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Reposted by siddhartha jena

Martin Jonikas @mjonikas.bsky.social · 1d

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...

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Kara McKinley @karalmckinley.bsky.social · 3d

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!

Çağrı Çevrim @cagricevrim.bsky.social · 3d

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...
🧵

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...

www.biorxiv.org

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Philip Ball @philipcball.bsky.social · 5d

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...

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.

www.quantamagazine.org

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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 7d

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/...

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Carl T. Bergstrom @carlbergstrom.com · 29d

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

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siddhartha jena @epijenatics.bsky.social · 19d

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!

Arnau Sebé-Pedrós @arnausebe.bsky.social · 19d

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...

siddhartha jena @epijenatics.bsky.social · 20d

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

Serena Sanulli Lab at Stanford Genetics @serenasanulli.bsky.social · 21d

Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!

bioRxiv Genetics @biorxiv-genetic.bsky.social · 22d

An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates https://www.biorxiv.org/content/10.1101/2025.09.21.676939v1

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Anders Sejr Hansen @andersshansen.bsky.social · 22d

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...

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Dr. Sedona Murphy @sedonamurphy.bsky.social · 25d

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/...

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...

www.science.org

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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · Sep 11

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

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siddhartha jena @epijenatics.bsky.social · Sep 12

Thank you Kaushik!

siddhartha jena @epijenatics.bsky.social · Sep 11

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

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siddhartha jena @epijenatics.bsky.social · Sep 11

Thank you!

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siddhartha jena @epijenatics.bsky.social · Sep 11

Thank you so much!

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siddhartha jena @epijenatics.bsky.social · Sep 11

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

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siddhartha jena @epijenatics.bsky.social · Sep 11

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

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 ...

www.biorxiv.org

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siddhartha jena @epijenatics.bsky.social · Sep 11

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

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siddhartha jena @epijenatics.bsky.social · Sep 11

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

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siddhartha jena @epijenatics.bsky.social · Sep 11

This process was able to alter cellular plasticity to transcription factor inputs: T cells expressing the tail mutant G4D displayed increased accessibility of heterochromatin-associated transcription factors and were able to respond to overexpression of those factors with proliferation! 5/9

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siddhartha jena @epijenatics.bsky.social · Sep 11

We were surprised to see that some mutations in the N-terminal tail of H4 caused outsized effects on chromatin structure- digging in deeper, we found that these mutations alter nucleosomes in cis, ablating the heterochromatin mark H3K9me3 and shaping spatial compartmentalization in the nucleus. 4/9

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siddhartha jena @epijenatics.bsky.social · Sep 11

The first step was defining sequence-to-function relationships. To do this, we turned to high-throughput screening of 1000s of variants for effects on chromatin accessibility and histone marks. We found that some single-residue changes have global effects on chromatin structure! 3/9

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siddhartha jena @epijenatics.bsky.social · Sep 11

Organisms across the tree of life, including humans, have evolved histone sequences that remodel chromatin in diverse ways. As I learned about these examples, I grew mildly obsessed with the idea of designing histones to do what *I* wanted them to do. 2/9

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siddhartha jena @epijenatics.bsky.social · Sep 11

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

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Mo Khalil @mokhalil.bsky.social · Jul 21

We traveled to DC to talk to Congressional Staffers about the impact of NIH and NIBIB funding. It enables us to develop synthetic biology tools to advance cell & genetic medicines for patients in need. REPOST to deliver the message that SCIENCE saves lives & makes America GREAT!

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City of Boston Streets Cabinet @streets.boston.gov · Jul 14

What'd you do over the weekend? Public Works began resurfacing the street in front of the Chipotle where Thomas Paine wrote Common Sense

Boston Public Works Department crews raising castings on School Street

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