Kaushik Ragunathan

Repression lite?

(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.

Some truth telling

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...

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...

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...

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. 🧵👇

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

Thanks for sharing. This was a really great conversation

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…

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...

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.

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👇

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...

🥳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...

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...

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...

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.

Was the indirect rate 15% or 55%? 🤔 Lovely pictures in any way event.

Yes! Been here for a week downing eight nalen gur rasagullas a day 😊

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

Street art in Kolkata. The everyday is quite stunning.

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:)

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...

Love the images and poster!

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

Proofs!

Check out this beautiful representation of our work by @munafomarzia.bsky.social uncovering the molecular bridge between sperm and egg! 🔑🤩

We had lots of fun brainstorming together with Marzia and seeing our discoveries come to life in this artistic rendition 🧵

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer Giant transposons called “Starships” mediate horizontal gene transfer in fungi to drive repeated evolution and rapid adaptation.

#TEsky Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer doi.org/10.1126/scia...

Gene behind orange fur in cats found at last After 60 years, scientists know why gingers, calicos, and tortoiseshells look the way they do

After 60 years, scientists finally know why ginger, calico, and tortoiseshell #cats look the way they do. scim.ag/3BpxRxY

A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor Reduced protein stability is the most frequent mechanism by which rare missense variants cause disease. A promising therapeutic avenue for treating destabilizing variants is pharmacological chaperones...

Can a single small molecule rescue the stability of nearly all mutations in a protein?
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...

Using biochemical and structural approaches, we show that FIGNL1 forms a ring around RAD51 and removes it from DNA. Mutating key regions of the FIGNL1 ring resulted in loss of RAD51 removal (3/7)

That’s a helpful axiom 😊

We all belong to an elite club. 😑 Let me know if I can be helpful