Massive effort from many in @anshulkundaje.bsky.social lab to train and curate this collection of 1000s of sequence-to-function deep learning models and the predictive features they learn - check out their blog posts on how to use the resource!

Chang M. Yun@chang-m-yun.bsky.social · 5h ago

Finally… Excited to share what I’ve been working on for the first half of my PhD! ENCODE GRAMMAR: One of the largest collections of regulatory DNA seq2func models to date (3,865 in total) trained across ENCODE, with full model interpretations and annotations tracks. Blog: tinyurl.com/3hmknhaa 1/

Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.

Fred Hutch Basic Sciences Division@basicsci.fredhutch.org · 12h ago

Join @FredHutch.org's Basic Sciences Division as an Assistant or Associate Professor and help shape the future of fundamental biology. We welcome applicants whose work will complement, extend, or bring new directions to the division.

Excited this multi-year collaboration is in print @NatureGenet with @mspivakov.bsky.social @MalyValerie @HelenR_J Low-input Capture Hi-C reveals promoter-anchored chromosomal interactions in human ILC3 prioritzing CLN3 & other genes as potential ILC3-specific mediators of genetic risk for #IBD

Mikhail Spivakov@mspivakov.bsky.social · 2d ago

Very happy to see this story finally out (link in comments)! We used low-input Capture Hi-C to profile promoter-anchored chromosomal interactions in Type 3 innate lymphoid cells (ILC3s) - rare tissue-resident lymphocytes that lack antigen receptors and regulate barrier immunity.

"Here we describe a systematic effort (‘Codebook’) to determine the sequence specificity of 332 putative and poorly characterized human TFs." www.nature.com/articles/s41...

An expanded codebook of human transcription factor DNA-binding specificity - Nature

Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.

nature.com

A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...

biorxiv.org

I will be opening my research group at the Max Delbrück Center later this year to unravel the principles governing the unique context sensing capacity of the liver www.mdc-berlin.de/schwayer and am looking for enthusiastic PhD applicants.

Schwayer Lab

The mammalian liver possesses a regenerative capacity that is unmatched by any other organ. Following injury, liver epithelial cells can proliferate or even change their identity, enabling the organ t...

mdc-berlin.de

Very happy to see the first story from my PhD now published! Genetic variants causing coding mutations in alternative isoforms are more common than we thought, plus a novel DPP9 isoform 🧬 @wbickmor.bsky.social @eliasfriman.bsky.social @simonbiddie.bsky.social www.nature.com/articles/s41...

Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms - Nature Communications

Isoforms are seldom considered in genetic variant interpretation. Here the authors map common and rare variants to alternative isoforms, which can be highly expressed and tissue-specific. A common DPP...

nature.com

Giovanna Weykopf@gweykopf.bsky.social · last yr.

Genetic variants can cause protein-coding mutations that result in disease. What about in alternative isoforms? Excited to share my first first-author pre-print! Here we show many variants reside in tissue-specific isoforms, causing coding mutations. 1/ https://bit.ly/455I6T6

Very happy to see this story finally out (link in comments)! We used low-input Capture Hi-C to profile promoter-anchored chromosomal interactions in Type 3 innate lymphoid cells (ILC3s) - rare tissue-resident lymphocytes that lack antigen receptors and regulate barrier immunity.

MRC Laboratory of Medical Sciences@mrc-lms.bsky.social · 2d ago

New research published today in Nature Genetics uses a technique called mini-Capture Hi-C to map 3D DNA folding in rare ILC3 immune cells, linking 100+ genes to immune disease risk in this cell type 🧬

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

We have a postdoc position available in the lab and would like to spread the word. Please apply if you are interested! www.cam.ac.uk/jobs/researc...

Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/

Jesse Engreitz@jengreitz.bsky.social · 2y ago

Introducing scE2G: a new model to link enhancers to target genes using single-cell data. Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body! Wonderful collaboration with @randersson.bsky.social @613weilin.bsky.social @mayayayas.bsky.social Thread👇

Read this article, get excited, and come to the Epigenome Editing symposium! Marianne Rots, Charlie Gersbach, and Angelo Lombardo (all featured in the piece) will be there in person!! Registration only 50€, talks from abstracts, plus Paris 😜 @natureportfolio.nature.com www.nature.com/articles/d41...

Epigenetic editing makes its mark

Researchers are rewriting the chemical tags on DNA and chromatin to tune gene expression.

nature.com

Maxim Greenberg@maxvcg.bsky.social · 5mo ago

Very excited to announce the FIRST symposium on epigenome editing! These tools are becoming widely used in mol bio, ag & therapy. It's time to bring leaders together to discuss this rapidly growing and exciting field. And why not in Paris! Please register & share! (1/2) ctrlepiedit.sciencesconf.org

Great to see this lovely functional genomics work from @gweykopf.bsky.social @jmarshlab.bsky.social @kennethbaillie.bsky.social @gorrellmsydney.bsky.social @simonbiddie.bsky.social published. What at first sight seemed to be non-coding turns out to be coding. www.nature.com/articles/s41...

Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms - Nature Communications

Isoforms are seldom considered in genetic variant interpretation. Here the authors map common and rare variants to alternative isoforms, which can be highly expressed and tissue-specific. A common DPP...

nature.com

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

1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

Is healthy ageing possible on a normal diet? Our new eLIFE paper describes metabolic re-engineering of yeast to avoid senescence The A2A mutant we created is super-fit late in life even on a rich high glucose diet… these cells stay healthy until they die! elifesciences.org/articles/111...

Sailing in @biorxivpreprint.bsky.social ready for summer, our study on the iconic Portuguese man o' war 🪼 is out: www.biorxiv.org/content/10.6.... We use (epi)genomics to understand a critter that fascinates me since childhood. Massive team effort with @obog.bsky.social, Cummins and Neely groups. 🧵

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

Now out from Bintu lab: compaction following transient KRAB recruitment tracks long-term epigenetic memory. But K9me3 decays after KRAB release and is replaced by DNA methylation. Does compaction help maintain K9me3, or slow its loss enough to facilitate the handoff to DNAme? tinyurl.com/ycay4mrh

Single-cell chromatin state transitions during epigenetic memory formation

Large-scale chromatin compaction quantitatively predicts the percentage of cells with durable epigenetic memory of gene silencing.

tinyurl.com

Japan has now joined Horizon Europe. Japan’s researchers can now partner with teams across the EU. Together, we will advance global research in health, digital technologies, and climate neutrality ↓ link.europa.eu/YP7MtB

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

Our study published today @science.org shows that X-chromosome inactivation (XCI) attracts L1 mutations to the human X chromosome: doi.org/10.1126/scie... With outstanding Perspective from @aurelien-doucet.bsky.social & @retrogenomics.bsky.social: doi.org/10.1126/scie...

This epic paper, which has been a heroic 10 year journey for the lead author, Ricardo Barrientos, is finally out in Cell today! Many thanks to all co-authors, especially Billie Meadowcroft and Andela Saric for their beautiful MD simulations www.cell.com/cell/fulltex...

Basement membrane turnover controls cell shape

Basement membranes are scaffolds of proteins, like collagen, that give organs shape. During development, basement membranes must adapt to the growing organ. We infer how fast the basement membrane ada...

cell.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-...

1/ New paper alert! 🎉🧬 Our study on #9p21 gene regulation is out in #CellGenomics: "Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes" (Torlai Triglia, Miller, et al. www.cell.com/cell-genomic... 🧵

Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...

The genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature Genetics

We show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...

nature.com

And we must continue to protect that ability because - counter-intuitively! - that is how the most useful things are eventually discovered.

That part may be true, but the real reason for distinguishing these two is to protect the ability of basic researchers to choose to understand how something works even if there is no immediate use for it at all.

Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders

Caroline Langley's primary thesis chapter from her time as a grad student in @memerman.bsky.social's and my lab is now published. She shows that HIV-1 Vif’s ability to maintain A3G antagonism depends on structural robustness, which permits adaptation, and epistasis, which imposes constraints.

@JohnGrossSF@johngrosssf.bsky.social · 2w ago

Strain-specific epistasis shapes fitness landscapes of APOBEC3G antagonism by HIV-1 Vif proteins | Science Advances www.science.org/doi/10.1126/... Congratulations on this beautiful work!