Ranjith Padinhateeri

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...

Congratulations Ed @irate-physicist.bsky.social on your new work. Look forward to reading it in detail. I missed this thread as I was away from social media for a few days!! Thank you for the comment -- let’s catch up sometime.

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...

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

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 ...

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...

Excellent work by my colleague Anirban Banerjee and team

The Big temple at Thanjavur, built around ~1000 CE.

500-year-old library at Thanjavur

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!).

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…

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...

logo for the IDLI method (Iteratively Defined Lengths of Inaccessibility)

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)

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 ...

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...

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.

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

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

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…

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!

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.

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.

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!

Are you in Mumbai?

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

Congratulations Vijay, Megan @martyyang.bsky.social and everyone in the team!

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...

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

Cool! Look forward to reading it. Congratulations Ed, Anders and the entire team.

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 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...

"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.

Talk by Rosana today. 5 pm IST sites.google.com/view/mbu-inf...

I found this Perplexity tool very good www.perplexity.ai . Better than Google because it's search+AI. Better than Chat GPT because it cites the source from where it gets information and is real-time. Unlike chat GPT, it doesn't cook up ("generate") stuff! It's reliable for factual queries.

For a dynamical system/network person, it would be fun to study the Twitter to Bluesky switching data! It will have interesting features of connectivity, collective effects, and all that!