Kaushik Ragunathan
@kaushikr.bsky.social
Brandeis Biology, Asst Prof,epigenetic inheritance,protein QC, learning to cope with uncertainty, hoping good coffee helps, thinking about poetry and those who do not have the permission to narrate.he/him http://www.ragunathanlab.org
Reposted by Kaushik Ragunathan
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
November 27, 2025 at 1:17 PM
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
Reposted by Kaushik Ragunathan
Please reshare, repost- Summer research opportunities in the NIH Intramural Research Program for currently enrolled undergraduates or High School Seniors who are U.S. citizen or permanent residents. You can choose one of the ~1100 labs. Keep an eye here -
www.training.nih.gov/research-tra...
www.training.nih.gov/research-tra...
www.training.nih.gov
November 27, 2025 at 12:11 PM
Please reshare, repost- Summer research opportunities in the NIH Intramural Research Program for currently enrolled undergraduates or High School Seniors who are U.S. citizen or permanent residents. You can choose one of the ~1100 labs. Keep an eye here -
www.training.nih.gov/research-tra...
www.training.nih.gov/research-tra...
Reposted by Kaushik Ragunathan
Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
October 17, 2025 at 12:47 PM
Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Reposted by Kaushik Ragunathan
Wonderful opportunity to work with Martin Howard and my group trying to understand how chromatin influences gene transcription and expression. Integration of theory, modelling, and experimentation. Come and join the team!
Please repost!
jobs.jic.ac.uk/Details.asp?...
Please repost!
jobs.jic.ac.uk/Details.asp?...
John Innes Centre
jobs.jic.ac.uk
October 8, 2025 at 9:04 AM
Wonderful opportunity to work with Martin Howard and my group trying to understand how chromatin influences gene transcription and expression. Integration of theory, modelling, and experimentation. Come and join the team!
Please repost!
jobs.jic.ac.uk/Details.asp?...
Please repost!
jobs.jic.ac.uk/Details.asp?...
Reposted by Kaushik Ragunathan
Super excited that this story by @borissieber.bsky.social is now on BioRxiv!
For decades, we thought there was no MAPK scaffold for the ERK-like cascade that promotes sexual reproduction in fission yeast ... until Boris found it !
See the thread 👇 and enjoy the paper!
doi.org/10.1101/2025...
For decades, we thought there was no MAPK scaffold for the ERK-like cascade that promotes sexual reproduction in fission yeast ... until Boris found it !
See the thread 👇 and enjoy the paper!
doi.org/10.1101/2025...
Mammalian cells have KSR, budding yeast has Ste5… and fission yeast has Sms1 as the MAPK scaffold for sexual reproduction!
Very excited to share my postdoc work where we discover that the hemi-arrestin Sms1 binds all components of the MAPK cascade, including ERK-like Spk1
doi.org/10.1101/2025...
Very excited to share my postdoc work where we discover that the hemi-arrestin Sms1 binds all components of the MAPK cascade, including ERK-like Spk1
doi.org/10.1101/2025...
September 25, 2025 at 7:48 PM
Super excited that this story by @borissieber.bsky.social is now on BioRxiv!
For decades, we thought there was no MAPK scaffold for the ERK-like cascade that promotes sexual reproduction in fission yeast ... until Boris found it !
See the thread 👇 and enjoy the paper!
doi.org/10.1101/2025...
For decades, we thought there was no MAPK scaffold for the ERK-like cascade that promotes sexual reproduction in fission yeast ... until Boris found it !
See the thread 👇 and enjoy the paper!
doi.org/10.1101/2025...
Reposted by Kaushik Ragunathan
This may be the most important paper ever published about NIH funded research.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
What if NIH had been 40% smaller?
Replaying history with less NIH funding shows widespread impacts on drug-linked research
www.science.org
September 25, 2025 at 9:20 PM
This may be the most important paper ever published about NIH funded research.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Kaushik Ragunathan
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
www.biorxiv.org
September 20, 2025 at 4:10 PM
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
Reposted by Kaushik Ragunathan
(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
May 7, 2025 at 8:53 PM
(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
Some truth telling
April 25, 2025 at 9:35 PM
Some truth telling
Reposted by Kaushik Ragunathan
Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...
Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase
Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide...
www.biorxiv.org
March 26, 2025 at 10:13 PM
Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...
Reposted by Kaushik Ragunathan
𝐍𝐞𝐰 𝐦𝐞𝐜𝐡𝐚𝐧𝐢𝐬𝐭𝐢𝐜 𝐢𝐧𝐬𝐢𝐠𝐡𝐭𝐬 𝐢𝐧𝐭𝐨 𝐭𝐡𝐞 𝐫𝐞𝐠𝐮𝐥𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐡𝐢𝐬𝐭𝐨𝐧𝐞 𝐬𝐮𝐩𝐩𝐥𝐲! Excited to share our latest collaboration led by tkjeong.bsky.social and ciaranfrater.bsky.social! Structural determination of the histone chaperone ASF1 and its regulator CODANIN-1 uncovers how CODANIN-1 counters ASF1 activity. 🧵👇
CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply
Nature Communications - CODANIN-1 negatively regulates the function of ASF1, the key chaperone for histone H3-H4 supply. Here the authors present the cryo-EM structure of the CODANIN-1_ASF1A...
rdcu.be
March 6, 2025 at 12:45 PM
𝐍𝐞𝐰 𝐦𝐞𝐜𝐡𝐚𝐧𝐢𝐬𝐭𝐢𝐜 𝐢𝐧𝐬𝐢𝐠𝐡𝐭𝐬 𝐢𝐧𝐭𝐨 𝐭𝐡𝐞 𝐫𝐞𝐠𝐮𝐥𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐡𝐢𝐬𝐭𝐨𝐧𝐞 𝐬𝐮𝐩𝐩𝐥𝐲! Excited to share our latest collaboration led by tkjeong.bsky.social and ciaranfrater.bsky.social! Structural determination of the histone chaperone ASF1 and its regulator CODANIN-1 uncovers how CODANIN-1 counters ASF1 activity. 🧵👇
Reposted by Kaushik Ragunathan
Post-doc in fungal molecular cell biology. Seeking person with an understanding of gene expression and phenotypic analysis, who is interested in epigenetic regulation in fungi, to explore mechanisms of antifungal resistance in Zymoseptoria tritici and Schizosaccharomyces pombe. Email me! #ECFG17
March 4, 2025 at 6:01 AM
Post-doc in fungal molecular cell biology. Seeking person with an understanding of gene expression and phenotypic analysis, who is interested in epigenetic regulation in fungi, to explore mechanisms of antifungal resistance in Zymoseptoria tritici and Schizosaccharomyces pombe. Email me! #ECFG17
Reposted by Kaushik Ragunathan
The realignment of research in our group @fmiscience.bsky.social is beginning to bear fruit. Proud of our captain @merleskribbe.bsky.social and the whole team!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin
Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyce…
www.sciencedirect.com
February 27, 2025 at 7:31 AM
The realignment of research in our group @fmiscience.bsky.social is beginning to bear fruit. Proud of our captain @merleskribbe.bsky.social and the whole team!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Kaushik Ragunathan
𝐇𝐨𝐰 𝐝𝐨 𝐜𝐞𝐥𝐥𝐬 𝐫𝐞𝐦𝐞𝐦𝐛𝐞𝐫 𝐰𝐡𝐨 𝐭𝐡𝐞𝐲 𝐚𝐫𝐞 𝐚𝐟𝐭𝐞𝐫 𝐃𝐍𝐀 𝐫𝐞𝐩𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧? Our new study “Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability” is out in 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘈𝘥𝘷𝘢𝘯𝘤𝘦𝘴. Led by @lleonie.bsky.social @biranalva.bsky.social 🧵 More below👇
Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability
Losing parental histones during DNA replication fork passage challenges differentiation competence and cell viability.
tinyurl.com
February 19, 2025 at 7:35 PM
𝐇𝐨𝐰 𝐝𝐨 𝐜𝐞𝐥𝐥𝐬 𝐫𝐞𝐦𝐞𝐦𝐛𝐞𝐫 𝐰𝐡𝐨 𝐭𝐡𝐞𝐲 𝐚𝐫𝐞 𝐚𝐟𝐭𝐞𝐫 𝐃𝐍𝐀 𝐫𝐞𝐩𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧? Our new study “Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability” is out in 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘈𝘥𝘷𝘢𝘯𝘤𝘦𝘴. Led by @lleonie.bsky.social @biranalva.bsky.social 🧵 More below👇
Reposted by Kaushik Ragunathan
🥳Just published @nature.com. Over 25 years after the discovery of SPO11 as the enzyme responsible for initiating meiotic recombination, we finally succeeded in reconstituting its DNA cleavage activity.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
SPO11 dimers are sufficient to catalyse DNA double-strand breaks in vitro - Nature
A biochemical system recapitulates the hallmarks of meiotic double-strand break formation, with mouse SPO11 catalysing break formation in the absence of any partners and remaining covalently atta...
www.nature.com
February 19, 2025 at 4:52 PM
🥳Just published @nature.com. Over 25 years after the discovery of SPO11 as the enzyme responsible for initiating meiotic recombination, we finally succeeded in reconstituting its DNA cleavage activity.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kaushik Ragunathan
Our latest preprint describes methods and tools that enable >99% efficient short homology-dependent genome editing in the human fungal pathogen Cryptococcus neoformans. Congratulations to Matt, Sanjita, and Manning!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Near 100% efficient homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans
We recently described CRISPR/Cas9-based short homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans , a haploid budding yeast that is the most common cause of fung...
www.biorxiv.org
February 18, 2025 at 10:23 PM
Our latest preprint describes methods and tools that enable >99% efficient short homology-dependent genome editing in the human fungal pathogen Cryptococcus neoformans. Congratulations to Matt, Sanjita, and Manning!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Sounds interesting. If expression levels are equalized across the two alleles not sure it directly accounts for sex determination but I like these examples of genetic compensation.
Diverse mechanisms of DDX3Y suppression by DDX3X https://www.biorxiv.org/content/10.1101/2025.02.08.637260v1
February 10, 2025 at 4:14 AM
Sounds interesting. If expression levels are equalized across the two alleles not sure it directly accounts for sex determination but I like these examples of genetic compensation.
Sometimes in the heat even the trees are thirsty. Backwaters in Kerala
December 31, 2024 at 7:16 AM
Sometimes in the heat even the trees are thirsty. Backwaters in Kerala
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
Street art in Kolkata. The everyday is quite stunning.
December 31, 2024 at 7:13 AM
Street art in Kolkata. The everyday is quite stunning.
Reposted by Kaushik Ragunathan
At this END of YEAR please check out our new paper on GENE ENDS and a convenient marker of transcription termination: RNAPII CTD T4ph! We think it is relevant to anyone studying human/animal #genes and #genome so put a lot of effort to make it easy to read. #RNABiology and #Epigenetics meet:)
Do you know where transcription of a gene actually stops? Hint: it is not the annotated gene end.
In our new paper in Nucleic Acids Research we argue that phosphorylation on threonine 4 of RNA Pol II CTD is a marker of transcription termination in animals... 🧵
academic.oup.com/nar/advance-...
In our new paper in Nucleic Acids Research we argue that phosphorylation on threonine 4 of RNA Pol II CTD is a marker of transcription termination in animals... 🧵
academic.oup.com/nar/advance-...
December 27, 2024 at 4:55 PM
At this END of YEAR please check out our new paper on GENE ENDS and a convenient marker of transcription termination: RNAPII CTD T4ph! We think it is relevant to anyone studying human/animal #genes and #genome so put a lot of effort to make it easy to read. #RNABiology and #Epigenetics meet:)
Reposted by Kaushik Ragunathan
Delighted to share our new preprint on the cell biology and genome of Stentor pyriformis, a giant ciliate that maintains Chlorella endosymbionts in surface-associated microtubule baskets.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 21, 2024 at 8:26 PM
Delighted to share our new preprint on the cell biology and genome of Stentor pyriformis, a giant ciliate that maintains Chlorella endosymbionts in surface-associated microtubule baskets.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Kaushik Ragunathan
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
December 12, 2024 at 7:16 PM
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
Reposted by Kaushik Ragunathan
