Vijay Ramani

Pseudouridine selects RNAs for extracellular transport RNAs move through the extracellular space to transmit information between cells, including mammalian neurons, yet how specific RNAs are channeled into these extracellular routes is unknown. Using geno...

RNAs outside of cells?! How did they get there?

(Thread coming soon 👀)

www.biorxiv.org/content/10.1...

Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology Stem cell differentiation is controlled by manipulating RNA condensates.

1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...

Now published in PLOS Biology! We found new retron containing bacteria in the wild, figured out defense mechanisms, and turned them into genome editors. From a cupful of dirt to new parts for genome editing in one story! journals.plos.org/plosbiology/...

The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1...
Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

Density* not sensory, d’oh.

We (ramani and narlikar labs) see the same thing for ISWI in mESCs (PMID37696956). seems possible (maybe even likely?) that CHD family remodelers are also sensory sensors! cool stuff!

A rendering of multiple Oct4 molecules bound to a chromatin fibre

🚨 🚨 🚨 New preprint alert!!! 🚨 🚨 🚨
In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level.
But what happens when you have a fibre of multiple nucleosomes?
www.biorxiv.org/content/10.1...
@rcollepardo.bsky.social @juliamaristany.bsky.social

Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41...

Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon

Brief thread 👇

Hello Boston! The lab is delighted to be at #ASHG25🧬
Check out our talks over the next few days - all unpublished stories.

Kicking things off is @michaelherger.bsky.social presenting "Saturation mutagenesis of 37 human splicing factor genes with pooled prime editing". Today @2pm, Rm205abc

Also 👇

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...

Lab’s 1st preprint!

Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.

@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.

He is on the job market!

Induction of menstruation in mice reveals the regulation of menstrual shedding During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...

I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵

SHAPIRO: OK, so you've spent your career creating television without Al, and I could imagine today you thinking, boy, I wish I had had that tool to solve those thorny problems... SIMON: What? SHAPIRO: ...Or saying... SIMON: You imagine that? SHAPIRO: ...Boy, if that had existed, it would have screwed me over. SIMON: I don't think Al can remotely challenge what writers do at a fundamentally creative level. SHAPIRO: But if you're trying to transition from scene five to scene six, and you're stuck with that transition, you could imagine plugging that portion of the script into an Al and say, give me 10 ideas for how to transition this. SIMON: I'd rather put a gun in my mouth.

David Simon, creator of ‘The Wire’, being interviewed by Ari Shapiro (NPR)

Induction of menstruation in mice reveals the regulation of menstrual shedding During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...

Congratulations @karalmckinley.bsky.social & lab on their groundbreaking recent preprint establishing + characterizing a chemically inducible model of menstruation in mouse:

www.biorxiv.org/content/10.1...

My jaw dropped when I heard this presented earlier this year. Incredible.

Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer Paraneoplastic syndromes arise when tumor-derived cytokines reprogram distant organs. Although mediators such as Interleukin-6 have been implicated, how these signals impair host organ function remain...

New paper: Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer
Liu, Miao, Wang, Ezequiel, Kim, Zhang, Sun, Binari, Asara, Yanhui Hu, Goncalves, Janowitz, Perrimon
doi: doi.org/10.1101/2025...

Independent research fellowships leading to tenured positions at the John Innes Centre.

Repost = nice. Thank you very much!!!

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...

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

🙏 spearheaded almost entirely by the inimitable @camille-moore.bsky.social!

Congratulations @jbuenrostro.bsky.social!!!

HDAC3 prevents enhancer hyperactivation to enable developmental transitions Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate tra...

Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...

EEE meeting is BACK! Early Embryogenesis & Epigenetics conference in Berlin 02/2026.
Checkout great program and over 12 slots for (not so) short talks for submitted abstracts!. Early registration now open -
w.molgen.mpg.de/embryo2026

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...

(8/7) ALSO: co-first author @palindromephd.bsky.social from our group is about to be on the job market, specifically seeking tenure-track liberal arts school teaching positions. You should hire her, period. Happy to share exactly why to anyone interested!

Will end w/ huge thank you to @fmattiroli.bsky.social & her team, esp Bruna, who spent time w/ us in SF thx to EMBO fellowship. This work exists bc of *international collaboration* & hard work across big time zone gap. We need MORE of this in the world, not LESS for the love of god.(7/7)

data visualization from preprint

(2) we observe intrinsic asymmetry in single-molecule fiber structures assembled on lagging and leading strands. This is neither resolved by CAF-1/ASF1, nor addition of active ISWI remodeler (Isw1a). Will be exciting to identify the factors that restore symmetry in reconstituted setting!(6/n)

footprint size distributions from replicated chromatin experiments

I'll leave details for interested readers to dive into, but here are two (of many) highlights: (1) 1st views of nucleosome wrapping states generated by the replisome alone (we see underwound nucleosomes!); we suspect this relates to our observations in mammalian cells in PMID39549698.(5/n)

Data visualization of SAMOSA-ChAAT data from reconstituted replication reactions

Next where our group came in. We applied our SAMOSA-ChAAT method (PMID37696956) to these reconstituted replication reactions. The method is spiced up even more, allowing us to footprint single chromatin fibers AND identify replicated DNA through strand-specific BrdUTP detection via PacBio.(4/n)

Coomaassie-stained protein gels for individual proteins / complexes for this reconstitution

Building on pioneering work of Kurat, Diffley & colleagues, Bruna, Inge, & Francesca have implemented the pure reconstitution of replication initiation, elongation and termination on fully chromatinized yeast origins. >70 proteins. Extremely challenging, extremely cool, extremely powerful.(3/n)

TL/DR: Working hand-in-hand with the absolutely brilliant scientists of the @fmattiroli.bsky.social group, we use single-molecule footprinting to study nascent chromatin fiber assembly by purely reconstituted yeast replisomes and associated factors.(2/n)