Maxim Greenberg
@maxvcg
Group leader at Institut Jacques Monod. When I say "epigenetics" what I really mean is "DNA methylation". www.maximgreenberglab.com
Very excited to host @chribue.bsky.social ( @maxperutzlabs.ac.at ) for double-duty @ijmonod.bsky.social ! Thesis jury on Thursday and a seminar on Friday (with some champagne in between 😜) If you're around Paris on Sept 25, don't hesitate to come listen!
I have to say, it warmed my heart to see Parisians congregate (in the dog days of August, no less) for a celestial event like it was Woodstock. 🌍 🌓🌞@ishier.bsky.social @arabette.bsky.social
Woke up remembering these old Occupy Wall Street protests, and it clicked why this QED 1% branding is so, so, so very awful
So we don’t think 5mC is “activating” enhancers in most cases, but we did find evidence that methyl-binding TFs might play a role in decommissioning (12/13)
We also took advantage of the genetics in the EpiLC system. We reasoned that if active enhancers required 5mC, they would lose activity in the Dnmt KO. We could find examples, but they were rare (11/13)
We noted the active methylated enhancers have the highest 5hmC signal. This indicates active demethylation rather than a requirement for 5mC (10/13)
Active enhancers are generally anti-correlated with 5mC, so we were motivated to dig into this. First, we developed hydroxymethyl-ATAC (hM-ATAC) to determine how much signal was 5mC vs 5hmC (9/13)
Now we could sort our ATAC peaks into different enhancer classes. We noted that: 1) H3K4me1, per se, is not really anti-correlated with 5mC (surprise), 2) primed enhancers have higher 5mC than active enhancers (not a surprise) and 3) there are still a lot of active methylated enhancers 🤔 (8/13)
Next, we implemented M-CUT&Tag to see how chromatin marks relate to 5mC levels. We did the classical marks of H3K4me1 (primed/active enhancers) and H3K27ac (active) (7/13)
Side note: we also devised a really nice way to visualize the data with a genome browser track (h/t @jrichardalbert.bsky.social) where we pile up the reads under our ATAC peaks and really see DNA methylation patterns emerge. As a 5mC biologist, I love this 🤩 (6/13)
What about the mutants? The Dnmt KO ATAC landscape was broadly misregulated. In the Tet KO, we could see an increase in 5mC (indicating Tet activity), but only subtle effects on accessibility (5/13)
Opening peaks (Cluster 1) exhibited less 5mC than closing peaks (C5). Not a surprise, but two things we noted: 1) signal from whole-genome data is always higher, which shows how M-ATAC brings unique info 2) even open peaks have a subset with high 5mC levels (4/13)
From its onset, our lab has been using the ESC-EpiLC transition to study the requirements of 5mC, as it is resilient to mutations in Dnmt or Tet machinery. Priscillia and I thought this would be an excellent system to employ her tools to study enhancer dynamics (3/13)
During her post-doc with @janeskok.bsky.social, Priscillia developed the "EpiMethylTag" technology to simultaneously assess accessibility with DNA Methylation (2/13)
Got my Father’s Day gift socks on, which also feel appropriate for my trip to Dublin today for Faseb Biological Methylation #BioMethylSRC 🍻 🍀 🧬
For students in the Paris region: free mental health support is available, and sessions can be held in Italian, Spanish or English if requested. Don't hesitate to share this info! www.apaso.fr/les-consulta...
I'm going to start playing this album in the lab to send a subliminal message
Was completely charmed by my long overdue trip to Strasbourg and @igbmc.bsky.social . Thank you @abardet.bsky.social for being a great host, organizing a walking visit, great dinner, thesis committee, institute visit and talk! Such stimulating discussions, and exciting collaborations to come!!
Also a good hang @mads100tist.bsky.social @nkonst4.bsky.social . We’ll be on the Seine for a while if you want to join 😉🍻
The was a straight up awesome talk. Beautiful work, @mads100tist.bsky.social , congratulations!
I think @upcite.bsky.social is trying to recreate the Maison Fond art installation that used to be in front of Gare du Nord
Exciting #CtrlEpiEdit conference update: Maja Jagodic @ki.se will be joining us in Paris! Check out her fantastic in vivo epigenome editing preprint here: www.biorxiv.org/content/10.6... And register for the symposium here 😉: ctrlepiedit.sciencesconf.org Please repost!
Bad week for @thermofishersci.bsky.social on this site!! @sholtodavid.bsky.social