Job Dekker

2026 STAT Madness 2026 bracket Welcome to STAT Madness, a bracket-style contest to find the best innovation in science and medicine. Explore groundbreaking innovations from

Time to vote for @umasschan.bsky.social in #STATMadness! The work of Job Dekker, PhD, on the 4D nucleome will help scientists decide how to approach specific research questions. Create an account and click on the UMass Chan logo to vote: https://direc.to/oYD4

@jobdekker.bsky.social @statnews.com

White House stalls release of approved US science budgets The US Congress rejected sweeping cuts to science agencies. But the NIH, the NSF and NASA have had their spending slowed.

Congress rejected massive cuts to US science budgets for 2026, but much of the money still isn’t flowing to researchers.

The culprit? The White House Office of Management and Budget (OMB) is quietly slow-walking the release of funds. 🧵👇

I was sad to learn that my postdoctoral mentor, David Botstein, died yesterday. I started with David as a postdoc in 1998, and he had a profound effect on both my life and scientific career. He was a giant in the field of genetics, making seminal contributions in both yeast and human genetics. 1/

What a great study! Must read!

Vote for #4Dnucleome !

🧵 Thread: What happens when transcription isn’t properly shut off during mitosis? Our new preprint explores just that 👇
www.biorxiv.org/content/10.6...

Please share: we're hiring a new tenure-track faculty member to our Department of Genetics at Albert Einstein College of Medicine.

faculty-einstein.icims.com/jobs/17847/a...

Terrific paper on a new chromosomal
compartment where extensive loop
extrusion isolates domains from
other such domains

excellent thread

This looks very interesting, I will study this in detail!

Seeing into Hi-C: How our scientific connectivity revealed the close connections in our DNA to be a work of art Scientific data can be beautiful. An example where the data itself have a particularly striking appearance even before any scientific meaning has been ascribed

I had the privilege to meet artist Mary Griffiths. Mary got inspired by Hi-C maps and over zooms we spoke about Hi-C maps, patterns and drawings. Mary’s Hi-C inspired art has been exhibited eg the Royal Academy. We wrote this piece about this art-science collaboration

pubs.aip.org/aip/bpr/arti...

Excited to share my PhD work from @riscalab.bsky.social on @biorxivpreprint.bsky.social CAD-C & CADwalks –repair-free, nucleosome-resolution chromosome conformation capture with engineered TEVp-activatable CAD. CADwalks: chromosome walks of ligated CAD footprints. doi.org/10.64898/202...
1/

Preprint alert: Jiangyuan Liu developed a new workflow for chromatin loop calling across Hi-C datasets, e.g., during differentiation. Most loops are shared between datasets/cell states. Important work for all interested in chromatin loops and how to identify them!

www.biorxiv.org/content/10.6...

Sorry but I will attend only virtually! Enjoy the meeting!

4D Nucleome Consortium produces detailed models of the 3D genome over time in cells The 4D Nucleome Consortium has extensively mapped and analyzed the 3-D folding of the human genome in human embryonic stem cells and immortalized fibroblasts over time.

Work by the 4D Nucleome Consortium, led by Job Dekker, PhD, reveals a systematic map of the structure and function of the human: direc.to/ooab

#genome @jobdekker.bsky.social @hhmi-science.bsky.social @nature.com @marionicodemi.bsky.social @creminslab.bsky.social @gladstoneinst.bsky.social

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm Nature Cell Biology - Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through...

Happy to share that my postdoc work with @jobdekker.bsky.social is out!
rdcu.be/eWHD2

We characterize interphase chromatin folding programs with distinct modes of mitotic inheritance and identify the chromosome-intrinsic capacity to form a microcompartment of active CREs during mitotic exit.

I launched my lab at UMass Amherst this fall. We study the mechanisms of meiotic homolog pairing using advanced live‑cell and super‑resolution imaging. Currently in budding yeast, with plans to expand to other eukaryotes. #Chromosome #Meiosis #Mitosis
www.umass.edu/biology/abou...

Unexpected allies: DNA packaging aids gene expression | Cornell Chronicle Researchers discovered that DNA packaging structures called nucleosomes, which have been traditionally seen as roadblocks for gene expression, actually help reduce torsional stress in DNA strands and facilitate genetic information decoding.

When gene expression goes wrong, it can cause abnormal cellular growth, cancer, & more. HHMI Investigator Michelle Wang (Cornell University) & collaborators have discovered that nucleosomes—long thought to be obstacles to gene expression—actually help the process work more smoothly. bit.ly/4q9xA6e

Really interesting paper! Cool approach that may be widely applicable.

Dynamics of microcompartment formation at the mitosis-to-G1 transition - Nature Structural & Molecular Biology Goel et al. produce high-resolution three-dimensional genome structure mapping from mitosis to G1 phase to show unseen interactions between enhancers and promoters in prometaphase. Polymer modeling in...

See this recent paper by @andersshansen.bsky.social that discovers similar microcompartmentalization during mitotic exit:

www.nature.com/articles/s41...

Inheriting chromosome conformation - Nature Cell Biology Chromosomes unfold and refold each time cells divide. A study by Schooley et al. demonstrates that chromosome-intrinsic and cytoplasmic factors uniquely contribute to interphase chromosome structure, ...

And also see this nice News and Views by @kyleeagen.bsky.social

www.nature.com/articles/s41...

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.

Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!

www.nature.com/articles/s41...

4D nucleome The 4D Nucleome (4DN) program, funded by the National Institutes of Health Common Fund, was established in 2015 to map the three-dimensional organization of ...

And for those that want to read even more about the 4D nucleome, Nature has put together this collection of 4DN-funded papers published in their portfolio over the last few years, all Open Access!!!

www.nature.com/collections/...

Systematic maps reveal how human chromosomes are organized Our genomes are highly structured, which facilitates gene regulation. An ambitious project has catalogued the organization of DNA in the nuclei of human cells.

Also nice to see this News&Views by Elzo de Wit @dewitlab.bsky.social

www.nature.com/articles/d41...

An integrated view of the structure and function of the human 4D nucleome - Nature The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!

www.nature.com/articles/s41...

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...

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.

Our study with @stadtfeldlab.bsky.social on the dual mechanism by which EHMT2 is repressing totipotency-associated vs lineage-specific loci is now out @emboreports.org. See thread by @cmuyehara.bsky.social who led the study with K Chatterjee. Full article here link.springer.com/article/10.1...

Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons We have investigated changes in chromosome conformation, nuclear organization, and transcription during differentiation and maturation of control and mutant motor neurons harboring hexanucleotide expa...

New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan.
www.biorxiv.org/content/10.1...

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...

New preprint with @gfudenberg.bsky.social

We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.

This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇

www.biorxiv.org/content/10.1...

RNA Pol II inhibition activates cell death independently from the loss of transcription When RNA polymerase II (RNA Pol II) is inhibited, the inhibition is sensed and signaled to mitochondria, leading to programmed cell death independently of the loss of RNA Pol II transcription activity...

I’m excited to highlight our latest paper, just published in Cell 🎉

We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.

1/n 🧪

www.cell.com/cell/fulltex...