Evgeny Kvon

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

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...

Buildings on the Lawrence Berkeley National Lab campus, with the San Francisco Bay and the Golden Gate Bridge in the background. It's sunset time, the sky is orange. On the left is the Integrative Genomics Building (IGB), which houses the JGI, NMDC and KBase. On the right is the BioEPIC building.

🧬 @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.

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

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...

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

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 Discovery Reveals Hidden DNA Element That Helps Switch On Genes from Afar - Charlie Dunlop School of Biological Sciences Irvine, Calif., July 2, 2025 — How do cells know which genes to activate, and when? For decades, scientists have puzzled over how distant parts of our DNA — sometimes […]

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...

Schematics depicting the dorsal and ventral sides of fins and limbs

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...

Structural variants in the 3D genome as drivers of disease - Nature Reviews Genetics Disruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects ...

🚀 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

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...

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

Thank you, Stefan. I am looking forward to attending more seminars in that series!

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 🙌

Two-panel cartoon set in a desert with mountains and cacti. Top panel: A green box labeled “ENHANCER” stands on the left, shouting weakly “Turn on, please?!?” toward a distant blue spiky blob labeled “GENE” on the right, who is asleep with a “Zzz.” Bottom panel: The enhancer now uses a microphone connected to a large purple speaker labeled “REX,” which amplifies the message “Turn on!!” in a bold speech bubble across the desert. The gene is now awake and alert with wide eyes and a happy expression. Image credit: Emma Visel

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

Lastly, special credit goes to @axelvisel.bsky.social, who proposed the name “Range Extender” for this new cis-regulatory element. 10/

HOME | kvonlab The Kvon Lab at UC Irvine. Regulatory Genomics, Enhancers, Evo-Devo

During these challenging times for federally funded research in the US, I want to thank the support from NIH Pathway to Independence and High-Risk, High-Reward programs, which provided us the freedom to conduct numerous high-risk experiments. www.kvonlab.org 9/

I want to thank my lab @ucibiosci.bsky.social, our collaborators @berkeleylab.lbl.gov @ucirvine.bsky.social @abardet.bsky.social @jlopezrios.bsky.social and reviewers for helpful suggestions. The paper includes important new experiments suggested by the reviewers that are not in the preprint. 8/‬‬

Our work shows that spatial specificity and long-distance activity are two separate and separable aspects of enhancer function. It also offers a plausible mechanistic explanation for why some enhancers are highly distance-dependent while others don’t seem to care. 7/

Importantly, we can rescue LHX-less ZRS by adding a REX element to it. Mice with LHX-less ZRS fused to REX develop nearly normal limbs! 6/

What about ZRS itself? It turns out it also has three LHX motifs. Without these motifs, ZRS only functions at short range but completely loses its long-range ability, as we demonstrate in KI mice. 5/

REX lacks CTCF or YY1 sites but contains two motifs for LIM-homeodomain TFs LHX2/9, which are essential for its function and are enriched in long-range limb enhancers throughout the genome. 4/

We describe a prototypical element, called the Range Extender (REX), located next to the long-range limb enhancer of Sall1. REX lacks enhancer activity by itself, but when combined with short- and medium-range enhancers, it allows them to function over more than 850 kb of genomic space! 3/

We show that medium- and short-range limb enhancers cannot operate over long genomic distance when transplanted in place of the long-range ZRS enhancer of Shh. 2/

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

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/

Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA Cis-regulatory elements (CREs) have a major effect on phenotypes including disease. They are identified in a genome-wide manner by analyzing the binding of transcription factors (TFs), various co-fact...

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...