Daniel MK Lee

HDAC3 prevents enhancer hyperactivation to enable developmental transitions Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate tra...

Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:

The E2G Portal! e2g.stanford.edu

This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.

Uses cases 👇

1/

Congratulations @julianeg.bsky.social ! Very happy for your grant and looking forward to seeing more cool stuff from your lab!

During Cassandra Extavour's visit to the MPIMG, I was honored to chair a session discussing how we can collectively improve diversity and inclusion in science.

As a next generation of scientist, it was truly inspiring and empowering.

Kudos to all the organizers that make it happen!

What controls condensate composition and function beyond binding stoichiometry? We show that condensate microenvironments play a key role, and can be probed by a micropeptide killswitch in live cells. www.nature.com/articles/s41... in @nature.com ‬ with @yaotianzhang.bsky.social Denes Hnisz & team.

Delighted to share a new preprint from the lab!

We identified zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) as insulator-binding proteins in Drosophila.
www.biorxiv.org/content/10.1...

Check out this 🧵 from @eimearlagan.bsky.social on our new Molecular Cell @cp-molcell.bsky.social paper! We show how the H3K27M Oncohistone reprograms chromatin in DMG, creating a specific dependency on CBX4/PCGF4-containing forms of cPRC1 👇

Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

Macromolecular interactions dictate Polycomb-mediated epigenetic repression The dynamic regulation of epigenetic states relies on complex macromolecular interactions. PRC2, the methyltransferase complex responsible for depositing H3K27me3, interacts with distinct accessory pr...

Excited to share a preprint from my lab on distinct specificity and functions of PRC2 subcomplexes: www.biorxiv.org/content/10.1...

I am thrilled to share our preprint where we take advantage of the unique opportunities offered by human blastoids to uncover a human-specific mechanism potentially playing a role in preimplantation 🧵. www.biorxiv.org/content/10.1...

Congrats to the very talented @oozguc.bsky.social 🔬

Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells Abstract. Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to dis

Happy to share the lab's latest publication from @eli-elder.bsky.social and team in @narjournal.bsky.social ! What happens when #DNAmethylation maintenance is transiently interrupted in mouse embryonic stem cells? Let's dive in (1/11). doi.org/10.1093/nar/...

1/ H3K27me3 mimicry has repeatedly emerged through evolution, but what's the physiological relevance?

We show that JARID2 and PALI1 mimic H3K27me3 to antagonise PRC2 in vivo and restrict the spread of Polycomb domains.
🧵
www.biorxiv.org/content/10.1...

Very happy that I attended the amazing SY-Stem symposium. I received so many nice feedback on my project and good to have another Curie BDD reunion.
@deborahbourchis.bsky.social
@dianapinheiro.bsky.social

Congrats Adri! Well deserved 🎉

Institut Pasteur decides to leave X The Institut Pasteur, a research organization which for more than 130 years has been committed to tackling infectious diseases, sharing knowledge and defending science, has decided to leave X because ...

The Institut Pasteur has decided to leave X (formerly Twitter) to join BlueSky! 🦋
The Institut Pasteur made this decision due to several serious issues observed on the X platform since its acquisition. Join us here to continue advocating for science. www.pasteur.fr/en/home/pres...

Congratulations Juliane🥳🥳🥳
So happy for u!

Come to be our colleague @pasteur.fr! center of Paris, great colleagues, outstanding facilities, permanent position, crème brûlée every Friday - what else could one want?

Thanks!

Hi Duncan.
Can you please add me?
Thanks!

Evolution and function of chromatin domains across the tree of life - Nature Structural & Molecular Biology Szalay et al. discuss cross-kingdom similarities and differences in 3D chromatin folding in relation to gene regulation, including in bacteria, archaea, mammals and plants. This comparison reveals cer...

🔺🔺🔺RED TRIANGLE ALERT 🔺🔺🔺
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!

Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!

SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...

Here it is! Congratuations to @jesskelley.bsky.social @edimitrova.bsky.social @neilblackledge.bsky.social @aleksszczurek.bsky.social and the rest of the team (Maciej, Amy, and Hieu). This was a fab collaboration with Arminja Kettenbach. Also see a lovely complementary paper from Fei Chen's group.