to make a chimeric mice, which we dubbed the "choano-mice". Then, we also reconstructed ancestral sequences in collaboration with the Hochberg group at the Max Plank, to find reveal that many of the ancestral Sox proteins have Sox2-like potential. Choanoflagellate POU is also remarkable, as very few species encode them, yet its DNA binding specificity is still very much like most homeodomains, not yet binding to the octamer, the preferred motif for animal POU orthologues. See the paper here:

https://www.nature.com/articles/s41467-024-54152-x

This research has sparked quite an unexpected love from the media outlets, and we got covered in several venues, including the Washington Post and Forbes:

https://www.washingtonpost.com/climate-environment/2024/11/28/lab-grown-mouse-stem-cells/

https://www.forbes.com/sites/scotttravers/2024/12/11/scientists-can-now-recreate-a-mouse-without-its-dna-heres-how-it-works/

All the way to a funnily titled version in a British tabloid:

https://www.dailystar.co.uk/news/billion-year-old-mouse-created-34152890

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