Ranjith Padinhateeri
@ranjithpa.bsky.social
Professor IIT Bombay, Mumbai, India. Physics & Biology. Chromatin. Self-assembly. https://www.bio.iitb.ac.in/~ranjith/
Reposted by Ranjith Padinhateeri
Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...
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...
www.science.org
October 2, 2025 at 10:55 PM
Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
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!
October 17, 2025 at 3:36 PM
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!
Reposted by Ranjith Padinhateeri
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 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...
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...
Reposted by Ranjith Padinhateeri
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
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...
www.biorxiv.org
September 3, 2025 at 4:20 PM
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
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
Reposted by Ranjith Padinhateeri
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
August 16, 2025 at 3:03 AM
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...
Excellent work by my colleague Anirban Banerjee and team
🚨“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...
@natmicrobiol.nature.com
www.nature.com/articles/s41...
April 13, 2025 at 1:01 AM
Excellent work by my colleague Anirban Banerjee and team
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!).
April 1, 2025 at 2:13 AM
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!).
Reposted by Ranjith Padinhateeri
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...
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…
www.sciencedirect.com
February 26, 2025 at 9:22 PM
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...
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Reposted by Ranjith Padinhateeri
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)
January 24, 2025 at 1:04 AM
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)
Reposted by Ranjith Padinhateeri
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 ...
www.biorxiv.org
January 24, 2025 at 1:04 AM
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...
Reposted by Ranjith Padinhateeri
Had a wonderful time discussing chromatin when some friends visited IIT Bombay, Mumbai! @vram142.bsky.social @dimplenotani.bsky.social @kaushikr.bsky.social
January 9, 2025 at 3:29 PM
Had a wonderful time discussing chromatin when some friends visited IIT Bombay, Mumbai! @vram142.bsky.social @dimplenotani.bsky.social @kaushikr.bsky.social
Reposted by Ranjith Padinhateeri
The Hooghly river drains into the Bay of Bengal. Just an absolutely gorgeous view of waters that nourish eastern India
December 31, 2024 at 7:15 AM
The Hooghly river drains into the Bay of Bengal. Just an absolutely gorgeous view of waters that nourish eastern India
Reposted by Ranjith Padinhateeri
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…
www.sciencedirect.com
December 27, 2024 at 9:00 PM
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!
Reposted by Ranjith Padinhateeri
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.
www.nytimes.com
December 12, 2024 at 6:57 PM
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.
Reposted by Ranjith Padinhateeri
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!
www.nature.com/articles/s41...
www.science.org/doi/10.1126/...
Interested? Please DM me!
November 30, 2024 at 12:32 PM
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!
www.nature.com/articles/s41...
www.science.org/doi/10.1126/...
Interested? Please DM me!
Reposted by Ranjith Padinhateeri
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
November 29, 2024 at 8:56 PM
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
Reposted by Ranjith Padinhateeri
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...
www.cell.com
November 15, 2024 at 3:35 PM
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
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!)
January 13, 2024 at 3:15 PM
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.
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...
www.nature.com
December 15, 2023 at 5:29 AM
"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.
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...
December 14, 2023 at 12:53 AM
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.
November 22, 2023 at 2:10 AM
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!
November 14, 2023 at 3:37 AM
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!