Looking forward to our @ihgatucsf.bsky.social yearly Genotech Symposium in collaboration this year with @ucsfstemcell.bsky.social on September 23rd. We have a great line up of speakers, networking options, amazing sponsors and registration is free of charge. Hope to see you there! genotech.ucsf.edu

Great technology feature by @eisensteinium.bsky.social in @nature.com on the use of massively parallel reporter assays (MPRAs) to characterize regulatory elements featuring our work and many other amazing labs. www.nature.com/articles/d41...

These powerful tools reveal the ‘control knobs’ of the genome

By accelerating the identification of DNA sequences that control gene expression, assays are revealing the hidden grammar of the regulatory genome — and giving scientists the means to rewrite it.

nature.com

Our bat–mouse limb paper is now on bioRxiv!
🦇https://www.biorxiv.org/content/10.64898/2026.04.07.717074v2 This was a collaborative effort across the @nadavahituv.bsky.social Nicola Illing, Dorit Hockman, Guy Kelman, Tommy Kaplan labs and my lab at @washugenetics.bsky.social

Looking forward to this meeting!

We invite you to join our information session at UCSF Mission Bay campus with Iris Jiang, Hodaka Kokeguchi, and Masame Terushita from @ss-f.bsky.social humangenetics.ucsf.edu/stellar-scie...

New work from @danfeldman.bsky.social's lab, exploring sensory representations in Scn2a loss of function mice. Whisker representations are blurred, akin to cortical visual impairment often seen in SCN2A kiddos. Rescuable w/ @nadavahituv.bsky.social's CRISPRa @P30! www.biorxiv.org/content/10.6...

Degraded sensory coding in a mouse model of Scn2a-related disorder and its rescue by CRISPRa gene activation

Heterozygous loss-of-function mutations in SCN2A, a sodium channel gene expressed in cortical pyramidal (PYR) cells, lead to a neurodevelopmental disorder characterized by autism, intellectual disabil...

biorxiv.org

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

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...

We are excited to inform you about the annual UCSF IHG Genotech Symposium, taking place on 9/22. The goal of this symposium is to foster collaboration and cross-fertilization between industry and academia in genetics and genomics. Hope to see you there! genotech.ucsf.edu/home

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...

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion

Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...

biorxiv.org

Neomers are short 16bp sequences missing in our genome. Cancer causes mutations, leading to their appearance, making them a great diagnostic tool from cell-free DNA. Amazing work by Ilias Georgakopoulos-Soares, Ofer Yizhar-Barnea, Ioannis Mouratidis, Martin Hemberg... www.nature.com/articles/s43...

Leveraging sequences missing from the human genome to diagnose cancer - Communications Medicine

Georgakopoulos-Soares, Yizhar-Barnea, Mouratidis et al. identify neomers, short (16 base pair) DNA sequences that are absent in the genomes of healthy individuals but appear in tumors due to mutations...

nature.com

Our protocol on growing adipocytes or adipose organoids for Adipose Manipulation Transplantation (AMT), by the amazing Kelly An and Yusuke Ito, is out in Bio-Protocol. Hoping it will be helpful in the adoption of this therapeutic technology for various conditions. bio-protocol.org/en/bpdetail?...

📣 We are recruiting! Please share!! Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺 We have two roles available 👇 🧵 1/4

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...

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...

embl.wd103.myworkdayjobs.com

Given two genomes, can you tell who’s taller or more prone to a disease? How confident can you be? A fresh take on phenotypic inference, now out: rdcu.be/exW4f See thread🧵👇:

Predicting the direction of phenotypic difference

Nature Communications - Here authors reveal a method to predict key information on phenotypes - their direction. This is achievable even for phenotypes with incomplete genotype-to-phenotype...

rdcu.be

Join us for our @ihgatucsf.bsky.social Genotech Symposium on September 22nd 9-6pm at our Mission Bay campus! We have a great lineup of speakers and registration is free. genotech.ucsf.edu

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...

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...

biorxiv.org

Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others. www.biorxiv.org/content/10.1...

Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity

Cis regulatory elements (CREs) interact with their target promoters over long genomic distances and can be identified using chromatin conformation capture (3C) assays. Their regulatory activity can be...

biorxiv.org

Comparison between a neuronal massively parallel reporter assay for 50,000 sequences and 20,000 variants with mouse enhancer assays provide complimentary information. Great work by Michael Kosicki, Dianne Laboy Cintrón, Len Pennacchio, Martin Kircher lab & many others. www.nature.com/articles/s41...

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity - Nature Communications

MPRAs and in vivo transgenic mouse assays are two potentially complementary ways to assay the impact of noncoding variants. Here, authors find a strong and specific correlation between the assays in n...

nature.com

Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others. www.nature.com/articles/s41...

Massively parallel jumping assay decodes Alu retrotransposition activity - Nature Communications

Here, the authors develop a high-throughput assay to measure the jumping potential of thousands of transposons in parallel.

nature.com

MPRAbase (mprabase.ucsf.edu) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos, @vagar.bsky.social, ilias Georgakopoulos-Soares & others. genome.cshlp.org/content/earl...

One of the toughest parts of the field of massively parallel reporter assays to measure >~thousands of elements is that there are hundreds of pubs using them, but no central repo to easily locate the results....until now! Great collab w/ Jingjing Zhao, Ilias G-S, and @nadavahituv.bsky.social!!

Was a lot of fun doing this podcast! Thanks @thermofishersci.bsky.social team! speaking-of-mol-bio.simplecast.com/episodes/fro...

From bats to cancer – the power of gene regulation | Speaking of Mol Bio

Dr. Nadav Ahituv, Professor and Director of the Institute for Human Genetics at UCSF, takes us on a journey through groundbreaking work in gene regulation, disease genetics, and the evolution of bats....

speaking-of-mol-bio.simplecast.com

I could not be more excited to have our lab's first story online where we report our discovery that HDACs ~reverse~ their activity to ADD acyl groups to lysine! We found this for our favorite ketone body, BHB, but this pathway controls other lysine modifications too!🧵 www.nature.com/articles/s41...

Reversible histone deacetylase activity catalyzes lysine acylation - Nature Chemical Biology

Tsusaka et al. discover that histone deacetylases, which are well known to remove protein modifications, such as lysine acetylation and β-hydroxybutyrylation, can also reverse their chemical activity ...

nature.com

Nice story about our adipose manipulation transplantation (AMT) cancer therapy written by Edward Winstead at NCI. www.cancer.gov/news-events/...

Genetically Modified Fat Cells Starve Tumors in Mice

White fat cells genetically engineered to aggressively consume glucose and other nutrients can shrink tumors in mice, a new study has found.

cancer.gov

Looking forward to this symopium in honor of Ray White. There is still time to register.

Institute for Human Genetics at UCSF@ihgatucsf.bsky.social · last yr.

Join us for our symposium in honor of Ray White! We have an amazing lineup of speakers. Please register before Friday March 21, 2025. humangenetics.ucsf.edu/ray-white-me...

#ResearchHighlight 🚨 @nadavahituv.bsky.social &Co developed a new therapeutic approach, adipose manipulation transplantation (AMT), in which engineered adipocytes are used to outcompete tumours for lipids and glucose to suppress cancer progression. 👀 ⬇️

Fighting cancer with fat

bit.ly

Looking for a new director for our Genetic Counseling Program at UCSF. Job ad below and feel free to contact me directly with any questions. sjobs.brassring.com/TGnewUI/Sear...

Looking forward to this meeting!

Wellcome Connecting Science Learning and Training@eventswcs.bsky.social · last yr.

Join leading experts working in #RareDisease research at our #GRD25 conference. 📅 Dates: 9-11 April 2025 💭 Share insights in person Explore the latest #genomics advances accelerating improvements in clinical care for rare disorders, globally. ⏰Secure your place by 11 March: bit.ly/3BpAe44