Professor IIT Bombay, Mumbai, India. Physics & Biology. Chromatin. Self-assembly. https://www.bio.iitb.ac.in/~ranjith/
Ranjith Padinhateeri
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Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...
An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...
Sharing our recent review with @ranjithpa.bsky.social on polymer models of chromatin
Polymer simulations of chromatin: connecting 3D organization and dynamics to function 👇
www.sciencedirect.com/science/arti...
🧵 (1/6)
#Chromatin #GenomeArchitecture #PolymerPhysics #ComputationalBiology
Exited to share Current Opinion review on how chromatin hubs involving multiple enhancers and promoters are formed, and their potential roles in gene regulation: www.sciencedirect.com/science/arti...
Our work on the interplay between loop extrusion and chromatin mechanics is finally out in @physrevresearch.bsky.social . Congrats @hosseinsalari.bsky.social for the hard work ! 👏
journals.aps.org/prresearch/a...
Our new preprint: Chromatin at ~10–100 kb scales behaves very differently from standard polymer expectations. DNA-PAINT data reveal broad fluctuations and sharp local bends. Our study suggests emergent active forces at these scales and quantifies the nature and strength of this activity
How does 3D chromatin organization affect translocations? Our work shows that translocation probability depends not just on local contact probability, but also on global chromatin compaction. Cool work by Anirudh (then an MTech student at IIT Bombay) with @shuvadipdutta.bsky.social et al.
We propose an active model for the coarse-grained chromatin polymer. The interplay of activity and elasticity determines chromatin properties. While fitting the data consistently with known chromatin features, many interesting details emerge. Read: www.biorxiv.org/content/10.6...
Folded chromatin stochastically extends far beyond even a random self-avoiding polymer, as if many internal interactions collectively break. It also bends with unusually acute local angles. How can this be explained consistently with the known nature of chromatin at 10nm scale?
Happy to share our Current Opinion review on the key challenges in accurately predicting 3D distances between chromatin segments and computing their dynamics. Thanks to @djost-physbiol.bsky.social @lucagiorgetti.bsky.social for the invitation to write this review! @shuvadipdutta.bsky.social
📖 The final version of our paper is out in press
Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption
authors.elsevier.com/a/1m%7EU03vV...
or www.cell.com/molecular-ce...
Chromosomes are complex biopolymers folded into dynamic loops via a loop-extrusion process and may experience various mechanical forces in vivo. We develop a force-dependent model of chromatin loop ex...
Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion
by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative
mechanistic basis for the gene...
New preprint from the lab !! Loop extrusion may provide mechanical robustness to chromatin. Great work by Hossein Salari. @cnrs.fr @lbmcinlyon.bsky.social
www.biorxiv.org/content/10.1...
Elphege Nora Lab at UCSF
Chromosomes are complex biopolymers folded into dynamic loops via a loop extrusion process and may experience various mechanical forces in vivo . We develop a force-dependent model of chromatin loop e...
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...
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 ...
