Job Dekker
@jobdekker.bsky.social
Biologist. Chromosomes | dinoflagellates | birds. Happy in academia! Umass Chan Medical School, HHMI
http://www.dekkerlab.org
http://www.dekkerlab.org
Reposted by Job Dekker
The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.
October 23, 2025 at 5:10 PM
The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.
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...
www.biorxiv.org/content/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...
www.biorxiv.org
September 23, 2025 at 9:13 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Job Dekker
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...
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...
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 ...
www.biorxiv.org
August 16, 2025 at 3:03 AM
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...
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...
Reposted by Job Dekker
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...
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...
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...
www.cell.com
August 15, 2025 at 6:35 PM
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...
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...
Very important work! Congratulations @nvictus.bsky.social and Thomas!
We're excited to share our new preprint, "Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development", led by Thomas Reimonn. www.biorxiv.org/content/10.1...
Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development
The spatial organization of chromosomes in the nucleus is fundamental to cellular processes. Contact frequency maps from Hi-C and related chromosome conformation capture assays are increasingly availa...
www.biorxiv.org
August 11, 2025 at 9:09 PM
Very important work! Congratulations @nvictus.bsky.social and Thomas!
Reposted by Job Dekker
Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions https://www.biorxiv.org/content/10.1101/2025.07.29.667515v1
August 1, 2025 at 8:33 PM
Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions https://www.biorxiv.org/content/10.1101/2025.07.29.667515v1
Reposted by Job Dekker
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
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www.biorxiv.org/content/10.1...
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July 15, 2025 at 8:11 AM
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/
www.biorxiv.org/content/10.1...
1/
Reposted by Job Dekker
The evolution of high-order genome architecture revealed from 1,000 species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/xjtu-omics/H...
July 8, 2025 at 6:31 PM
The evolution of high-order genome architecture revealed from 1,000 species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/xjtu-omics/H...
Reposted by Job Dekker
🧬 @science.org Rules of engagement for condensins and cohesins guide mitotic chromosome formation | Science www.science.org/doi/10.1126/...
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
April 14, 2025 at 5:40 AM
🧬 @science.org Rules of engagement for condensins and cohesins guide mitotic chromosome formation | Science www.science.org/doi/10.1126/...
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
Excited to share our latest work on how cells fold their genomes, and build mitotic chromosomes! Out in Science today!
Lots of interesting results and proposals for those interested in loop extrusion, and chromosomes!
With @golobor.bsky.social, Leonid Mirny, Bill Earnshaw labs.
See thread below:
Lots of interesting results and proposals for those interested in loop extrusion, and chromosomes!
With @golobor.bsky.social, Leonid Mirny, Bill Earnshaw labs.
See thread below:
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Rules of Engagement
YouTube video by Johan Gibcus
www.youtube.com
April 11, 2025 at 4:06 PM
Excited to share our latest work on how cells fold their genomes, and build mitotic chromosomes! Out in Science today!
Lots of interesting results and proposals for those interested in loop extrusion, and chromosomes!
With @golobor.bsky.social, Leonid Mirny, Bill Earnshaw labs.
See thread below:
Lots of interesting results and proposals for those interested in loop extrusion, and chromosomes!
With @golobor.bsky.social, Leonid Mirny, Bill Earnshaw labs.
See thread below:
Reposted by Job Dekker
Job Dekker, PhD, and colleagues identify simple rules for genome folding during mitosis: direc.to/naBG
Rules of engagement for chromosome folding machines define how cells organize genomes. Understanding how cells achieve mitosis may provide insights into genetic mutations. #ScienceSky
Rules of engagement for chromosome folding machines define how cells organize genomes. Understanding how cells achieve mitosis may provide insights into genetic mutations. #ScienceSky
UMass Chan scientist co-leads study identifying simple rules for folding the genome
UMass Chan Medical School scientists detail simple rules for folding the genome during mitosis
direc.to
April 11, 2025 at 12:44 PM
Job Dekker, PhD, and colleagues identify simple rules for genome folding during mitosis: direc.to/naBG
Rules of engagement for chromosome folding machines define how cells organize genomes. Understanding how cells achieve mitosis may provide insights into genetic mutations. #ScienceSky
Rules of engagement for chromosome folding machines define how cells organize genomes. Understanding how cells achieve mitosis may provide insights into genetic mutations. #ScienceSky
Nice work! Go TADs!
In this study, Huang et al. demonstrate how a single enhancer independently controls the expression of two distal and functionally unrelated genes.
Learn more here:
➡️ tinyurl.com/gd352235
Learn more here:
➡️ tinyurl.com/gd352235
March 14, 2025 at 3:21 PM
Nice work! Go TADs!
Reposted by Job Dekker
Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…
www.sciencedirect.com
February 26, 2025 at 9:22 PM
Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Fantastic work! Congratulations!
Two papers out in Nature today! Super exciting work by an amazingly talented team - Hefei Zhang and Xuhang Li. Proud and thrilled to see these out.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A systems-level, semi-quantitative landscape of metabolic flux in C. elegans - Nature
A strategy is introduced that infers whole-animal metabolic flux wiring from transcriptional phenotypes in the nematode Caenorhabditis elegans and several features in its adult metabolism are discover...
www.nature.com
February 26, 2025 at 11:32 PM
Fantastic work! Congratulations!
Reposted by Job Dekker
Important paper showing that acetylation of trans-acting factors rather than histones controls transcriptional bursting dynamics www.cell.com/molecular-ce...
www.cell.com
February 25, 2025 at 11:53 AM
Important paper showing that acetylation of trans-acting factors rather than histones controls transcriptional bursting dynamics www.cell.com/molecular-ce...
Reposted by Job Dekker
A must read for any (systems) biologist!
www.cell.com/cell-systems...
www.cell.com/cell-systems...
Should biology put complexity first?
The dictum “Everything should be made as simple as possible, but no simpler” poses
a problem for biology. How simply can it be told without doing damage to its complex
nature? The answer might be foun...
www.cell.com
February 20, 2025 at 1:42 PM
A must read for any (systems) biologist!
www.cell.com/cell-systems...
www.cell.com/cell-systems...
Reposted by Job Dekker
Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
February 20, 2025 at 11:15 AM
Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
Reposted by Job Dekker
Excited to share our work on archaeal 3D genome! This paper revealed how an archaeal SMC complex sculpts TAD-like domains by cooperating with a roadblock NAP and physical properties of DNA. Many congrats to our talented PhD student Kodai!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure - Nature Communications
Eukaryotic chromosomes are organized into arrays of compact domain structures called TADs. Here the authors show that a member of the Archaea, the prokaryotic domain closest to the Eukarya, uses a euk...
www.nature.com
February 19, 2025 at 12:20 PM
Excited to share our work on archaeal 3D genome! This paper revealed how an archaeal SMC complex sculpts TAD-like domains by cooperating with a roadblock NAP and physical properties of DNA. Many congrats to our talented PhD student Kodai!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Go TADs!
Very nice and elegant study showing enhancer-promoter connectivity within TADs
genesdev.cshlp.org/content/earl...
Very nice and elegant study showing enhancer-promoter connectivity within TADs
genesdev.cshlp.org/content/earl...
Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
genesdev.cshlp.org
January 29, 2025 at 11:54 AM
Go TADs!
Very nice and elegant study showing enhancer-promoter connectivity within TADs
genesdev.cshlp.org/content/earl...
Very nice and elegant study showing enhancer-promoter connectivity within TADs
genesdev.cshlp.org/content/earl...
Fabulous study! Congratulations!
Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵
A short thread to highlight some of our findings 🧵
January 20, 2025 at 9:22 PM
Fabulous study! Congratulations!
Reposted by Job Dekker
New discovery from our #CDlab reported in Cell @cp-cell.bsky.social today:
SMC motor proteins have a left-right ‘gearbox’ and can switch direction in DNA loop extrusion!
www.sciencedirect.com/science/arti...
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SMC motor proteins have a left-right ‘gearbox’ and can switch direction in DNA loop extrusion!
www.sciencedirect.com/science/arti...
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January 16, 2025 at 4:11 PM
New discovery from our #CDlab reported in Cell @cp-cell.bsky.social today:
SMC motor proteins have a left-right ‘gearbox’ and can switch direction in DNA loop extrusion!
www.sciencedirect.com/science/arti...
1/
SMC motor proteins have a left-right ‘gearbox’ and can switch direction in DNA loop extrusion!
www.sciencedirect.com/science/arti...
1/
Reposted by Job Dekker
Mandatory curriculum for any graduate student or post-doc 😆
www.youtube.com/shorts/vavfB...
www.youtube.com/shorts/vavfB...
#воронгоша #raven #ravengosha #animal #ravenbird #birds #nature
YouTube video by Ворон TV
www.youtube.com
January 9, 2025 at 11:30 PM
Mandatory curriculum for any graduate student or post-doc 😆
www.youtube.com/shorts/vavfB...
www.youtube.com/shorts/vavfB...