siddhartha jena

The image shows DNA nucleosomes arranged from histones in archaea. DNA is portrayed as an incandescent metal in a heated environment.

February's PDB Molecule of the Month is for "Histones Across the Tree of Life".

I wanted to focus on the histones of archaea Methanothermus fervidus which thrives at 83°C in sulfur pools in Iceland.

I call the image: "Compacting DNA at nearly boiling water."

Papers are like buses... You wait for ages, then two come along at once.

Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published!

www.nature.com/articles/s41...

We've got two exciting chromatin talks coming up on Wednesday next week:

@epijenatics.bsky.social from @jbuenrostro.bsky.social's lab and @ambystoma22.bsky.social!

register and join us: us06web.zoom.us/webinar/regi...

😍

Had a great time at #EMBOevoChromo25 learning about some really cool work at the interface of chromatin and evolution. Really an amazing community of scientists! Thank you to all the organizers :) and can't wait for the next one!

The fitness costs of reproductive specialization scale inversely with organismal size The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...

1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size!

www.biorxiv.org/content/10.6...

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 Histones are small basic proteins that form the proteinaceous core of the nucleosome, the repeating building block of chromatin in all eukaryotes. Long thought to be exclusive to eukaryotes, histones ...

A little reading before the Christmas break by the one and only @nucleosomepolice.bsky.social in @annualreviews.bsky.social

The expanding Histone universe: Histone-Based DNA organization in noneukaryotic organisms

www.annualreviews.org/content/jour...

Phenomenal work!

Signal control during tissue regeneration in adult animals Nature Reviews Molecular Cell Biology, Published online: 11 November 2025; doi:10.1038/s41580-025-00917-1The ability to track single cells in vivo, combined with insights into chromatin structure, immune–tissue crosstalk, bioelectric and metabolic cues and quantitative modelling, is changing our understanding of how tissues are repaired and renewed. This Review discusses how signals are regulated during regeneration and future directions for a more quantitative understanding of regenerative biology.

New Online! Signal control during tissue regeneration in adult animals

Ancient amino acid sets enable stable protein folds https://www.biorxiv.org/content/10.1101/2025.10.29.685319v1

As a mammalian-cell bioengineer interested in plants, it was great to connect with Sebastian, and I can assure you you’ll learn a TON from talking to him (if you haven’t already from his posts)

Algal pyrenoids—condensates that mediate ~1/3 of Earth’s CO2 fixation—change size and number as cells divide. Our data suggest a simple control mechanism: a kinase that continuously ejects material from the condensate! ☀️🌍🔬💧 #Biophysics #Photosynthesis
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!

Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.

I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...

Game changer for cell-based plant genetics: the labs of Caixia Gao & Jin-Long Qiu have developed very efficient self-replicating vectors and they just published a very nice proof-of-concept paper.
#plantscience
www.science.org/doi/10.1126/...

How competition propels scientific risk-taking Kevin Gross∗ Department of Statistics North Carolina State University Raleigh, NC USA Carl T. Bergstrom† Department of Biology University of Washington Seattle, WA USA (Dated: September 9, 2025) In science as elsewhere, attention is a limited resource and scientists compete with one another to produce the most exciting, novel and impactful results. We develop a game-theoretic model to explore how such competition influences the degree of risk that scientists are willing to embrace in their research endeavors. We find that competition for scarce resources—for example, publications in elite journals, prestigious prizes, and faculty jobs—motivates scientific risk-taking and may be important in counterbalancing other incentives that favor cautious, incremental science. Even small amounts of competition induce substantial risk-taking. Moreover, we find that in an “opt-in” contest, increasing the stakes induces increased participation—which crowds the contest and further impels entrants to pursue higher-risk, higher-return investigations. The model also illuminates a source of tension in academic training and collaboration. Researchers at different career stages differ in their need to amass accomplishments that distinguish them from their peers, and therefore may not agree on what degree of risk to accept.

1. What does a Cold War-era game theory problem known as the silent duel have to do with high-risk research strategies, publication in Cell/Nature/Science glamor journals, and the academic job market?

Kevin Gross and I tackle these questions in our latest arXiv preprint: arxiv.org/abs/2509.06718

This is a great initiative, and would be an invaluable resource to learn more about (and maybe borrow from!) the diversity of cellular organization and regulation across evolution!

very cool image-based screening of HP1 condensates and implications for RNA in regulating mesoscale structures!

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...

Kinetic organization of the genome revealed by ultraresolution multiscale live imaging Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...

Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...

Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1

Thank you Kaushik!

It’d be so cool to screen evolutionarily divergent CENP-A and map effects on centromere organization!

Thank you!

Thank you so much!

One last thing - I am on the job market! My lab will extend this approach to decode resilient chromatin: adaptations in proteins/DNA that allow for survival in harsh environments. These hold the 🔑 to designing cells that thrive under stress, esp. as we push the limits of where we take them ❄️🚀🪐🌱9/9

Engineered histones reshape chromatin in human cells Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between ...

Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9

This work is a proof of concept towards fully programmable chromatin, something I think will become very common. By combining evolutionary insights, high-throughput assays and predictive/generative modeling, we should be able to uncover some true “superpowers” of chromatin (more on this soon!) 7/9

Finally, we set out to achieve what I’d always wanted. Using screen data and sequence embeddings, we trained a classifier to predict heterochromatin repression, and used it to design totally synthetic histones we called synH4s that demonstrate optimized heterochromatin-repressing activity. 6/9