Daniel MK Lee
@dannimklee.bsky.social
MSCA postdoctoral fellow at Max Planck Institute for Molecular Genetics. PhD alumnus at Institut Curie. Epigenetics, DevBio, Transcriptional regulation, Organoids
Happily, our fly stock room has been restored to 18°C and the labs are now a chilly 30°C. We will see how the hot week ahead progresses.
Bardin Lab@bardinlab.bsky.social · 2mo agoHow HOT is TOO HOT to work in lab? 33°C? 35°C? 37°C? Our aircon in the BDD @institutcurie.bsky.social , which hasn't worked well for years, is now dead. This is our "18°C" room for important fly stocks (now at 29°C!). It is 33°C in the labs today, and will only increase over the next 6 days!
JIT 4 summer, the latest preprint from our lab, brilliantly led by @kaitezhang.bsky.social w/ support from Collepardo lab (@juliamaristany.bsky.social / @janhuemar.bsky.social). www.biorxiv.org/content/10.6... describes a new single-molecule epigenomic method, & discoveries it enables ... (1/n)
Single-molecule nucleosome spacing coordinates chromatin fiber interactions
Nucleosome spacing influences higher-order chromatin fiber organization in vitro but how this relates to cellular chromosome structure remains contentious. To address this, we developed Ligation Analy...
biorxiv.org
I am extremely honored and grateful to see our work featured on PreLights @prelights.bsky.social. If you want a quick dive into how acute loss of PRC2 impacts TLS formation, check out this excellent breakdown by María @mariamafau.bsky.social. I had a great time discussing the work with her.🔬👇
María Mariner@mariamafau.bsky.social · 3mo ago🚨Happy to share a new PreLight covering the latest #preprint by the Meissner lab (@molgen.mpg.de) on acute SUZ12 degradation during TLS formation. A work brilliantly executed by @dannimklee.bsky.social et al. Get to know more about him and his work here ⤵️ prelights.biologists.com/highlights/t...
We are offering Postdoc & PhD positions 🥼 If you are interested in the intersection of X chromosome inactivation, epigenetics, aging, sex-biased disease, and allele-specific multi-omics, feel free to reach out or share this with interested candidates. More info: portal.mytum.de/jobs/wissens...
Very excited to have Alex Meissner @molgen.mpg.de visit @upcite.bsky.social (jointly hosted by Pierre Defossez from the Epigenetics and Cell Fate Centre and me @ijmonod.bsky.social). If you want to see the cutting edge of DNA methylation in mammals, come to our big amphitheater on June 5!
Very excited to share our newest findings! A very long team effort pursued by multiple team members -to frantically reproduce everything over and over-, we show mTOR-Polycomb synergy at promoters of developmental master regulator TFs in ESCs prior to their expression. www.biorxiv.org/content/10.6...
biorxiv.org
'Look, it's going to be an easy paper. Trust me. Six months. Tops'
A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organis...
cell.com
New paper out in @cp-cellstemcell.bsky.social. We uncover unexpected complexity in how metabolism changes when the embryo implants or when stem cells exit naive pluripotency, revealing a central role for dynamic TCA cycle rewiring in cell fate decisions. www.cell.com/cell-stem-ce...
TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency
Using carbon tracing and functional experiments, Kafkia, Pladevall-Morera, et al. show that TCA cycle rewiring underlies mouse embryo implantation and the exit from naive pluripotency. In this context...
cell.com
New Preprint alert!🚨 Super excited to share my postdoc work now on BioRxiv. How does PRC2 loss lead to developmental failures? We combined rapid protein degradation with TLS embryoid models to uncover temporal and lineage-specific dependencies 🧬. Preprint: doi.org/10.64898/2026.04.18.719361
Big congrats to Julia! Besides doing amazing science, she has always been a super kind, supportive colleague. I can not wait to hear more about her cool work and so so happy for her for her new journey!
FMI science@fmiscience.bsky.social · 4mo agoIn this interview, @juliabatki.bsky.social, FMI’s newest group leader, reflects on the early curiosity that drew her to science, why FMI is the right home for her lab, how studying cell clearance could help us understand disease, and her love of improv. www.fmi.ch/news-events/...
Polycomb repressive-deubiquitinase complex safeguards oocyte epigenome and female fertility by restraining Polycomb activity www.nature.com/articles/s4...
With the human embryo model field rapidly expanding, it would be good if those venturing into it properly acknowledge the history of the field and give credit where credit's due. I doubt hTLS would be there w/o mouse gastruloids @amartinezarias.bsky.social @susannevandenbrink.bsky.social & TLS.
🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...
A dual role for CTCF in development
CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 637587, 865459 Dutch Research Council, https://ror.org/04jsz6e67, 016.161.316, VI.C.222.049 Dutch Cancer Society, https://ror.org/0368jnd28, N/A
biorxiv.org
I am very happy to share that I've started my new position @upcite.bsky.social and opened my lab @institutimagine.bsky.social 🎉 In the lab we will study how differences in X-linked gene dosage between the sexes affect fetal growth and survival and contribute to sex differences later in life 👩🔬🧪🧬🧫
🚨JOB ALERT🚨PLEASE SPREAD and RT Searching for a motivated Master’s student @bokelab.bsky.social @crg.eu @prbb.org to investigate how proteostasis in oocytes influences dormancy and fertility. Reach out to me (adriano.bolondi@crg.es) to join us in sunny Barcelona! See details below👇
If you want to explore ncRNA dynamics during mammalian development, love microscopy, and are not afaraid of transposons biology, apply‼️ We are looking for a postdoc to join our team at @imbavienna.bsky.social More details 👇🏻
Institute of Molecular Biotechnology@imbavienna.bsky.social · 5mo agoWe are hiring! Join the Jachowicz lab as a postdoctoral researcher. The project focuses on understanding the dynamics of ncRNAs using high-resolution and single-molecule microscopy approaches. Link below 👇
Find our latest Perspective article in Nature Genetics on "The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements" at www.nature.com/articles/s41..., with implications for the future of research on the cause of human disease.
The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements - Nature Genetics
This Perspective explores the co-evolution of transposable elements and KRAB zinc-finger proteins in relation to their integration into human gene regulatory networks, highlighting their potential eff...
nature.com
Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.
Redirecting
doi.org
Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation: www.sciencedirect.com/science/arti...
Are you a DNMT3 enthusiast wondering how they achieve specificity at CpG islands during development? And why is DNMT3B specifically required for methylation on the inactive X? We set out to dissect the mechanism, now published in Genes & Development genesdev.cshlp.org/content/earl... [1/12]
Chromatin binding and N-terminal domains of DNMT3B1 confer specificity for developmentally regulated CpG island methylation
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
genesdev.cshlp.org
Very excited to share our new Molecular Cell paper on missense mutations in Polycomb genes and how they can disrupt chromatin regulation to drive neurodevelopmental disorders. A huge thank you to everyone involved, and to our amazing collaborators! www.cell.com/molecular-ce...
Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders
Borges, González-Blanco, Arigela, et al. report new missense mutations in the PRC1 genes RNF2 and RING1 in individuals with neurodevelopmental disorders. Functional dissection of a deleterious variant...
cell.com
During germline epigenetic reprogramming, Polycomb must be restricted in the gametes to ensure proper genome regulation in the fertilized embryo. 2 must-read papers assess what happens when Ezhip (Polycomb antagonist) is lost. They come to highly similar conclusions and should be read in tandem 1/4
Now final version out: Our manuscript connecting histone modifications with metabolism: How H4K16 acylations regulate inter +intranucleosomal interactions and confer resilience to metabolic challenges in vivo. Thanks to the team+ @sandrani.bsky.social Enjoy 👇👇 www.cell.com/molecular-ce...
H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations
Nitsch et al. show that short-chain acylations of histone H4K16, acetylation (C2), propionylation (C3), and butyrylation (C4) modulate chromatin structure in vitro. These effects can translate in vivo...
cell.com
Do you want to play a key role in running a cutting-edge stem cell and embryology lab at reNEW @ucph.bsky.social ? We’re hiring a Lab Manager to support our team and help with stem cell and animal work. Apply before Feb. 1st : rb.gy/d5uf17
Academic employee for Research Group, Dept. of Biomedical Sciences, reNEW
rb.gy
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉 We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
Escape from X inactivation is directly modulated by Xist noncoding RNA
Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...
rdcu.be
🧬 Are you interested in synthetic biology, CRISPR-Cas9 genome editing and cutting-edge genomics? Apply by 07.01.2026 to join Stefan Mundlos’ lab @stemundi.bsky.social at the MPIMG. #IMPRS-BAC #gradschool! @nataliabenetti.bsky.social 👉 www.molgen.mpg.de/5124667/Mund...
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost! www.biorxiv.org/content/10.6...
SET1/MLL complexes control transcription independently of H3K4me3
Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...
biorxiv.org
Happy to see Atsuhiro Taguchi's work on genes involved in liver zonation published in Dev @cellpress.bsky.social. Kudos to all authors at @molgen.mpg.de #MeissnerLab #HniszLab. Grateful for the opportunity to help! www.sciencedirect.com/science/arti...
Single-cell activation screen identifies hepatic maturation regulators with zonal resolution
The maturation of lineage-committed embryonic hepatocytes requires both the timed activation of metabolic gene regulatory networks (GRNs) and silencin…
sciencedirect.com
IMPRS-BAC Open Call: Current IMPRS student Marcel Wittmund talks about what pursuing a PhD means to him and how the IMPRS program supports his doctoral studies at the MPIMG. Apply by Jan 7th, 2026! www.molgen.mpg.de/IMPRSPhDproj... #IMPRSBAC @freieuniversitaet.bsky.social @maxplanck.de