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Jan 12, 2023 12 tweets 7 min read Read on X
New preprint! 🥳

biorxiv.org/content/10.110…

Led by @aledjohnparry & @ChristelKrueger we asked why #DNAmethylation and oxidation often target overlapping genomic regions at the exit of #pluripotency.

Great collaboration with @Tim_Lohoff, @StevenWingett & @stefanschoenfe1.

🧵👇
Excellent work by @SchubelerLab, @rulandsgroup, Jaenisch lab, Meissner lab, @CarellThomas and others has shown that DNA methylation turns over genome wide as cells exit naïve pluripotency, especially at enhancer elements.

We discussed this here: rdcu.be/b8bfM Image
But what is the function of methylation turnover?

To find out, we modelled pluripotency exit in vitro (transitioning ESCs to EpiLCs) and performed a thorough molecular characterisation in wild type cells and in cells lacking DNA methylation (Dnmt TKOs) or oxidation (Tet TKOs).
This was a lot of data to wrangle (>300 datasets! 🥵), so we developed new computational approach.

We clustered promoter - promoter interacting region (PIR) pairs (identified by PCHi-C) using the expression, interaction strength and epigenetic information from both regions. Image
This identified pairs of elements including promoters interacting with active enhancers, primed enhancers or poised enhancers. Image
So what happens at enhancers in Dnmt and Tet TKO epiblast-like cells?

Excitingly we found that H3K4me1 is depleted from enhancers in both knockouts, but H3K27ac is reduced only in the Tet TKOs. Image
So we reasoned that methylation turnover is required for H3K4me1 deposition at active enhancers.

We have previously identified WRD5, a member of the MLL3/4 containing WRAD complex, as a strong binder of 5fC - this is one possible mechanism.
doi.org/10.1186/gb-201… Image
Is methylation turnover important for enhancer priming too?

To find out, we differentiated TKO ESCs into embryoid bodies (EBs). In Tet TKO EBs, activation of genes associated with the blood lineage was especially perturbed.
Excitingly we could already see defects at primed enhancers associated with key blood transcription factor (TF) genes in Tet and Dnmt TKO epiblast like cells, long before these genes are expressed.
Primed enhancers lost H3Kme1 . . . Image
. . . and interaction strength between these primed enhancers and their associated genes was often reduced.

Thus TET and DNMT activity (and therefore methylation turnover?) are both important for priming of enhancers associated with genes encoding blood specific TFs. Image
For example, two blood TF genes, Klf1 and Lyl1, share a number of primed enhancers.

These enhancers and the interactions between them were clearly perturbed in Tet TKO epiblast-like cells, potentially explaining why the genes aren’t upregulated upon differentiation. Image
Perhaps DNA methylation turnover at enhancers can explain the paradoxical finding that mutations in DNMT and TET genes are both causally linked to blood cancer. Enhancer activity is disrupted if either methylation or oxidation is perturbed.

We’d love to know your thoughts!

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More from @ReikLab

Jan 17, 2023
Time really does *fly* by when you’re enjoying journal club🪰

This week we discussed the newly released Aging Fly Cell Atlas by @TzuChiaoLu, @mariabrbic, @HongjieLi5, @StephenQuake and colleagues!

doi.org/10.1101/2022.1…
This valuable new resource provides insights into the changes in cellular composition and transcriptional patterns across the whole animal during the aging time course of Drosophila, and provides an understanding of cell-type specific aging features.
We were interested by the fact that the majority of cell types see significant transcription changes early in aging. This leaves us curious as to why certain cell types are seemingly resilient in maintaining their transcriptional and cellular identities.
Read 5 tweets
Apr 8, 2022
Now published in @eLife! 🎉 We show that transient iPSC reprogramming can substantially rejuvenate human fibroblast cells (many markers suggest by about 30 years)! Congratulations to @Diljeet_Gill who led the work. Thread below 👇🧵
elifesciences.org/articles/71624
During the process, which we call maturation phase transient reprogramming (MPTR), we express the Yamanaka factors (OSKM) in fibroblast cells for 10-17 days (until the "maturation phase") before removing their expression and allowing the cells to revert back.
Cell morphology and gene expression levels change at the intermediate stage, but then return to a fibroblast state following removal of the Yamanaka factors (based on morphology, transcriptome and methylome). We think epigenetic memory at enhancers is important for reversion.
Read 6 tweets

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