Andy Katznelson

When I was a mphil student, Prof Gurdon attended a joint journal club I was presenting. I chose an underwhelming paper. He printed out and marked up the paper, was clearly the only person in the room who'd read it. We had never met. What a towering figure and example for a generation of scientists.

Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their ...

🚨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...

Federal investment in UC research Federal funds are the university’s single most important source of support for research, accounting for more than half of UC’s total research awards. Many of California’s leading industries grew from UC research, including biotechnology, computing, semiconductors, telecommunications and agriculture. Providing health care at UC University of California Health (UC Health) is one of the nation’s largest public academic health systems, serving as a critical part of the California safety net. UC trains approximately 36% of the medical residents in California

The university of California is a powerhouse of innovation, healthcare, and social mobility for California and the US.

Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity Transcription factors (TFs) regulate gene expression by binding specific DNA motifs, yet only a fraction of putative sites is occupied in vivo. Intrinsically disordered regions (IDRs) have emerged as ...

1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?

www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics

ASB7 is a negative regulator of H3K9me3 homeostasis The maintenance of H3K9me3 involves the recognition of pre-existing modifications by HP1, which recruits methyltransferase SUV39H1 to methylate the adjacent newly incorporated histones, thereby establ...

🧬@science.org ASB7 is a negative regulator of H3K9me3 homeostasis | Science www.science.org/doi/10.1126/...
#epigenetics #chromatin #genetics #histone

I’m excited to announce that my paper describing non-canonical mitotic mechanisms in the early mouse embryo is out in @science.org ! (link at end of 🧵)

Clinical trials test the safety of stem-cell therapy for Parkinson’s disease Transplanting dopamine-releasing neurons into the brain is a promising regenerative therapy for Parkinson’s disease. Two clinical trials show that it is safe, but more evidence is needed to prove its ...

It has taken decades to get to this point, but stem cells for Parkinson's disease showing promise in 2 clinical trials
nature.com/articles/d41...
nature.com/articles/s41...
nature.com/articles/s41...

Harvard has set an example for other higher-ed institutions - rejecting an unlawful and ham-handed attempt to stifle academic freedom, while taking steps to make sure students can benefit from an environment of intellectual inquiry, rigorous debate and mutual respect. Let’s hope others follow suit.

Fairly sure my UG course used primate 16s rDNA or mitochondrial genes to learn tools of the trade. And then once more sophisticated, re-analysis of viral genomes to track epidemiological spread via character evolution etc.

As a Jew I will feel a lot safer at Columbia knowing that there are fewer graduate students toiling in labs to cure cancer and drug addiction.

Structures of TFs bound to core histone (Sox2, Cramer, PU.1/FoxA1 Bai, OCT4 Halic, ect) shows a mechanistic solution for stable binding on nuc. Of course stable structures would be biased for in the cryoEM densities.
I do like the idea of transient interactions, but these are hard to study! By FRET?

The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucle...

Many have tested this! Most compelling IMO are that foxa1 re-ChIP’s with core histone, overlapping MNase-resistant chromatin (Iwafuchi/Zaret) pmc.ncbi.nlm.nih.gov/articles/PMC...
And C&R distinguish pioneering/nuc binding events by fragment size (Meers/Henikoff)
pmc.ncbi.nlm.nih.gov/articles/PMC...

Cis-regulatory chromatin contacts form de novo in the absence of loop extrusion NIPBL promotes chromatin loop extrusion by the cohesin complex until it stalls at convergently oriented CTCF sites, leading to the formation of structural loops. However, to what extent loop extrusion...

Recently joined Bluesky, so sharing here. Our latest work on bioRxiv. Using cell-cycle dynamics and NIPBL depletion, we show that long-range enhancer-promoter interactions can form de novo without loop extrusion. www.biorxiv.org/content/10.1...

NIH cuts billions of dollars in biomedical funding, effective immediately The move halts a large slice of money for most universities and research institutions virtually overnight, imperiling vital research in everything from cancer to heart disease.

Another assault on US competitiveness at a time when biomedicine is roaring with innovation, an own-goal in a high-stakes international tournament. Of course the real losers are American people needing medicines and cures.

www.washingtonpost.com/health/2025/...

Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and a...

Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin?
By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient!
#chromatin #3Dgenome #generegulation
www.science.org/doi/10.1126/...
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Also… the Waymo seats are super comfy

Hah, an n-of-1 of someone being inconvenienced seems better than the reality of hundreds of car deaths per day

Before Christmas I did threads on the application areas of genomics in rare disease (bsky.app/profile/ewan...) and in common disease (bsky.app/profile/ewan...) - now I am going to focus on Cancer genomics

Fantastic convo. And at times contained painful lessons that made me reflect on my own process. Thank you for this!!

Has anyone had success modeling histone peptides (with PTMs) or nuclesomes (with histone tail PTMs) with chromatin reader proteins using Alphafold or Chai1? If so, any tips? Most iterations I try have the histone tail flopping off to the side #Chromatin #Alphafold #Epigenetics

Late to the party, but alphafold is mind blowing. A high confidence heterodimer that would take an entire team months can be predicted by a grad student procrastinating writing, in minutes, on coffee shop wifi.

Wow, big congrats to Jailynn and co!

"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...

So. Much. Cool. Science. Here. Really invigorating. To my old friends and new, hi 👋