banner
vram142.bsky.social
Vijay Ramani
@vram142.bsky.social
1.6K followers 570 following 95 posts
PI @ Gladstone Institutes & UCSF. Molecular technologies & the genomics / molecular biology / biochemistry of gene regulation. Views here mine & do not represent those of my affiliated institutions.
Posts Media Videos Starter Packs
Pinned
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
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
2 40 74
Reposted by Vijay Ramani
perrimonlab.bsky.social
Perrimon Lab @perrimonlab.bsky.social · 4d
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...
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...
doi.org
2 3
Reposted by Vijay Ramani
tunglejic.bsky.social
Tung Le @tunglejic.bsky.social · 5d
Independent research fellowships leading to tenured positions at the John Innes Centre.

Repost = nice. Thank you very much!!!
johninnescentre.bsky.social
John Innes Centre @johninnescentre.bsky.social · 5d
Shortlisted candidates will be invited to give a seminar at the Fellows Conference, which will be held on 10 March 2026.

Candidates who win Fellowships will be offered a Tenure Track Group Leader position from the outset, initially for 5 years.

Find out more: www.jic.ac.uk/training-car...
Independent Research Fellowships Leading to Tenured Faculty Positions | John Innes Centre
The John Innes Centre (JIC), is a world leading centre of excellence in plant and microbial sciences based on the Norwich Research Park, UK. We are inviting applications from outstanding researchers…
www.jic.ac.uk
83 46
Reposted by Vijay Ramani
camille-moore.bsky.social
Camille Moore @camille-moore.bsky.social · 6d
Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
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
4 34 84
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 6d
🙏 spearheaded almost entirely by the inimitable @camille-moore.bsky.social!
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 7d
Congratulations @jbuenrostro.bsky.social!!!
broadinstitute.org
Broad Institute @broadinstitute.org · 8d
Leading epigenetics researcher and longtime Broad member
@jbuenrostro.bsky.social has been named core institute member of the Broad. His lab will study how cells change in response to life experiences, and how those alterations affect health and disease.
Jason Buenrostro named core institute member at Broad
An expert in epigenetics and longtime member of the Broad community, Buenrostro will focus on how life experiences can alter the epigenome and increase risk of disease.
broad.io
1
Reposted by Vijay Ramani
jzylicz.bsky.social
Jan Żylicz @jzylicz.bsky.social · 20d
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...
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...
www.biorxiv.org
6 22 67
Reposted by Vijay Ramani
jacob-hanna.bsky.social
Jacob (Yaqub) Hanna - يعقوب حنا @jacob-hanna.bsky.social · 10d
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
12 28
Reposted by Vijay Ramani
andersshansen.bsky.social
Anders Sejr Hansen @andersshansen.bsky.social · 17d
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...
5 34 76
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
(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!
3
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
1 1
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
(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)
data visualization from preprint
1 1 2
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
footprint size distributions from replicated chromatin experiments
1
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
Data visualization of SAMOSA-ChAAT data from reconstituted replication reactions
1 1
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
Coomaassie-stained protein gels for individual proteins / complexes for this reconstitution
2 4
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
1 1
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · 18d
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)
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
2 40 74
Reposted by Vijay Ramani
jopkind.bsky.social
Jop Kind @jopkind.bsky.social · 21d
1/ 🧵 I am excited to share a new preprint from our group:
Single-cell Dam&T-seq during mouse corticogenesis reveals how genome–lamina interactions regulate long neuronal genes.
doi.org/10.1101/2025...
#Neurodevelopment #Epigenetics @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social
MeCP2 binding and genome–lamina reorganization precede long gene activation during mouse corticogenesis
During corticogenesis, neural gene expression is tightly coordinated by chromatin and epigenetic changes, whose misregulation can lead to neurodevelopmental disorders[1][1]–[4][2]. The role of spatial...
doi.org
2 15 40
Reposted by Vijay Ramani
natmethods.nature.com
Nature Methods @natmethods.nature.com · 26d
TDAC-seq is a method for targeted chromatin accessibility profiling that uses cytidine deaminases and long-read sequencing to resolve the effects of CRISPR edits on single chromatin fibers.

www.nature.com/articles/s41...
Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase - Nature Methods
This paper presents TDAC-seq, a targeted chromatin-accessibility-profiling method using cytidine deaminases and long-read sequencing, to resolve the effects of CRISPR edits on single chromatin fibers.
www.nature.com
1 4 11
Reposted by Vijay Ramani
jlsteenwyk.bsky.social
🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 28d
Major overhaul on my personal website is now live!

jlsteenwyk.com
1 8
Reposted by Vijay Ramani
dportik.bsky.social
Dan Portik @dportik.bsky.social · 28d
This could be a neat method for species detection in #metagenomic datasets, but why on earth are we simulating PacBio and ONT error rates at >10%? 🫣🤔🫠

PacBio HiFi has had >99% accuracy since 2019.

Very hard to interpret the results based on 90% accuracy.

www.biorxiv.org/content/10.1...
TIPP-SD: A New Method for Species Detection in Microbiomes
In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a modified version of TIPP3, which is a recently develo...
www.biorxiv.org
1 1 1
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · Aug 17
My only question is what all is earmarked for sambar and what isn’t 😂😂?
1
Reposted by Vijay Ramani
elphegenoralab.bsky.social
Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · Aug 16
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...
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
1 50 110
Reposted by Vijay Ramani
benoitbruneau.bsky.social
Benoit Bruneau @benoitbruneau.bsky.social · Aug 15
Thoughts on Illumina pip-seq in general and vs 10X?
1 2 1
vram142.bsky.social
Vijay Ramani @vram142.bsky.social · Aug 13
very cool. quick q: are VEFS phenotypes similar to what weber, crabtree & colleagues observed in PMID34117481 upon BRG1 degradation? Wondering if mSWI/SNF-mediated coactivation in distal cis is somehow constraining PRC2 activity to target sites.
1 1
Reposted by Vijay Ramani
sarahmoser.bsky.social
Sarah Moser @sarahmoser.bsky.social · Aug 13
Thrilled to share our latest work, just published in @nature.com ⬇
www.nature.com/articles/s41...

We discovered that PARP inhibitors 💊 trigger histone eviction from the chromatin and this creates a hidden vulnerability in PARPi resistant tumors.
🧵 (1/8)
NASP modulates histone turnover to drive PARP inhibitor resistance - Nature
PARP inhibitor treatment triggers histone release from the chromatin in cancer cells; consequently, targeting the histone chaperone NASP renders cells vulnerable to PARP inhibition.
www.nature.com
3 32 81