Our study on giant transposons Starship 🚀🧬 in the genome of the lichen fungus Xanthoria is now out in @pnas.org! What did we find out about Starships in #lichen fungi? 👇Updated thread below 🖥️ 🧪 🦠 🧫 #SymbioSky 1/6 www.pnas.org/doi/10.1073/...

(1/n) Excited to share close collab w @bloodgenes.bsky.social led by Varshini & Chun-jie et al How to induce expression of key genes while silencing much of the genome during Erythropoiesis? A: Matchmaker CREs load cohesin near key genes to promote looping & exp: www.biorxiv.org/content/10.6...

🎉 this paper is now out - we show how subicular plateaus are linked to reward locations. Congratulations to the whole team! www.cell.com/cell-reports...

Subicular plateaus signal reward locations during goal-directed behavior

Using in vivo whole-cell recordings during goal-directed navigation, Bhatia, Adel, and Grienberger identify plateaus as a prominent feature of subiculum activity. These events preferentially occur nea...

cell.com

Christine Grienberger@cgrienberger.bsky.social · 6mo ago

🚀 New preprint from the lab! Our first foray into the subiculum uses in vivo whole-cell recordings to show that dendritic plateaus are a prominent, learning-dependent signaling mode of subicular neurons. Feedback is welcome! www.biorxiv.org/content/10.6...

Very interesting finding from the Ragunathan lab showing that a CHD remodeler in a NuRD-like complex called SHREC can trigger H3K9me2/3!

Kaushik Ragunathan@kaushikr.bsky.social · 2w ago

Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...

Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...

Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback

In Schizosaccharomyces pombe , the conserved CHD remodeler Mit1 function within the SHREC remodeler-deacetylase complex (a homolog of the metazoan Mi-2/NuRD complex), which is essential for H3K9 methy...

biorxiv.org

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

Next summer's Epigenetics GRC (I'm co-chairing with Deborah Bouch'is) is shaping up nicely with an all-star lineup of speakers working on a broad range of organisms and systems and everything from molecular mechanisms to new phenomena. Apply and put it on your calendar! www.grc.org/epigenetics-...

Douglas Weidemann, Silke Hauf @silkehauflab.bsky.social and colleagues @virginiatech.bsky.social establish MS2–MCP-based single-molecule RNA visualisation in Schizosaccharomyces pombe. journals.biologists.com/jcs/article/...

Delighted to share our paper on neo-chromosomes! We induced centromere fission using CRISPR in Arabidopsis and increased the chromosome count from n=5 to n=6. The broken chromosomes ends quickly “healed” by adding telomeres de novo and the new karyotype is stable through mitosis and meiosis! 1/3

Ian Henderson@hendersi.bsky.social · 3w ago

CRISPR-mediated centromere fission generates neochromosomes with distorted meiotic inheritance in Arabidopsis biorxiv.org/content/10.6... new preprint from us - includes changing the Arabidopsis karyotype from 5 -> 6 chromosomes using Cas9 & outcomes of 5/6 chromosome hybrid meiosis

Very interesting study showing that active non-equilibrium fluctuations are required to explain chromatin organization at the 10-100kb scale:

Ranjith Padinhateeri@ranjithpa.bsky.social · 3mo ago

Our new preprint: Chromatin at ~10–100 kb scales behaves very differently from standard polymer expectations. DNA-PAINT data reveal broad fluctuations and sharp local bends. Our study suggests emergent active forces at these scales and quantifies the nature and strength of this activity

If you like ethological learning, structural plasticity, and the idea that homeostatic setpoints are malleable, this paper is for you! Congrats to Diane and the whole team on the culmination of a long and fascinating journey #dianebissen.bsky.social, #neuroskyance

@dianebissen.bsky.social · 4w ago

Back to Bluesky to share the most exciting news: my postdoctoral research is now published in Neuron! We used cricket hunting to show how ethological learning persistently rewires juvenile (but not adult!) visual circuits by co-opting homeostatic plasticity. Full story www.cell.com/neuron/fullt...

How do transposons jump when they’re released from host control? I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs. Here’s what we found & excited to share my 1st postdoc paper: “piRNA loss unleashes episodic transposition bursts” www.biorxiv.org/content/10.6...

piRNA loss unleashes episodic transposition bursts

In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...

biorxiv.org

Excited to see this collaboration now in print. Dye chemistry meets AI-designed proteins. Three small, orthogonal tags; lifetime modulation; split versions. Request the free dyes at dyes.janelia.org www.science.org/doi/10.1126/...

De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging

Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostabilit...

science.org

The talented @isa-ozdemir.bsky.social wrote a review of CHD remodelers, discussing all 9 family members and their roles in ES cells and early development. dx.doi.org/10.1002/bies... 1/2

Molecular Acrobats: How CHD Remodelers Shape the Genetic Playground to License Cell Identity

In eukaryotes, DNA is not a naked repository of genetic information but is tightly wound around histone octamers to form nucleosomes. While this packaging solves the spatial problem of fitting 2 mete...

dx.doi.org

"American propaganda has always been about the spectacle of the city upon a hill on whom the world’s eyes are turned...Now the spectacle is about the demonization of immigrants, the sickening rituals of hunting them down in the streets with masked government enforcers, zeteo.com/p/250-americ...

'250 Years of Cruelty' – Viet Thanh Nguyen on the ‘American Empire' and How to Save the U.S.

The liberation of the American peoples cannot be achieved without the shedding of imperial weight, writes the Pulitzer prize-winning author in this somber essay marking the semiquincentennial.

zeteo.com

Introns have a hidden regulatory role! 🧬🎉 Delighted to share our latest paper showing that inefficiently spliced introns and spliceosomal proteins direct RNA methylation, engaging RNAi to silence retrotransposons and regulate gene expression nature.com/articles/s41...

1/11 New preprint from the Sternberg lab in collaboration with the Fernández lab! We are excited to share our structure-function study of DRT10, a bacterial defense-associated reverse transcriptase that synthesizes long tandem-repeat DNA.🧵 Read the full story here: www.biorxiv.org/content/10.6...

Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase

Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection[1][1],[2][2]. We previously showed that DRT10, a tripartite system comprising an RT, a...

biorxiv.org

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

Bacteria sense virus-induced genome degradation via methylated mononucleotides

Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...

science.org

Osterman Ilya@ostermanilya.bsky.social · last mo.

Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️

Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️

Bacteria sense virus-induced genome degradation via methylated mononucleotides

Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...

science.org

Osterman Ilya@ostermanilya.bsky.social · 9mo ago

Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...

Much of the genome is made up of repetitive DNA sequences that trace back to ancient mobile elements. Two new studies from the @marcbuhler.bsky.social group, now published in @cp-molcell.bsky.social, show how cells keep these potentially disruptive sequences under control. www.fmi.ch/news-events/...

How cells keep genomic hitchhikers under control

Much of the genome is made up of repetitive DNA sequences that trace back to ancient mobile elements, many of which have lost their ability to copy themselves into new locations but can still cause pr...

fmi.ch

Meet SpudCell, a synthetic cell made from lifeless ingredients that feeds, grows, divides, and experiences selection. If it doesn't have all the hallmarks of life, it has a lot! Here's my story. Gift link: nyti.ms/4vCbTih

Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...

Bacterial and human exonucleases mediate interkingdom antiviral immunity

All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...

biorxiv.org

Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates

Anders Sejr Hansen@andersshansen.bsky.social · 2y ago

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!

Replication-stress-induced chromatin loops protect fork stability - Nature

Replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks.

nature.com

It is out 😍 check it out!! Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. @cschwayer.bsky.social @silviabarbiero.bsky.social @davidbrueckner.bsky.social @ehannezo.bsky.social www.cell.com/cell/fulltex...

Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning

During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...

cell.com

My first PhD paper is out in Nucleic Acids Research! We describe "Ab-trapping" - an antibody artifact that distorts assays relying on antibody diffusion (microscopy, CUT&Tag, CUT&RUN). The revisions made the story much stronger. Check it out! doi.org/10.1093/nar/...

Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus

Abstract. Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome’s most essential functions. Many microscopy and geno

doi.org

This is an important read. One Day, Everyone Will Have Always Been Against This, by Omar El Akkad.

One Day, Everyone Will Have Always Been Against This - National Book Foundation

On October 25, 2023, after just three weeks of the bombardment of Gaza, Omar El Akkad put out a tweet: “One day, when it’s safe, when there’s no personal downside to calling a thing what it is, when i...

nationalbook.org

How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926

@zjmaggiexu.bsky.social's story on suctorian trap structure adaptation is now online in @currentbiology.bsky.social , with new evolutionary analyses and modeling! This fall, Maggie will keep exploring predatory protists as a PD in @nbellono.bsky.social group; keep an eye out for her she's amazing!

Scott Coyle@cellraiser.bsky.social · 9mo ago

How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926

How did animal senses evolve? Max Coyle et al. used choanoflagellates to uncover TRPW, ancient ion channels predating animal somatosensory receptors. TRPW links microbial prey ecology to evolution of receptor structure, sensory organelles, & multicellular processing. www.biorxiv.org/content/10.6...