Nathan Gamarra Ph.D.

Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how proteins co-occupy individual fibers, especially at ...

What an amazing assay.

DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...

This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...

Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.

In a new preprint, we share some clues about when, how, and why this happens!

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

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...

Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...

Mosaic anatomy in an early fossil squamate - Nature Breugnathair elgolensis gen. et sp. nov., an early squamate identified from a newly discovered Middle Jurassic skeleton on the Isle of Skye, provides new evidence on the origins of snakes.

Benson, R.B.J., Walsh, S.A., Griffiths, E.F. et al. Mosaic anatomy in an early fossil squamate. Nature (2025). doi.org/10.1038/s415...

Meiotic cohesin RAD21L shapes 3D genome structure and transcription in the male germline Deletion of the meiotic subunit RAD21L alters 3D chromatin structure and transcription in the mammalian male germ line.

🚨 New from our lab in #ScienceAdvances!

RAD21L cohesin acts as both a 3D genome architect and a transcriptional gatekeeper in the male germline. Its loss disrupts both structure and function—highlighting the tight link between genome folding and gene regulation

www.science.org/doi/10.1126/...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...

Are viruses capable of regulating protein synthesis in the nuanced way of cellular organisms? Kinda! I’m excited to share some of my postdoc work that leveraged giant DNA viruses to address this question.

We have developed hyper-migratory CAR T cells that alleviate ovarian cancer metastatic burden and improve prognosis.

We transduce synthetic modular "velocity" receptors that promote fast and deep infiltration of CAR T cells into mets in the liver.

More here: www.biorxiv.org/content/10.1...

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.

How do #stemcells integrate information to coordinate fate decisions? Delighted to finally see our work showing how growth factors regulate the mechano-osmotic state of the #nucleus and #chromatin to control #pluripotency exit out! www.nature.com/articles/s41... see 🧵 👇

ProteinDJ logo

I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign

🏈 GB 40 - 40 DAL
FINAL

✅ That's Scorigami!! It's the 1093rd unique final score in NFL history.

PDB101: Irina Bezsonova Gallery PDB-101: Training, Outreach, and Education portal of RCSB PDB

You can find my previous inktober works here: pdb101.rcsb.org/sci-art/bezs...

Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...

📝New preprint! #MicroSky

🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy.

🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.

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

YouTube video by Stowers Institute for Medical Research How Stowers Scientists Found the DNA Site Where Robertsonian Chromosomes Fuse

🚂 The T2T train keeps rolling: "The formation and propagation of human Robertsonian chromosomes" with Gerton and Garrison labs is out! What's a Robertsonian chromosome? Let Jen tell you herself in this great video, or read our paper: [1/3]
📺 youtu.be/JmlY5omxQVc
📄 www.nature.com/articles/s41...

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...

Our Boettiger lab paper on live-cell imaging of DNA motion across genomic scales is out! www.science.org/doi/10.1126/...

Aging by the clock and yet without a program - Nature Aging Meyer and colleagues refute the idea that, as aging can be tracked precisely by clocks, it must be driven by a biological program. They propose that imperfect maintenance and repair processes resultin...

🕰️ Is aging driven by a programmed/programmatic mechanism, or by the unavoidable burden of imperfect maintenance? Our perspective argues that aging reflects finite maintenance and reduced evolutionary pressure🧵🧪 www.nature.com/articles/s43... @bjornschumacher.bsky.social @alexeimaklakov.bsky.social

PIEZO channels link mechanical forces to uterine contractions in parturition Mechanical forces are extensively involved in pregnancy and parturition, but their precise roles and mechanisms remain poorly understood. Here, we identify mechanically activated ion channels PIEZO1 a...

New preprint alert! The uterus expands ~500-fold in pregnancy, yet we know little about how pressures are sensed. Led by @yunxiao-dr.bsky.social, we show PIEZOs are required for contractions and birth in mice, with dual roles of PIEZO1 in muscle and PIEZO2 in neurons
www.biorxiv.org/content/10.1...

Senegal rolls out “six-in-one” jab, making life easier for families and health workers The hexavalent vaccine – introduced into Senegal’s routine vaccination schedule in July – protects kids against six diseases with a single shot. That means fewer injections for babies, fewer clinic vi...

Senegal just introduced a single shot hexavalent vaccine which covers:
Tetanus, diphtheria, whooping cough, polio, hepatitis B, and Haemophilus influenzae type b
www.gavi.org/vaccineswork...

Sonoepigenetic Modification Mechanoprimes Early Osteogenic Commitment in Mesenchymal Stem Cells Cells effectively balance and integrate numerous pathways to adapt to external signals in an attempt to regain homeostasis, although the complex nuclear mechanotransduction mechanism through which thi...

EpiSci - 🧬 - 🧪 - 👇🏽👇🏽👇🏽👇🏽👇🏽👇🏽👇🏽
We just submitted an updated version of the previous preprint.

Sonoepigenetic Modification Mechanoprimes Early Osteogenic Commitment in Mesenchymal Stem Cells

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

Flagellar gliding in choanoflagellates Freire-Delgado and Brunet discover a new mode of cell motility in choanoflagellates, the closest relatives of animals. Under mild confinement, choanoflagellate move over surfaces without cell deformat...

New short paper from our lab @currentbiology.bsky.social, in which we discover of a new mode of cell motility for choanoflagellates: flagellar gliding. www.cell.com/current-biol... - A 🧵

Simulation of the formation of a chromatin-attached condensate, which is visited by a gene undergoing transcriptional activation.

Read more about it here:

nyaspubs.onlinelibrary.wiley.com/doi/10.1111/...

Fine structural organization of the interphase nucleus in some mammalian cells, Monneron & Bernard, 1969

Gotta love these classic papers about nuclear architecture. In hindsight, all that we understand and discover today was already contained in their images.

www.sciencedirect.com/science/arti...

Gerald Scarfe, “Belgrano Nightmare—Thatcher Wakes Screaming” (1982), pen and ink on paper, 59.5 x 84 cm.

Edith Heard

Exciting day for @crick.ac.uk today: Edith Heard takes over as Director

We're looking forward to this new chapter in the story

www.crick.ac.uk/about-us/lea...

CUT&TIME captures the history of open chromatin in developing neurons Chromatin structure plays a central role in defining cell identity by regulating gene expression. During development, shifts in chromatin structure facilitate changes in gene expression needed to spec...

"Honey, wake up. New CUT protocol just dropped" www.biorxiv.org/content/10.1...

Opinion | We Ran the C.D.C.: Kennedy Is Endangering Every American’s Health

9 CDC Directors going back to 1977 speak out. What RFK Jr has done to our nation’s public health system "should alarm every American."

It "is unlike anything we have ever seen at the agency, and unlike anything our country has ever experienced." www.nytimes.com/2025/09/01/o...

De-novo promoters emerge more readily from random DNA than from genomic DNA Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab!

"De-novo promoters emerge more readily from random DNA than from genomic DNA"

This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

Scientists found the missing nutrients bees need — Colonies grew 15-fold Scientists have developed a breakthrough food supplement that could help save honeybees from devastating declines. By engineering yeast to produce six essential sterols found in pollen, researchers pr...

This feels like a spot of good news

www.sciencedaily.com/releases/202...

It bears repeating that nearly the entire US enterprise in science and technology has been irreversibly gutted. This is shocking.

All this loss has occurred without any real benefit to the average US citizen. Except we now have the biggest, best funded secret police force perhaps ever.

Yay for us!