Srinivas Ramachandran
@4everbiochemist.bsky.social
Reposted by Srinivas Ramachandran
As usual this time of year, started drafting the list of gene regulation conferences for 2026, enjoy! generegulation.org/conferences-...
Know of a relevant event that’s missing? Please reply below
Know of a relevant event that’s missing? Please reply below
Conferences & Schools – 2026 – Gene Regulation – Teif Lab
generegulation.org
December 29, 2025 at 3:29 PM
As usual this time of year, started drafting the list of gene regulation conferences for 2026, enjoy! generegulation.org/conferences-...
Know of a relevant event that’s missing? Please reply below
Know of a relevant event that’s missing? Please reply below
Reposted by Srinivas Ramachandran
This went under the radar but answers a fundamental question in Epigenetics...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers
The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...
www.biorxiv.org
January 5, 2026 at 12:51 PM
This went under the radar but answers a fundamental question in Epigenetics...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
Reposted by Srinivas Ramachandran
Our Perspective article on Computational Strategies for Cross-Species Knowledge Transfer is now published in @natmethods.nature.com!
This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵
www.nature.com/articles/s41...
This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵
www.nature.com/articles/s41...
January 6, 2026 at 3:15 PM
Our Perspective article on Computational Strategies for Cross-Species Knowledge Transfer is now published in @natmethods.nature.com!
This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵
www.nature.com/articles/s41...
This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵
www.nature.com/articles/s41...
Reposted by Srinivas Ramachandran
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.
December 25, 2025 at 2:44 AM
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.
Reposted by Srinivas Ramachandran
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
December 24, 2025 at 3:51 PM
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
Reposted by Srinivas Ramachandran
Excited for this work by Michael Cortazar, an @JagannathanLab Postdoc, to be out as a preprint.
So much hard work went into it, but it was well worth it 🤓
So much hard work went into it, but it was well worth it 🤓
Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay https://www.biorxiv.org/content/10.64898/2025.12.20.695734v1
December 25, 2025 at 1:19 AM
Excited for this work by Michael Cortazar, an @JagannathanLab Postdoc, to be out as a preprint.
So much hard work went into it, but it was well worth it 🤓
So much hard work went into it, but it was well worth it 🤓
Reposted by Srinivas Ramachandran
A thread on our latest paper from the Whitehouse lab
Hi all!
We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids.
www.biorxiv.org/content/10.6...
#3DGenome #chromatin #Cohesin #centromere
We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids.
www.biorxiv.org/content/10.6...
#3DGenome #chromatin #Cohesin #centromere
CAD-C reveals centromere pairing and near-perfect alignment of sister chromatids
Three-dimensional (3D) genome organization plays a central role in gene regulation, chromatin folding, and genome stability. Although chromosome-conformation capture (3C)-derived methods have revoluti...
www.biorxiv.org
December 20, 2025 at 5:11 PM
A thread on our latest paper from the Whitehouse lab
Reposted by Srinivas Ramachandran
@pravrutharaman.bsky.social got super intrigued about EZHIP/CATACOMB, previously identified as a histone H3K27M mimic of PRC2. You can read about her efforts here: www.biorxiv.org/content/10.6... We hope these analyses will help spur more analyses in this very cool gene! 1/
Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals
The Polycomb Repressive Complex 2 (PRC2) is an ancient, conserved chromatin-interacting complex that controls gene expression, facilitating differentiation and cellular identity during development. It...
www.biorxiv.org
December 13, 2025 at 10:08 PM
@pravrutharaman.bsky.social got super intrigued about EZHIP/CATACOMB, previously identified as a histone H3K27M mimic of PRC2. You can read about her efforts here: www.biorxiv.org/content/10.6... We hope these analyses will help spur more analyses in this very cool gene! 1/
Reposted by Srinivas Ramachandran
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
December 16, 2025 at 4:06 PM
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones)
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
www.biorxiv.org
December 16, 2025 at 7:50 PM
Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones)
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
Reposted by Srinivas Ramachandran
Calling all archaeal enthusiasts! 🔬🔥 From molecular machines to microbial communities, Archaea never fail to surprise us!
We are excited to announce the 2026 EMBO Workshop on the Molecular Biology of Archaea, 6–10 July in Cambridge, UK!
Sign up here: meetings.embo.org/event/26-arc...
#ArchaeaSky
We are excited to announce the 2026 EMBO Workshop on the Molecular Biology of Archaea, 6–10 July in Cambridge, UK!
Sign up here: meetings.embo.org/event/26-arc...
#ArchaeaSky
December 16, 2025 at 2:18 PM
Calling all archaeal enthusiasts! 🔬🔥 From molecular machines to microbial communities, Archaea never fail to surprise us!
We are excited to announce the 2026 EMBO Workshop on the Molecular Biology of Archaea, 6–10 July in Cambridge, UK!
Sign up here: meetings.embo.org/event/26-arc...
#ArchaeaSky
We are excited to announce the 2026 EMBO Workshop on the Molecular Biology of Archaea, 6–10 July in Cambridge, UK!
Sign up here: meetings.embo.org/event/26-arc...
#ArchaeaSky
Reposted by Srinivas Ramachandran
New online: Evolution of promoter-proximal pausing enabled a new layer of transcription control
Evolution of promoter-proximal pausing enabled a new layer of transcription control
Nature Structural & Molecular Biology, Published online: 15 December 2025; doi:10.1038/s41594-025-01718-yHere, the authors generated and analyzed run-on sequencing data to observe transcription in species across the tree of life to uncover the origins of the promoter-proximal pause.
go.nature.com
December 16, 2025 at 3:17 AM
New online: Evolution of promoter-proximal pausing enabled a new layer of transcription control
Reposted by Srinivas Ramachandran
Rotational settings quantize nucleosome movement by chromatin regulators https://www.biorxiv.org/content/10.64898/2025.12.12.693854v1
December 16, 2025 at 1:16 AM
Rotational settings quantize nucleosome movement by chromatin regulators https://www.biorxiv.org/content/10.64898/2025.12.12.693854v1
Reposted by Srinivas Ramachandran
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
December 13, 2025 at 7:00 AM
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Reposted by Srinivas Ramachandran
Took us a bit, but proud of this published version. We now examine the genetic interaction of phosphorylation with oligomerization and where bulk and phospho-Swi6 localize. Wonder if chromatin affinity tuning to enable Suv39 H3K9me3 spreading is a conserved mechanism ?
doi.org/10.1093/nar/...
doi.org/10.1093/nar/...
December 12, 2025 at 11:37 PM
Took us a bit, but proud of this published version. We now examine the genetic interaction of phosphorylation with oligomerization and where bulk and phospho-Swi6 localize. Wonder if chromatin affinity tuning to enable Suv39 H3K9me3 spreading is a conserved mechanism ?
doi.org/10.1093/nar/...
doi.org/10.1093/nar/...
Reposted by Srinivas Ramachandran
Excited to share that this work is now published in its final form!
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 15, 2025 at 2:37 PM
Excited to share that this work is now published in its final form!
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Reposted by Srinivas Ramachandran
Very happy with the final version of this work showing menin-MLL is a vulnerability in liver cancer and an interesting re-localization of NF-Y in response to menin inhibition. Menin-MLL1 complex cooperates with NF-Y to promote hepatocellular carcinoma survival: Cell Reports doi.org/10.1016/j.ce...
Redirecting
doi.org
December 15, 2025 at 2:54 PM
Very happy with the final version of this work showing menin-MLL is a vulnerability in liver cancer and an interesting re-localization of NF-Y in response to menin inhibition. Menin-MLL1 complex cooperates with NF-Y to promote hepatocellular carcinoma survival: Cell Reports doi.org/10.1016/j.ce...
Reposted by Srinivas Ramachandran
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
SET1/MLL complexes control transcription independently of H3K4me3
Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...
www.biorxiv.org
December 11, 2025 at 6:09 AM
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Srinivas Ramachandran
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
December 9, 2025 at 3:14 PM
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
Reposted by Srinivas Ramachandran
Giovana Breda Veronezi, who also earned her PhD this year, was first author on a research article
doi.org/10.1016/j.ce...
doi.org/10.1016/j.ce...
Redirecting
doi.org
November 24, 2025 at 7:15 PM
Giovana Breda Veronezi, who also earned her PhD this year, was first author on a research article
doi.org/10.1016/j.ce...
doi.org/10.1016/j.ce...
Reposted by Srinivas Ramachandran
🔔This Wednesday , in #FragileNucleosome seminar, we are excited to host @ishtiaqueh.bsky.social of Pastor lab and Prof. Sarah Teichmann, @teichlab.bsky.social, to tell us about their exciting studies!
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
November 18, 2025 at 9:43 AM
🔔This Wednesday , in #FragileNucleosome seminar, we are excited to host @ishtiaqueh.bsky.social of Pastor lab and Prof. Sarah Teichmann, @teichlab.bsky.social, to tell us about their exciting studies!
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
Reposted by Srinivas Ramachandran
Congratulations to Molecular Biology PhD student Giovana Maria Breda Veronezi of Srinivas Ramachandran's lab @4everbiochemist.bsky.social for successfully completing her PhD defense!
November 7, 2025 at 11:27 PM
Congratulations to Molecular Biology PhD student Giovana Maria Breda Veronezi of Srinivas Ramachandran's lab @4everbiochemist.bsky.social for successfully completing her PhD defense!
Reposted by Srinivas Ramachandran
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 Srinivas Ramachandran
On our three year lab anniversary (give or take a few days!), I'm proud to share the first original work produced within the Meers Lab: Plate-CUT&Tag! Take a look: www.biorxiv.org/content/10.1... 1/3
A protocol for high-throughput microplate-based CUT&Tag
Cleavage Under Targets & Tagmentation (CUT&Tag) is a versatile method for measuring genomic occupancy of chromatin-associated proteins with high sensitivity and specificity. CUT&Tag has low sequencing...
www.biorxiv.org
September 22, 2025 at 4:38 PM
On our three year lab anniversary (give or take a few days!), I'm proud to share the first original work produced within the Meers Lab: Plate-CUT&Tag! Take a look: www.biorxiv.org/content/10.1... 1/3
Reposted by Srinivas Ramachandran
In yeast spores, polarity emerges from a different playbook.
Dr. Michael McMurray (University of Colorado Anschutz) reveals how Bud8, Bud5, and Cdc42 machinery help spores establish polarity without relying on classic cortical landmarks.
www.molbiolcell.org/doi/10.1091/... #ASCB #CellBiology
Dr. Michael McMurray (University of Colorado Anschutz) reveals how Bud8, Bud5, and Cdc42 machinery help spores establish polarity without relying on classic cortical landmarks.
www.molbiolcell.org/doi/10.1091/... #ASCB #CellBiology
August 22, 2025 at 12:05 PM
In yeast spores, polarity emerges from a different playbook.
Dr. Michael McMurray (University of Colorado Anschutz) reveals how Bud8, Bud5, and Cdc42 machinery help spores establish polarity without relying on classic cortical landmarks.
www.molbiolcell.org/doi/10.1091/... #ASCB #CellBiology
Dr. Michael McMurray (University of Colorado Anschutz) reveals how Bud8, Bud5, and Cdc42 machinery help spores establish polarity without relying on classic cortical landmarks.
www.molbiolcell.org/doi/10.1091/... #ASCB #CellBiology