We often say cancers reactivate embryonic programs, but how often does this happen? and is it always bad? In this study, we develop EmbryoRadar to detect widespread expression of preimplantation transcriptional programs across all cancers, with varied patient outcomes www.biorxiv.org/content/10.6...
In this episode of the Epigenetics Podcast, we talked with @meleckmas.bsky.social from the Peter McCallum Cancer Center about her work on DPPA2 and DPPA4 as Chromatin Priming Factors. #podcast#epigenetics
Listen here: activemotif.com/podcasts-mel...
Thrilled to share my freshly "baked" Baker lab paper. We took a bottom-up approach to designing transcriptional regulators. Instead of relying on natural activation domains, we designed compact proteins that recruit specific cofactors. Activators for now, repressors to come!
Thoroughly enjoying the 6th Danube #epigenetics meeting in Budapest. Lots of great talks so far. Come fine me over coffee if you want to learn about our work on bivalent chromatin our our latest EmbryoRadar preprint www.biorxiv.org/content/10.6..., or to talk about #chronatin more generally!
Had a great time last week at the #CancerEpigenetics meeting in Paris where I had the opportunity to share our latest work on bivalent chromatin dynamics in cancer. Thanks Pierre-Antoine Defossez for organising and ensuring the conference success despite all the protests!
We often say cancers reactivate embryonic programs, but how often does this happen? and is it always bad? In this study, we develop EmbryoRadar to detect widespread expression of preimplantation transcriptional programs across all cancers, with varied patient outcomes www.biorxiv.org/content/10.6...
Interestingly, similarity to the trophectoderm, the precursor to the placenta, is highly detrimental for skin and breast cancers. This tumour intrinsic property is independent of known clinical and molecular attributes, and can predict dependencies to several key preclinical targets including MYBL2
We often say cancers reactivate embryonic programs, but how often does this happen? and is it always bad? In this study, we develop EmbryoRadar to detect widespread expression of preimplantation transcriptional programs across all cancers, with varied patient outcomes www.biorxiv.org/content/10.6...
EmbryoRadar is a suite of 7 independent classifiers that detects transcriptional similarity to maternal, ZGA, morula, epiblast, trophectoderm, pluripotent stem cells and adult cell types, and can be applied to any bulk transcriptome data. Code is available on GitHub: github.com/eckmaslab/EmbryoRadar
Whilst all cancers upregulate early embryonic programs, the impact on patient survival is context dependent. Surprisingly, similarity to maternal stage embryos is protective in kidney cancer. Further analysis revealed this signal comes form the stroma, not the tumour, in response to the cancer cells
(1/9) Excited to share my preprint on Polycomb 3D chromatin interactions from my postdoc with @andersshansen.bsky.social!
We were surprised to find that canonical PRC1 doesn't seem to be the only contributor to these interactions:
www.biorxiv.org/content/10.6...
1/ Most genes and variants matter somewhere but look silent in any one cell model. Can we build conditions that reveal phenotypes? With @kanishkadey.bsky.social, we engineer cell states to expose hidden disease biology and trace how genetic risk reaches disease genes. www.biorxiv.org/content/10.6...
Pathway to Independence – an interview with Evan Healy
In this interview, we learn about @evhealy.bsky.social's career path, what he hopes to gain from the Pathway to Independence programme, and what questions he hopes to tackle with his own group.
doi.org/10.1242/dev....
1\ We know a bit about how 3D chromatin interactions are formed, but what do we know about how they are disrupted? We asked this question in our latest preprint: doi.org/10.64898/202..., focusing on the massive loss of promoter interactions during neuronal differentiation.
Sad to hear about Terri’s passing. I have fond memories of her from my graduate student days at CSHL. and am grateful for some rather direct career advice she gave me at the time. My thoughts are with all those close to her. She will be missed
Deeply saddened to learn of the death of my colleague Terri Grodzicker. She was an amazing molecular biologist who did fundamental work on adenovirus. Many will know her as the charismatic long-time editor of Genes & Development and organizer of CSHL meetings 1/2
en.wikipedia.org/wiki/Terri_G...
🚨 #Postdoc position open.
Want to understand non-canonical #epigenetic regulation of mammalian transcription? Come work @uoe-igc.bsky.social in Edinburgh!
We’re looking for a motivated & collaborative colleague with a strong track record.
📅 14 October 2026
📢 Please share
Apply here 👇
Reposting this ongoing search (any discipline of biology) for an Assistant to Associate level colleague in the Division of Basic Sciences at Fred Hutch.
Great city, great colleagues, great core facilities, great trainees.
Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.
Ready to take the next step in your research career? 👨🔬
We're seeking an outstanding researcher to establish an independent research program as an EMBL Australia Group Leader at the Australian Regenerative Medicine Institute (ARMI) @monashuniversity.bsky.social
🗓️ Apply by 2 October
🔗 bit.ly/4qHYtjb
Had a great time visiting @vonmeyenn.bsky.social at ETH Zürich yesterday and sharing some of the labs latest work. Thanks for the invite, lively discussions and good food!
Next stop Heidelberg for the #EMBLTranscript meeting that starts later today
Our lab had an international brunch where everyone brought in something from their culture to share. They even printed out little place-cards with flags and ingredients. So much delicious food!
Preprint from Katerina Gurova's group looking at oncogenic competency. Using barcoding and scRNAseq, suggest all cells respond to oncogenic insults, yet only some stabilise as transformed. Explores many of the concepts we regularly discuss in the lab. www.biorxiv.org/content/10.6...
Latest from @arnaudkr.bsky.social on TF cooperation at enhancers, liked the combination of single-molecule footprinting at ectopic vs endogenous loci in mESCs. Curious if the cumulative activation frequency model holds for other less proliferative/plastic cell types? www.nature.com/articles/s41...
Intestinal stem cells count divisions and Polycomb/trithorax proteins are involved in the counting, implicating chromatin control. Love the model but would be great to know if it’s truely counting and not time, and how mechanistically replication dilution of histone mods ensures 9 cell cycles?
The ARC has released their new set of grant schemes ▶️ www.arc.gov.au/news-and-pub...
Before implementing them, they’re now going to “consult with the sector”. Hopefully genuinely, not just with a few disengaged DVCRs.
In the meantime, there’ll be another round of Discovery Projects (DP28).
New paper 🧵 What if the "landscape" that guides cell differentiation isn't fixed, but is sculpted, in real time, by the very cells moving through it?
We call this a 'sandscape' : grains of sand that carve dunes as they move, while the dunes' shape simultaneously steers where the grains go next.
1/ Very excited to share the first publication from my lab!
In this work, we developed an efficient strategy to precisely mutate mammalian histone genes in their native genomic context using CRISPR prime editing: www.nature.com/articles/s41...
We just started our summer break, but we're also planning our September-December seminar schedule!
If you have an exciting chromatin/transcription story that will be ready for the spotlight by then, use the survey below to nominate yourself to give a #FNucleosome talk 🧬🧬
forms.gle/1EKYN2Nt79ar...
If you're in Melbourne and interested in genomics and epigenetics, come along to the #Melbourne#Epigenetics club 4pm today.
Visit the website to get club email updates:
https://www.eckmaslab.com/melbourne-epigenetics-club
📢 We are looking for a Junior Group Leader to join us at @institutcurie.bsky.social!
Having joined the department just over a year ago, I can honestly say that it is an exceptionally stimulating and supportive scientific environment, filled with outstanding colleagues — all in the heart of Paris.
Exciting breakthrough technology from the lab, now live in
@cellcellpress.bsky.social
! Instead of cutting the genome where proteins bind (e.g., Cut&Tag), D&D-seq scars the DNA with a deaminase, allowing single cell genome mapping of TFs and chromatin remodellers!
Delighted to share the lab's latest led by superstar Janith and funded by @snowmedical.bsky.social.
What happens when embryonic factors are reawakened in cancers? We uncovered how DPPA2/4 amplify chromatin states in non-small cell lung cancer 🧬🔬🧪
genesdev.cshlp.org/content/earl...
Tutorial 👇 (1/8)
𝗔𝗽𝗽𝗹𝗶𝗰𝗮𝘁𝗶𝗼𝗻𝘀 𝗮𝗿𝗲 𝗻𝗼𝘄 𝗼𝗽𝗲𝗻 𝗳𝗼𝗿 𝘁𝗵𝗲: 𝗔𝗘𝗽𝗶𝗔 𝗦𝘂𝘀𝗮𝗻 𝗖𝗹𝗮𝗿𝗸 𝗔𝘄𝗮𝗿𝗱 𝗳𝗼𝗿 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗘𝘅𝗰𝗲𝗹𝗹𝗲𝗻𝗰𝗲
@aepia.bsky.social is excited to open applications for the Susan Clark Award for Research Excellence, recognising outstanding contributions in epigenetics research, leadership, and advocacy.
ChromSMF preprint is out!🚀
tinyurl.com/ChromSMF
We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting!
In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬
What does this unlock? ⬇️
𝗢𝘂𝘁 𝘁𝗼𝗱𝗮𝘆: Research at Peter Mac led by @meleckmas.bsky.social has uncovered a surprising driver behind aggressive lung cancer — embryonic proteins that are normally only active before birth.
Read more: www.petermac.org/about-us/new...#LungCancerResearch#LungCancer
Delighted to share the lab's latest led by superstar Janith and funded by @snowmedical.bsky.social.
What happens when embryonic factors are reawakened in cancers? We uncovered how DPPA2/4 amplify chromatin states in non-small cell lung cancer 🧬🔬🧪
genesdev.cshlp.org/content/earl...
Tutorial 👇 (1/8)
If we introduce DPPA2/4 in non-small cell lung cancer cells where it's not usually expressed, it binds active CpG rich regions. Here it changes the chromatin states at over half its binding sites to a more active state (as determined by ChromHMM) (7/8)
We propose DPPA2/4 act as chromatin amplifiers in a context dependent manner. In embryonic stem cells they amplify bivalent H3K4me3-H3K27me3 chromatin, while in lung cancer cells they alter H2AK119ub and H3K27ac. Thanks to all who contributed to the study! (8/8) genesdev.cshlp.org/content/earl...
Delighted to share the lab's latest led by superstar Janith and funded by @snowmedical.bsky.social.
What happens when embryonic factors are reawakened in cancers? We uncovered how DPPA2/4 amplify chromatin states in non-small cell lung cancer 🧬🔬🧪
genesdev.cshlp.org/content/earl...
Tutorial 👇 (1/8)
PRC2 is at these sites, but not it's product H3K27me3. We noticed H3K27ac was also there so hypothesised it might be blocking PRC2 activity. However removing H3K27ac (using A-485), at least for 24hrs, did not lead to an increase in H3K27me3 (5/8)
What happens if DPPA2/4 is removed? Surprisingly, the classic bivalent marks it regulates in stem cells (H3K4me3 and H3K27me3) are unaltered. Neither is transcription or chromatin accessibility. Instead we see a loss of H2AK119ub at these unique active sites (6/8)
Delighted to share the lab's latest led by superstar Janith and funded by @snowmedical.bsky.social.
What happens when embryonic factors are reawakened in cancers? We uncovered how DPPA2/4 amplify chromatin states in non-small cell lung cancer 🧬🔬🧪
genesdev.cshlp.org/content/earl...
Tutorial 👇 (1/8)
Chromatin profiling in lung cancer cells that endogenously express DPPA2/4 revealed they like to bind open CpG rich regions of the genome. This is similar to their binding profiles in embryonic stem cells (see www.nature.com/articles/s41... and others) (3/8)
Interesting, some of these DPPA2/4 bound active regions had PRC1-deposited H2AK119ub but not PRC2-deposited H3K27me3. We applied our reChIP protocol (link.springer.com/article/10.1...) to confirm co-occurrence of H2AK119ub with H3K4me3, and rule out cellular heterogeneity. (4/8)
Delighted to share the lab's latest led by superstar Janith and funded by @snowmedical.bsky.social.
What happens when embryonic factors are reawakened in cancers? We uncovered how DPPA2/4 amplify chromatin states in non-small cell lung cancer 🧬🔬🧪
genesdev.cshlp.org/content/earl...
Tutorial 👇 (1/8)
Co-expression of Developmental Pluripotency Associated 2 and 4 (DPPA2/4) is linked with worse survival, in particular for non-small cell lung cancer. So we generated a series of knockdown, over-expression and knockout cell models to understand molecularly why this is (2/8)
We are looking for a new group leader to join the IGH (Montpellier, France). I can’t wait to meet my future colleague! Apply :-) More infos here: igh.cnrs.fr/join-igh-as-...
We;re hiring Junior Group Leaders! 🔬✨
We’re looking for researchers in immunology, chemical biology, AI in biology, or protein design to launch their own independent groups in our collaborative, international environment.
www.nki.nl/news-events/...