Maxim Greenberg
@maxvcg
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Group leader @IJMonod . When I say "epigenetics" what I really mean is "DNA methylation".
Paris, France
Joined April 2010
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Pinned Tweet
The version for *posterity* is out
@NAR_Open
! Congrats to lead authors
@AnaMonteagudo4
&
@jrichardalbert
, our friend/collaborator
@DaanNoordermeer
& engineer extraordinaire Margherita Scarpa! Findings largely intact, but short 🧵 on changes since preprint
🚨New Preprint🚨 In this study, we set out to determine how the de novo DNA methylation program impacts the 3D cis regulatory landscape. Comments welcome! Here's a thread detailing our study's key findings (1/12)
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Homemade PCR tube magnetic rack: 10€ in resin for the 3D printer and 4€ worth of magnets compared with about 300€ from a commercial supplier 🤩🤩🤩
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Instead of using the word "interestingly" every five sentences, what if we start incorporating exclamation points in the scientific literature? Why is this taboo?
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In five (ten?) years we should organize a conference for the labs that had to start during the pandemic so we can trade war stories.
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I've been reflecting on this, and I think singular most memorable moment of
#ScienceTwitter
was when that lady faked the death of her pseud (and implied the pseud was also her lover) and even had a Zoom funeral. That was BONKERS.
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I know the consensus here is to kill reviewers who ask for RT-qPCR validation of RNAseq data, but we just did some RT that totally invalidated an RNAseq run that we were getting very excited about....
#JustSayin
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This paper is far too cool to be in Cell. Did they steal it off the Current Biology editor's desk?
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Waking up, and it's dawning on me that the 3 billion invested in Altos Labs is about 50% more than last year's ERC budget to fund ~1000 labs across the sciences. Wow.
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This Human Developmental Cell Atlas figure has gotten a lot of developmental biologists riled up, so I modified it a bit to make it more *palatable*
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I'm not a zebrafish guy, I'm not an embryologist, I'm certainly not a microscopy guy. But how this 7 second video makes me feel is pretty much why I'm an academic and there's no other job I want to have. So that's my 2 cents to the current discourse.
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🚨Preprint Alert🚨 I am very proud to present our latest work, describing how DNA methylation shapes the polycomb landscape. A team effort, led by
@jrichardalbert
,
@teresa_urli
, and
@AnaMonteagudo4
in the lab. Here's a 🧵 highlighting 🗝️ findings (1/12)
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So today we're getting lectured by HHMI professors that citing journal names in our talks is "prestige signaling". i had no idea I have been so insensitive all these years. my deepest apologies to all those feeling worthless upon seeing my PLoS and EMBO and eLife titles... 🙄
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Beef and lamb are the H3K36 methyl-marks that you waste your budget sequencing and all you can do is make some crappy meta-plots. Beans and peas are K4me3 and K27ac. Much better returns. Sum of all is MNase seq. (I'll show myself out)
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I think the most twisted mental gymnastics we scientists do is get excited / day-dream / imagine a paper about a hypothesis for many months or over a year, then one key experiment clearly refutes it, and we just are like "ah, ok. well that's science" and move on
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Forcefully recommend that anyone who refers to their research as "epigenetics" to take a few minutes and read this highly insightful perspective from Sui Huang
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Hey, even if it's really not the end of Twitter, why not let everyone know how we feel. Here's my
#ScienceTwitter
#SciTwitter
Mt Rushmore:
@HarmitMalik
@mbeisen
@OdedRechavi
@Caroline_Bartma
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TIL that some single-celled dinoflagellates have eyes built from endosymbiotic organelles. Nature never ceases to amaze
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🚨 First Greenberg Lab publication 🚨 There were some very cool papers from last year that I wanted to incorporate into our broader understanding of DNA methylation reprogramming in vivo (with a dash of speculation about why this all evolved)
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28 (😳) histone mutations. I feel like that alone is worth a big paper; whatever else they find is gravy.
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🚨New Preprint🚨 In this study, we set out to determine how the de novo DNA methylation program impacts the 3D cis regulatory landscape. Comments welcome! Here's a thread detailing our study's key findings (1/12)
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"Alain Aspect, our new Nobel Prize winner in physics, says that he has had time to conduct this research. In France, researchers lack time. They are devoured by bureaucratic activity. Let's trust them, let them work, otherwise they will leave."
Alain Aspect, notre nouveau prix Nobel de physique, dit avoir eu le temps de mener ces recherches. En France, les chercheurs manquent de temps. Ils sont dévorés par l'activité bureaucratique. Faisons leur confiance, laissons-les travailler, faute de quoi, ils partiront.
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This one really triggered me. Almost two million engagements on this tweet, giving hope to families dealing with these cruel diseases… go to his bio, and it’s all incomprehensible tech bro speak. Pure hucksterism
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In Parisian bus literally listening to
@PodSaveAmerica
when I spotted this guy at Parisian cafe. Unreal.
@jonfavs
@danpfeiffer
@TVietor08
@jonlovett
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There's data viz that helps readers quickly understand and digest a complex data set, and then there are gene interaction graphs
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I think I'm losing it. Agathe has been a PI for like 5 minutes, she's kind, she's funny, she has exactly *1* PhD student and made a good joke about a long running trope of how to take pipette tips from a box. Who are these people. I mean, what the f*ck are we doing here.
Apparently to go viral on scitwitter you just need to joke about firing your trainees. Gross 🤮
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I'm not being provocative, just asking naively: are witnessing the future of proteomics unfold (no-pun intended)?
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Getting ready to shut my brain off for a little bit of🎄⛷️🍾. Before I do, here is an incomplete list of some of my favorite DNA methylation papers from 2022 🧵
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I know people generally turn a blind eye to it anyway, but I wish self-plagiarism for methods was actually formally acknowledged as OK. How many different ways are you supposed to describe HeLa cell culture, or whetever.
I feel like people conflate a lot of things when discussing plagiarism. Someone using identical phrases in the Methods section of several of their papers is not plagiarism. Self-plagiarism in general is moot to me (the number of ways you can write the same thing is limited)
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I saw a tweet about "negative data" papers today, and I was thinking about how some of my favorites are in this genre. They are usually very thorough and diligently executed (even if the journal "IF" doesn't necessarily reflect their importance). Here are three bangers (1/4)
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We should start compiling a
#ScienceTwitter
glossary
1. "Paper is finally out!": The review process was a nightmare
2. "Glad to see this finally published!": This has been on bioRxiv for literally over a year
3. "Many thanks to our anonymous reviewers": You can burn in hell
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I made myself a promise (that I usually keep) to make this account generally about science and DNA methylation, so I made this GIF
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Dammit, time to re-write the textbooks again.... (btw it should be noted that Tim Bestor showed something similar in
@jbiolchem
a few years back). Meissner group,
@NatureSMB
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I’d love to read the “I played the game really well, got tenure, a bunch of grants and published in the top journals, but ultimately my scientific legacy is pretty forgettable” autobiography for a change
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🚨New Review🚨 There's a long history of evidence for DNAme antagonism of CTCF in mammals. How important is it in normal dev. or disease contexts?
@DaanNoordermeer
@AnaMonteagudo4
and I put together a summary in this collaborative review
@NatureSMB
(1/4)
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I'm seeing a lot of posts about PhD rejection (I got rejected by Harvard, UCSF, Stanford and Berkeley), but keep in mind this is NOT undergrad/law school/med school! Prestigious names mean so little compared to the work you can do in a great *lab* which are at every university!
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Fun fact about French research: when you become a PI you need to do a *second* defense in order to mentor PhD students. Not a joke! Anyway, mine is this Thursday and is open to the public. If your interested (or morbidly curious), DM me and I can share the Zoom info!
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Maybe I'm old fashioned and will get piled on for saying this, but I think it's really cool when students decide to work extra long hours because they are very excited to get a result.
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I love you Adobe Illustrator (even if I feel like I have only mastered ~0.1% of the program after nearly 2 decades of use). But your price is too damn high. As of today, I am an Affinity Designer user.
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I think today is a good day to make an official announcement: I found out I was awarded start-up funds from the ATIP-Avenir program to launch my independent research group at Institut Jacques Monod in Paris!!!!
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It's crazy how one satisfying PCR can offset an otherwise absolutely shitty morning. Look at all those positive clones 🤩
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This
@NatureGenet
paper from Matt Lorincz and co. is one of the studies of the year for the mammalian developmental epigenetics crowd imo. The divergent mechanisms between the male and female germlines are so striking. It's like they're different species!
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Mammals keep germline genes at bay with DNA methylation. Hagfish (and lampreys) just eliminate them altogether 😳
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After a couple of virtual visits, so stoked to actually interact with this truly special group of Munich chromatin researchers in person! And maybe have one (or more) of those famous Munich beverages. Can't wait!! 🧬🍻
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Weird to come into the lab and realize
@AnaMonteagudo4
won't be coming in today 😢. She was our first post-doc, and the engine that got our lab's research off the ground. We wish her nothing but the best of luck for the next phase of her career in industry in her native Spain!!
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How many people got a Science and a Nature paper with the same title, except with one word reversed? 🧑🍳💋
@pablonavarroLAB
@CRougeulle
Molecular Coupling of Xist Regulation and Pluripotency (Science, 2008)
Molecular Coupling of Tsix Regulation and Pluripotency (Nature, 2010)
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In my opinion,
@PSarkies
is one of the most original thinkers in the chromatin field. A non intuitive premise for an article that is food for thought for both the epigenetics and metabolism crowd
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This was published back in June, but it's is one of the most clear-eyed, nuanced reviews about the role of DNA methylation at mammalian enhancers I have come across (from
@ElisaKre
and
@arnaud_kr
-- mieux vaut tard que jamais, as Arnaud might say)
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The hazards of raising French kids: today the told me they can’t set the table for lunch because they’re on strike 😂 😂 🇫🇷🇫🇷
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Two important papers about PRC1 in mouse development just out in
@NatureGenet
: 1) Yi Zhang's group 2) the inaugural paper from Azusa Inoue's group (
@a_z_usa__
). Check them out! You can read more about them here in a N&V from myself and
@jrichardalbert
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Tremendously exciting news for our lab! Priscillia Lhoumaud
@lhoump01
was ranked 4th for the highly competitive CNRS tenured position!!! She has developed powerful tools to analyze DNA methylation at enhancers, and now will have long term security to pursue her line of research.
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Non-genetic intergenerational inheritance of glucose intolerance: Not via 5meC per se, but rather misregulated mat. TET3, leading to incomplete reprogramming of pat. genes in the zygote. Craziest to me is the pat. hyper 5meC persists through ground state..
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This is a massive effort that will be a tremendous resource for the chromatin field (Bartke Lab
@epigeneticsHMGU
)
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Nice in vivo genetics to finally demonstrate what people have been hand waving about for years
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Just finished up a JC on this nice paper from the Hochedlinger group. In a roundabout way, it's a great case study demonstrating the importance of DNMT3A vs TET competition at enhancers during a cellular transition.
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🚨Review Drop🚨
@jrichardalbert
& I explored the cutting edge of non-canonical imprinting. We also added our thoughts on the developmental and evolutionary importance of the phenomenon. A great exercise to think deeply about mammalian epigenetics (1/5)
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First cryoEM of de novo methylation shows DNMTs interacting with entire nucleosome (not just histone tails). Interesting choice to use cat. inactive isoform of DNMT3B instead of DNMT3L (DNMT3-Like-Like?)
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Today is our one year labbiversary 🎂! This year took some, ahem, unexpected twists and turns. I have had incredible institutional support
@IJMonod
and tremendous colleagues, but I want to take a moment to thank the
#SciTwitter
community, especially for the last 6 months. (1/4)
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Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development (Siddharth Dey and Alexander van Oudenaarden)
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Really cool paper about de novo DNA methylation right after fertilization. The kicker: mom's DNMT3A methylates dad's DNA, controlling paternal expression. (i'm also slightly biased bc Julien Albert—the first author—will be my post-doc!)
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📢I am recruiting! I am looking for a motivated post-doc to join my group in an
@ERC_Research
supported project on DNA methylation in mammals. Come to Paris! Come to
@IJMonod
! Link here: Please RT!!!
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I tried to explain to my sobbing 9 year old that in Argentina there’s a 9 year old just like him who’s having the best day of his/her life, and he could be happy for them. His response was “yeah, and?”
#sports
#parenting
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Things are getting intense!
@ericmiska
is leading a roundtable about what is real and what is heresy in epigenetics. As you can imagine, a lot of nuanced thoughts in this crowd.
#EMBOepigenome
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I had the pleasure of watching the brilliance of Danny, Michel et al develop these ideas (they were a floor above
@institut_curie
), and you will be hard pressed to find more thoughtful dissection of epigenetic memory than in this paper.
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Awesome figure for intro slides about TEs as drivers of phenotype/adaptation
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Thrilled to announce our team will be part of an
@AgenceRecherche
funded formal collaboration with the
@DefossezPierre
and
@S_Spicuglia
labs. Really looking forward to investigate how DNA methylation regulates SARS-CoV-2 (joking!!!). Seriously, this will be a lot of fun!
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Really nice study on DNA methylation signature of developmental enhancers (which become PRC2 regulated). Implication is PRC2 prevents de novo DNA methylation in somatic tissues:
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I am starting to cook with my daughter using a French cookbook for kids (spaghetti bolognese, chicken cordon bleu, etc), and I've learned that the secret to making anything delicious is just to throw a whole stick of butter into whatever you're making.
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Wow, another exciting breakthrough in the epigenetic editing therapy space! Really clever to use the H3 tail in the construct to stimulate DNMT3A activity. Similar to Lombardo lab, seems ZnFs tool of choice for targeting
@jswlab
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📢We are recruiting! Fun, international lab located
@IJMonod
in Paris in need of support on multiple fronts. See the ad for more details, and don't hesitate to contact me with your questions. Please RT!
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Absolutely thrilled and honored to be afforded this tremendous opportunity. I am also incredibly grateful for the support I received from
@IJMonod
and
@CNRS
. Congratulations to all the awardees!!! 🇪🇺👨🔬
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Shamelessly stealing the “paper not rejected yet celebration” concept from the
@GribnauLab
😂
🚨Preprint Alert🚨 I am very proud to present our latest work, describing how DNA methylation shapes the polycomb landscape. A team effort, led by
@jrichardalbert
,
@teresa_urli
, and
@AnaMonteagudo4
in the lab. Here's a 🧵 highlighting 🗝️ findings (1/12)
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We know CGIs are enriched at promoters, but 1/4 are in gene bodies. Usually gene bodies are DNA methylated, so this means their presence must be selected for. Whats is their function then? Nice review from experts on the subject
@rjoakey2012
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My goodness, Dnmt Tet 6KO by zygotic injection of CRISPR base editors 😳. This is such powerful technology
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Got our first batch of
@plasmidsaurus
sequences back. I sequenced a vector we use ALL the time for inducible expression constructs to see what we'd see. The top bar is the sequence we thought we had, the bottom bar shows all the mismatches (in red)....
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My lab’s still in the early embryonic development stage, and I’m so impressed by the motivation, enthusiasm and courage from this crew to take on the challenge. I started 2019 with so much anxiety, but I’m starting 2020 with so much excitement thanks to these guys!
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Transcriptional Memory ✅
Chromatin Modifications ✅
Transmission across meiosis ✅
Did Susan Strome et al satisfy everyone's definition?? Plus she defined the E-word in the first paragraph 🥹. As usual, very elegant work to boot (no pun intended).
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This is a nice adapted CUT&Tag protocol for looking at multiple marks in the same cell from Thomas Fazzio's group
@UMassMedical
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I spent a morning last week designing cloning to test this very idea! Ah well, I guess it's best to be "scooped" without having to touch a pipette 😀
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I strongly urge native English speakers esp. in English-speaking countries to read this thread. Before moving to France, I was completely non-empathetic to the mental burden of dealing with a language barrier, and I have a feeling I was not an isolated case.
How hard is it to do science in a language that’s not your first language? We quantified the severity of
#languagebarriers
for non-native English speakers when reading/publishing papers and attending/presenting at international conferences.
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Thrilled to announce that one month from today, Anne Ferguson-Smith will be coming to Paris!! Can't wait to hear what exciting mammalian epigenetics research she will tell us about! (wish I could do this👩🏼👩👩🏻👩🏽👩🏾👩🏿 with the🐁 emoji).
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Steve Jobs must be rolling over in his grave because of this design
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In the face of a pandemic, these scientists dropped everything they were doing and basically didn't sleep until they got the structure of this protein. Oh and they made all their results open.
1/ It's been a very busy few weeks in the Walsh group
@diamondLightSou
but extremely happy to announce that in collaboration with Frank von Delft group’s at Diamond we have been able to perform a full X-ray fragment based drug discovery experiment on the SARS-CoV-2 main protease
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I think my favorite euphemism in molecular biology for a minor effect is "fine tuning"
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I can't get this out of my head: in
@heard_lab
@LonelyPipette
interview, she said when she was training all that time waiting for maxipreps to drip allowed her to think and reflect. Now trainees have so many things going at once, it's harder to find the time. I agree and it 💔
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📢 Epigenetics Summer School in Montpellier 🌅! Join us for a fantastic week of chromatin biology with researchers from France and Japan! I am thrilled to be part of this excellent program! Students: Check the link for more details
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