The Kim Lab (sskimlab.org) at UC Irvine is recruiting motivated grad students interested in uncovering how transcriptional regulators direct cell fates. We accept students through the CMB (cmb.uci.edu) and MCSB (ccbs.uci.edu/education/mcsb/) PhD programs. Please share with prospective grad students!

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇

👀Next Wednesday, Oct 22nd, at #FragileNucleosome seminar, we are excited to host @alicelaigle.bsky.social and @seungsookim.bsky.social to tell us about amazing work they are doing! 🗓️Register here for upcoming session and the entire series: us06web.zoom.us/webinar/regi...

What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters www.biorxiv.org/content/10.1...

The #CSHA meeting on Systems Biology of Gene Regulation & Genome Editing kicks off next Monday! ⏳ Don’t miss your shot to dive into cutting-edge science. 👉 Check out the full program and register now on www.csh-asia.org?content/2767 Location: Suzhou. China | Oct.20-24, 2025

The @crick.ac.uk is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov www.crick.ac.uk/careers-stud...

If you’re interested in exploring the relationship between chromatin organization and epigenetic memory using chromatin tracing microscopy, my group is recruiting a talented PhD student 🥳

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇

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...

Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr

Congrats to Aurelie Hinterman aurhin.bsky.social, Chase Bolt chasebolt.bsky.social, and Brent Hawkins @homeobox.bsky.social! Coverage in NYTimes by @carlzimmer.com: www.nytimes.com/2025/09/17/s...

Most neurodevelopmental disorders are caused by having 1 functional gene copy. Using SCN2A, we show that upregulating the functional copy rescues neuronal phenotypes. Amazing work with @neurobender.bsky.social led by Serena Tamura, Andrew Nelson, Perry Spratt & others. www.nature.com/articles/s41...

Very interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...

Join this year's CSH Asia Systems Biology of Gene Regulation & Genome Editing meeting in beautiful Suzhou, China, Oct 20-24. Let's bring the international communities together! Abstract deadline Sept 19! Infos and registration at csh-asia.org?content/2767. Please repost!

Welcome Alex Stark @alex-stark.bsky.social to Bluesky!

Become our colleague at @fmiscience.bsky.social! The FMI is a very special place to start your lab: a vibrant international institute with world-class research groups and facilities, core funding, fantastic trainees, great colleagues😅, and a collegial culture. Get in touch if you're interested!

Honored to lead off such an amazing set of speakers 🧬 🌟

Join the Fragile Nucleosome Seminar featuring @gracebower.bsky.social, who will discuss our recent discovery of the Range Extender Element. (www.nature.com/articles/s41...)

Abstract deadline for CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing is extended to September 5th.

1) I am delighted to present this terrific tour de force research conducted by my post-doc Dr. Gayani Senevirathne @gayani.bsky.social and published today in Nature - www.nature.com/articles/s41...

New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...

Abstract deadline for CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing is extended to September 5th.

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

🚨New preprint from the lab🚨 🧬 What keeps certain chromatin domains anchored at the nuclear periphery? Our new genome-wide HiDRO screen uncovers a key role for RNA-binding protein hnRNPK. www.biorxiv.org/content/10.1...

“Our findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data, underscoring the continued need for expanding resources for enhancer discovery.” Great paper and very important finding - many congrats Axel & team! 👏👏

Enhancers are "just DNA" - finding all of them in the genome is hard. www.nature.com/articles/s41...

Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome? Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more www.nature.com/articles/s41...

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

Outstanding Faculty opportunity in the broad area of 'life sciences engineering' @EPFL School of Life Sciences, open to both junior and senior researchers. We may prefer metabolism-centric applications but remain open to outstanding applications across domains: www.epfl.ch/about/workin...

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

🧬 @jgi.doe.gov is hiring! We're seeking an Advanced Analysis Manager to lead data infrastructure and software engineering supporting the generation, analysis, and dissemination of genomics data Hybrid | SF Bay Area | Apply by Aug 7 jobs.lbl.gov/jobs/advance... @biosci.lbl.gov @berkeleylab.lbl.gov

Huge congratulations to Dr. Ethan Hollingsworth @ewholling.bsky.social for successfully defending his PhD thesis. Well done!

No new genes needed to fly - just rewire what you have! 🦇🧬 Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social doi.org/10.1038/s415... #EvoDevo #SingleCell #BatWings

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab. www.biorxiv.org/content/10.1... 1/

Some personal news…

Attend the CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing, organized by Len Pennacchio, Alex Stark, Zhiping Weng, and Wei Xie (all blueskyless), featuring a great lineup of speakers and a beautiful location in Suzhou. Abstract submission deadline: August 18th.

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

New research on range extenders, or REX genetic enhancer elements, from @ucirvine.bsky.social, #BioEGSB scientists @berkeleylab.lbl.gov & international collaborators! These bits of DNA that regulate gene expression allow enhancers to work far away from their target. www.bio.uci.edu/new-discover...

We take for granted that our hands have two sides and can articulate in an endless number of ways. But what about a fish’s fin? Can a fish know something “like the back of its fin,” or have its future told with a fin palm reading? Check out this bluetorial to find out 👇🧪🧬🐟 doi.org/10.1101/2025...

🚀 Thrilled to share our new review on how structural variants reshape 3D genome architecture and cause disease! 🧬🔀 Out now in Nature Reviews Genetics: www.nature.com/articles/s41... #3D-Genome #StructuralVariants #uksh

In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11

Speaking of T-Rex

I very much look forward to @andersshansen.bsky.social's talk on 'Spatiotemporal Mechanisms of Distal Gene Regulation by Enhancers' in @enhancedgenomics.bsky.social seminar series 'The 3D Regulatory Genome'. 📅 July 3rd 2025 (tomorrow!) ⏰ 4pm GMT Pleaase join us and register at: lnkd.in/eeRnyjC5

The Range Extender For enhancers to function At long distances #ChromatinHaiku

A dream come true: my first first-author publication! 🧬 🎉 Working to unravel the mysteries of long-range gene regulation has been an incredible journey. Endless gratitude to Evgeny, the lab, and all of the amazing collaborators who helped make this happen 🙌

Getting the message across from a distance: 🧬REX🧬 is a “Range EXtender” element that can turn short-range into looooooooooooong-range enhancers Great collaboration led by @gracebower.bsky.social and @evgenykvon.bsky.social www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.gov

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Lentivirus massively parallel reporter assays integrate & enrich for specific sequences in the genome. We utilize this to test their epigenetic modifications & open chromatin alongside their regulatory activity. Amazing work by Zicong Zhang, Fumitaka Inoue & others. www.biorxiv.org/content/10.1...