Pinned
Ed Banigan
@irate-physicist.bsky.social
· Dec 15
Our (Viraat Goel, @andersshansen.bsky.social et al) paper Dynamics of microcompartment formation during the M-to-G1 transition is in this month's @natsmb.nature.com -- thanks to NSMB editors and staff for the cover space and art! www.nature.com/nsmb/volumes...
See quoted posts for quick summary
See quoted posts for quick summary
Reposted by Ed Banigan
Check out the News & Views by @kyleeagen.bsky.social : 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, ...
www.nature.com
December 29, 2025 at 1:05 PM
Check out the News & Views by @kyleeagen.bsky.social : www.nature.com/articles/s41...
Reposted by Ed Banigan
We co-submitted this article with the work of @andersshansen.bsky.social , @irate-physicist.bsky.social , and authors, who characterize similar cre microcompartments : rdcu.be/eWK1u
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...
rdcu.be
December 29, 2025 at 1:05 PM
We co-submitted this article with the work of @andersshansen.bsky.social , @irate-physicist.bsky.social , and authors, who characterize similar cre microcompartments : rdcu.be/eWK1u
Reposted by Ed Banigan
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.
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.
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...
rdcu.be
December 29, 2025 at 12:39 PM
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.
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.
Reposted by Ed Banigan
🚨Our work on the impact of DNA replication on 3D genome is out in Genome Biology: replication-dependent loop extrusion by sister-forks, wave of replication, no evidence for large-scale replication factory. Great collab with @aurelepiazza.bsky.social. More here: link.springer.com/article/10.1...
December 23, 2025 at 1:04 PM
🚨Our work on the impact of DNA replication on 3D genome is out in Genome Biology: replication-dependent loop extrusion by sister-forks, wave of replication, no evidence for large-scale replication factory. Great collab with @aurelepiazza.bsky.social. More here: link.springer.com/article/10.1...
Reposted by Ed Banigan
Excited to share a News & Views highlighting a new, excellent paper from @jobdekker.bsky.social and @allanaschooley.bsky.social!
www.nature.com/articles/s41...
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, with new possibilities for how gene expression programs are passed from mother cells to daughter cells.
www.nature.com
December 23, 2025 at 2:51 AM
Excited to share a News & Views highlighting a new, excellent paper from @jobdekker.bsky.social and @allanaschooley.bsky.social!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ed Banigan
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...
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.
www.nature.com
December 22, 2025 at 11:45 AM
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...
www.nature.com/articles/s41...
Reposted by Ed Banigan
New publication from our lab! Can semiflexible polymers (lamin fibers, dsDNA, actin, etc) alter the shape of elastic shells or lipid vesicles? Indeed, the nematic/random ordering of these polymers on the surface could tune their shapes.
Read more on: pubs.rsc.org/en/content/a...
Read more on: pubs.rsc.org/en/content/a...
pubs.rsc.org
December 16, 2025 at 2:02 PM
New publication from our lab! Can semiflexible polymers (lamin fibers, dsDNA, actin, etc) alter the shape of elastic shells or lipid vesicles? Indeed, the nematic/random ordering of these polymers on the surface could tune their shapes.
Read more on: pubs.rsc.org/en/content/a...
Read more on: pubs.rsc.org/en/content/a...
Our (Viraat Goel, @andersshansen.bsky.social et al) paper Dynamics of microcompartment formation during the M-to-G1 transition is in this month's @natsmb.nature.com -- thanks to NSMB editors and staff for the cover space and art! www.nature.com/nsmb/volumes...
See quoted posts for quick summary
See quoted posts for quick summary
December 15, 2025 at 3:02 PM
Our (Viraat Goel, @andersshansen.bsky.social et al) paper Dynamics of microcompartment formation during the M-to-G1 transition is in this month's @natsmb.nature.com -- thanks to NSMB editors and staff for the cover space and art! www.nature.com/nsmb/volumes...
See quoted posts for quick summary
See quoted posts for quick summary
Reposted by Ed Banigan
Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Cohesin drives chromatin scanning during the RAD51-mediated homology search
Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...
www.science.org
December 4, 2025 at 9:50 PM
Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Ed Banigan
Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41...
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
October 20, 2025 at 6:36 PM
Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41...
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
Reposted by Ed Banigan
Very happy that this insightful story by @andersshansen.bsky.social is out @natsmb.nature.com, www.nature.com/articles/s41.... A nice press release explaining the progress also from the home institute @mitdeptofbe.bsky.social here: news.mit.edu/2025/surpris...
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...
www.nature.com
October 20, 2025 at 9:30 AM
Very happy that this insightful story by @andersshansen.bsky.social is out @natsmb.nature.com, www.nature.com/articles/s41.... A nice press release explaining the progress also from the home institute @mitdeptofbe.bsky.social here: news.mit.edu/2025/surpris...
Reposted by Ed Banigan
ICYMI: New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
Dynamics of microcompartment formation at the mitosis-to-G1 transition
Nature Structural & Molecular Biology, Published online: 17 October 2025; doi:10.1038/s41594-025-01687-2Goel 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 indicates the interactions are facilitated by chromosome compaction.
go.nature.com
October 18, 2025 at 10:00 AM
ICYMI: New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
Reposted by Ed Banigan
The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
Characterization of induced cohesin loop extrusion trajectories in living cells
Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...
rdcu.be
October 16, 2025 at 8:17 PM
The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
Previous experiments observed a transient spike in transcription of a subset of genes during ana/telophase. We now observe that these spiking genes are associated with microcompartments that peak in interactions during ana/telo, suggesting a 3D-genome-based mechanism for this transcriptional spike!
October 17, 2025 at 2:58 PM
Previous experiments observed a transient spike in transcription of a subset of genes during ana/telophase. We now observe that these spiking genes are associated with microcompartments that peak in interactions during ana/telo, suggesting a 3D-genome-based mechanism for this transcriptional spike!
Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in @natsmb.nature.com www.nature.com/articles/s41...
Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking
Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking
October 17, 2025 at 2:58 PM
Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in @natsmb.nature.com www.nature.com/articles/s41...
Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking
Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking
Reposted by Ed Banigan
New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
Dynamics of microcompartment formation at the mitosis-to-G1 transition
Nature Structural & Molecular Biology, Published online: 17 October 2025; doi:10.1038/s41594-025-01687-2Goel 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 indicates the interactions are facilitated by chromosome compaction.
go.nature.com
October 17, 2025 at 9:59 AM
New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
thanks! reading your paper (I see now accepted, congrats) really inspired the approach that made sense of the physics for me
October 1, 2025 at 2:20 PM
thanks! reading your paper (I see now accepted, congrats) really inspired the approach that made sense of the physics for me
I didn’t really complete the thought earlier: these papers point toward some of the key principles governing compartmentalization-extrusion interplay and are definitely worth reading!
September 3, 2025 at 7:48 PM
I didn’t really complete the thought earlier: these papers point toward some of the key principles governing compartmentalization-extrusion interplay and are definitely worth reading!
Postscript: for a long time I was very confused about the PDS5-WAPL depletion expts+sims & how extrusion alters compartments. I was fortunate to eventually stumble across @ranjithpa.bsky.social's preprint www.biorxiv.org/content/10.1... & later this by Chan/Rubinstein www.pnas.org/doi/abs/10.1...
September 3, 2025 at 4:23 PM
Postscript: for a long time I was very confused about the PDS5-WAPL depletion expts+sims & how extrusion alters compartments. I was fortunate to eventually stumble across @ranjithpa.bsky.social's preprint www.biorxiv.org/content/10.1... & later this by Chan/Rubinstein www.pnas.org/doi/abs/10.1...
I also want to point out another interesting and relevant recent preprint by @elphegenoralab.bsky.social and @gfudenberg.bsky.social
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
September 3, 2025 at 4:22 PM
I also want to point out another interesting and relevant recent preprint by @elphegenoralab.bsky.social and @gfudenberg.bsky.social
Thanks to our other co-authors who had essential contributions: Ryotaro Kawasumi, Roman Stocsits, Wen Tang, Kota Nagasaka, Lorenzo Costantino, Ralf Jansen, Kouji Hirota, Dana Branzei
September 3, 2025 at 4:21 PM
Thanks to our other co-authors who had essential contributions: Ryotaro Kawasumi, Roman Stocsits, Wen Tang, Kota Nagasaka, Lorenzo Costantino, Ralf Jansen, Kouji Hirota, Dana Branzei
Summary
-PDS5 facilitates NIPBL dissociation from cohesin by invading NIPBL binding site
-PDS5 strengthns CTCF boundaries by limiting NIPBL-cohesin life
-PDS5 lowers avg extrusion speed/depletion ups processivity
-Compartmentalization governed by competition of extrusion &polymer relaxation dynamics
-PDS5 facilitates NIPBL dissociation from cohesin by invading NIPBL binding site
-PDS5 strengthns CTCF boundaries by limiting NIPBL-cohesin life
-PDS5 lowers avg extrusion speed/depletion ups processivity
-Compartmentalization governed by competition of extrusion &polymer relaxation dynamics
September 3, 2025 at 4:20 PM
Summary
-PDS5 facilitates NIPBL dissociation from cohesin by invading NIPBL binding site
-PDS5 strengthns CTCF boundaries by limiting NIPBL-cohesin life
-PDS5 lowers avg extrusion speed/depletion ups processivity
-Compartmentalization governed by competition of extrusion &polymer relaxation dynamics
-PDS5 facilitates NIPBL dissociation from cohesin by invading NIPBL binding site
-PDS5 strengthns CTCF boundaries by limiting NIPBL-cohesin life
-PDS5 lowers avg extrusion speed/depletion ups processivity
-Compartmentalization governed by competition of extrusion &polymer relaxation dynamics
Can PDS5 therefore strengthen CTCF boundaries by limiting NIPBL-cohesin processivity (=speed x residence time)?
Hi-C in cells depleted of PDS5 & now partially of NIPBL recover some of CTCF boundaries (+ also compartments)
Hi-C in cells depleted of PDS5 & now partially of NIPBL recover some of CTCF boundaries (+ also compartments)
September 3, 2025 at 4:20 PM
Can PDS5 therefore strengthen CTCF boundaries by limiting NIPBL-cohesin processivity (=speed x residence time)?
Hi-C in cells depleted of PDS5 & now partially of NIPBL recover some of CTCF boundaries (+ also compartments)
Hi-C in cells depleted of PDS5 & now partially of NIPBL recover some of CTCF boundaries (+ also compartments)
To understand this Iain did 3-color single-molecule expts w/loop-extruding NIPBL-cohesin.
PDS5+NIPBL could colocalize on cohesin leading to NIPBL unbinding! Loops often released but sometimes shrunk & NIPBL returned.
So PDS5 slows loop growth + speeds NIPBL unbinding by facilitated dissociation!
PDS5+NIPBL could colocalize on cohesin leading to NIPBL unbinding! Loops often released but sometimes shrunk & NIPBL returned.
So PDS5 slows loop growth + speeds NIPBL unbinding by facilitated dissociation!
September 3, 2025 at 4:20 PM
To understand this Iain did 3-color single-molecule expts w/loop-extruding NIPBL-cohesin.
PDS5+NIPBL could colocalize on cohesin leading to NIPBL unbinding! Loops often released but sometimes shrunk & NIPBL returned.
So PDS5 slows loop growth + speeds NIPBL unbinding by facilitated dissociation!
PDS5+NIPBL could colocalize on cohesin leading to NIPBL unbinding! Loops often released but sometimes shrunk & NIPBL returned.
So PDS5 slows loop growth + speeds NIPBL unbinding by facilitated dissociation!