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...

Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature

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...

nature.com

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

📖 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...

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

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...

cell.com

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 12mo ago

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...

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...

Daniel Jost - Physical Biology of Chromatin group@djost-physbiol.bsky.social · 10mo ago

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...

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

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.

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...

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

Glad to share our latest work that came out recently. We dive into the mechanisms of how Transcription Factors (TFs) like the nuclear receptor, ERα navigate the genome to find their targets.

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization. www.science.org/doi/10.1126/...

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

science.org

The lab is in a celebratory mood as we head into the Diwali weekend🪔. Wishing everyone a bright, joyful, and prosperous Diwali!🌟. Kudos to Sai, Siddharth, Sriya, Surabhi and team for making this beautiful rangoli!

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

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...

nature.com

Ed Banigan@irate-physicist.bsky.social · 2y ago

been lurking here a while but time to spend less time in the bad place Here's my latest work in collab w/ Viraat Goel, @andersshansen.bsky.social, Leonid Mirny, Nick Aboreden, Gerd Blobel et al. Dynamics of microcompartment formation at the mitosis-to-G1 transition www.biorxiv.org/content/10.1...

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...

Excited to share our preprint w/Gordana Wutz, Iain Davidson, Leonid Mirny, Jan-Michael Peters www.biorxiv.org/content/10.1... Evidence that PDS5A/B limits NIPBL-cohesin life w/effects on CTCF boundaries & chrm compartments, +mechanisms of compartment-extrusion interplay & cohesin regulation by PDS5

PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes

Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heter...

biorxiv.org

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...

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 ...

biorxiv.org

Excellent work by my colleague Anirban Banerjee and team

@anirban-banerjee.bsky.social · last yr.

🚨“Ripping bacteria to shreds” 🚨 VCP/p97, a cellular AAA-ATPase, targets and then using its tweezer like action rips apart bacteria, protecting us from infections. A thread 🦠💥#MolecularMachines #HostDefense #cellularimmunity #microbiology @natmicrobiol.nature.com www.nature.com/articles/s41...

Was at Thanjavur this weekend. Visited the Big Temple, which is one of the most amazing historical structures in the world (1,000 years old), and the oldest library I have ever seen (~500 years old). It houses millennia-old manuscripts (many of them probably still unread!).

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...

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…

sciencedirect.com

We’ve hoped (suspected?) that nondestructive chromatin fiber mapping (pioneered by us & others) captures structural aspects missed by nuclease-based techniques. Here, we keep the tiffin cart rolling w/ IDLI: an approach that infers subnuc-res structure from m6dA long-read footprinting data. (3/n)

Amid concerning times, sharing a bit of positivity: our 1st preprint of 2025 (funded VIA NIH COMMON FUND), heroically led by Marty Yang (@martyyang.bsky.social) w/ huge assist from @genophoria.bsky.social lab. Lots to cover so let’s get this tweetorial started (1/n)! www.biorxiv.org/content/10.1...

Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers

We present a genome-scale method to map the single-molecule co-occupancy of structurally distinct nucleosomes, subnucleosomes, and other protein-DNA interactions via long-read high-resolution adenine ...

biorxiv.org

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

Martin Karplus obituary: theoretical chemist who first simulated proteins using molecular dynamics

The Nobel prizewinner used quantum and molecular mechanics to model the dynamics of complex chemical systems.

nature.com

Had a wonderful time discussing chromatin when some friends visited IIT Bombay, Mumbai! @vram142.bsky.social @dimplenotani.bsky.social @kaushikr.bsky.social

The Hooghly river drains into the Bay of Bengal. Just an absolutely gorgeous view of waters that nourish eastern India

Closing 2024 with a review! Excited to share the latest (short) review from our lab, written by amazing Ramani/Narlikar lab grad student Aaron Corin in collaboration with @elphegenoralab.bsky.social! We focus on CTCF's myriad functions beyond regulating loop extrusion; tons to dig into!

Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion

CCCTC-binding factor (CTCF) is a key regulator of 3D genome organization and transcriptional activity. Beyond its well-characterized role in facilitat…

sciencedirect.com

Dommaraju Gukesh, an 18-year-old Indian grandmaster, won the World Chess Championship in Singapore on Thursday. In so doing, Gukesh became the 18th and youngest undisputed world champion in history.

Dommaraju Gukesh, 18, Becomes Youngest World Chess Champion

It had been an unexpectedly close contest in Singapore with Ding Liren. When he won, the normally stoic Gukesh clasped his hands at the board and burst into tears.

nytimes.com

We are seeking a motivated postdoc to join our lab!  Our research focuses on live-cell imaging/analysis to reveal how chromatin behaves in living cells and how its behavior contributes to cellular functions. www.nature.com/articles/s41... www.science.org/doi/10.1126/... Interested? Please DM me!

As a chemical engg student interested in biology, I couldn’t attend any mol biol class. So Prof KK Rao taught me the entire class, meeting for hours AFTER he’d already taught the class. FOR 2 ENTIRE SEMESTERS! Then wrote me a letter that got me into grad school #scienceoriginstory #Thanksgiving

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

The single-molecule accessibility landscape of newly replicated mammalian chromatin

By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

cell.com

Prof. Muthukumar(UMass Amherst) working out every bit of the phase separation theory of polymers in a workshop we organized at IIT Bombay, Mumbai, India. Can't remember the last time when Biologists were so curious to understand an equation (here the Flory-Huggins theory for phase separation!)

"How high-impact papers from Indian researchers are shaping science". www.nature.com/articles/d41... One of these from my colleague Samir Maji's lab at IIT Bombay, Mumbai. Samir has pioneered work on aggregation & phase separation of proteins associated with neurodegenerative diseases.

How high-impact papers from Indian researchers are shaping science

Studies to tackle air quality in Delhi and solve the mystery of an emerging pathogen are among those helping to raise the profile of Indian science. Studies to tackle air quality in Delhi and solve th...

nature.com