Happy to share the definitive version of our last paper about the role of TET enzymes and DNA demethylation in retinal development @clark-lab-retina.bsky.social journals.plos.org/plosbiology/...

Congrats Revathi!

Congrats to @ismaelhdeznunez.bsky.social for taking on this project that included 9 different genotypes of TET mutants, and a special thanks to all other co-authors and collaborators.

Identifying genome-wide locations of active DNA demethylation. Studies were performed in an ongoing, fruitful collaboration with John R Edwards and Alaina Urman, helping us integrate the new methylation profiling with previous studies from the Dyer and Nathans labs.

Our work on the TET enzymes in retinal development is out. We identified that rod fate is inhibited when DNA demethylation is prevented by removal of the TET enzymes. Interestingly, photoreceptor numbers are normal. We utilized WGBS and bACE-seq to profile the precise localization of 5mC and 5hmC,…

Great to see you in attendance but sorry we didn’t get the chance to talk/officially meet!

Looking forward to having that conversation 🤣

Congrats Kris and well deserved!

Well, the Biology and Development of the Eye (BDE) study section has been postponed (previously scheduled for Thurs/Fri).
I’m very disappointed on behalf of the applicants and reviewers, who all want this meeting to happen. I’m also grateful to the NIH staff who work so hard to make science happen.

Special thanks to WUSTL DOVS, RPB and NEI for their support of me, my lab, and our research.

This work is the result of hard work by @ismaelhdeznunez.bsky.social and Alaina Urman, in collaboration with @phruzycki.bsky.social and John Edwards at WashU, and Rajesh Rao at Michigan. Our work extends both past and current work on DNA demethylation from Dmitri Ivanov's and Jeff Gross' labs.

We also show that 10% of CpGs in the retina normally have 5hmC, which is mostly lost in Tet tcKO retinas, and that gene body 5hmC levels correlate with gene expression. Furthermore, we show that Tet3 and 5hmC are lost in retinoblastoma cells, a cone-derived cancer.

We propose a model by which photoreceptor precursor cells can adopt rod fate only after the NRL and NR2E3 loci (and likely others) are demethylated. The mechanisms by which the TET enzymes are recruited to these loci, however, remains a mystery.

Using immunohistochemical and transcriptomic analyses, we observe that Tet triple mutant retinas (tcKO) display greatly reduced rod specification, instead resulting in a cone-dominant retina. Base-pair resolution methylation analyses (WGBS and bACE-seq) identified dramatic changes to methylation.

In an effort to better understand how retinal cell fates are determined, we assessed the significance of DNA demethylation by the TET enzymes on retinal cell fate decisions. Using conditional TET mutants, we show that DNA demethylation is required for proper retinal development and function.

First post on this platform is to announce that our preprint is posted to bioRxiv:

bioRxiv 2025.02.03.636318; doi: doi.org/10.1101/2025...