Happy to share two post-doc papers co-authored with the amazing @AnaMonteagudo4 and @teresa_urli. We had amazing collaborators for both projects, even our supervisor @maxvcg joined in on the experimenting!.1: 2:

RT @CNRSbiologie: #ResultatScientifique🔎| Les signaux épigénétiques : comment les marques de l’ADN façonnent le plan de la vie. 🤝 @CNRS @CN….

RT @cw_hanna: Happy to see this was published yesterday! It was great working on this with Shankar and @ShifaanT. And thank you to the grea….

RT @GenSocUK: Congratulations to our 2024 Genetics Society medal winner, Robert Martienssen. Rob is sharing his work on Germline small RNAs….

RT @RobertEdgarPhD: "Protein structure alignment by Reseek improves sensitivity to remote homologs" published in Bioinformatics https://t.….

RT @PeterLewisLab: The HuSH complex silences retrotransposable elements. We identify HuSH2, centered on TASOR2, targeting KRAB-ZNFs and int….

RT @LukeGilbertSF: excited to share COMET! A scalable CRISPR approach we (@carwils) developed to identify multidomain proteins that modulat….

RT @deMendoza_Alex: Does 6mA exist in eukaryotic DNA? This is our take on this dispute: yes it does, and can be very abundant, but mostly c….

Finally, thank you to @frm_officiel for their generous post-doc funding! These more long-term (3 years versus 2. ) fellowships are important for biology researchers who's projects frequently span 2++ years!.

What would happen to Zdbf2 expression if we prevented 5mC deposition at its upstream 5mC/H3K27me3 antagonism region or CTCF binding site in the developing embryo? Hmm!

Keep in mind that the 5mC deposited at these regulatory DNA elements occurs one week after fertilisation and is maintained in the adult - potentially conferring life-long effects.

All in all, these papers highlight two underappreciated facets of DNA methylation in regulating the mouse genome. While 5mC-sensitive CTCF and H3K27me3 loci are rare in the genome, they are nevertheless crucial for regulating some genes, as shown at Zdbf2 and others.

Here is Max’s drawing about what we think is happening at the Zdbf2 locus, which really helped wrap my brain around these loops

. and when we KO the 5mC-sensitive CTCF binding site plus treat cells with a chemical inhibitor of PRC2, we get robust Zdbf2 expression!

So we genetically removed the 5mC-sensitive CTCF binding site, which should allow promoter-enhancer interactions to happen again. No change in Zdbf2 expression.

1. CTCF insulates the promoter from its enhancers, and 2. H3K27me3 over the promoter further impedes transcription. During differentiation, global 5mC deposition over the SWR and CTCF binding site alleviates both silencing pathways.

Anyway, these results were amazing as they shined a spotlight on Zdbf2 promoter-enhancer interactions, which may be required for its proper expression. We hypothesized that in ESCs, Zdbf2 is regulated by two converging, 5mC-dependent mechanisms.

So, while CTCF binding is sensitive to 5mC, it only affects ~1% of all CTCF binding sites. I was eager to dig into those 43 5mC-sensitive CTCF loops, and then to my great dismay a CTCF loop upstream Zdbf2 was at the top of the list. again!

That’s where the second project focused on CTCF provided invaluable insight into this locus. Using the same differentiation model in the presence/absence of 5mC, we found (very few) 5mC-depending CTCF-CTCF loops.

However, 5mC gain was seemingly sufficient to antagonise H3K27me3, but did not lead to activation of Zdbf2. How come Zdbf2 wasn’t being activated in the absence of 5mC and H3K27me3?.

We also had the converse system: increasing 5mC levels in hypomethylated ESCs. This was trickier to get going, and we only observed a robust (but moderate) gain of 5mC at Zdbf2.