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
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!
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!