Elphege Nora Lab at UCSF

First preprint from the lab 🚨 How can enhancers regulate target promoters across vast genomic distances, and what is the role of cohesin loop extrusion in the process? biorxiv.org/content/10.110… (1)

@elphegenoralab.bsky.social

Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation Read this Research Article by James McGehee and Angelike Stathopoulos @Angela_Stathop @stathlab: journals.biologists.com/dev/article/15…

Ecstatic to share the first story from my post-doc, co-led with Megan Ostrowski, out now in final form (cell.com/cell/fulltext/…)!

Thrilled to share our new preprint, 'A genome wide code to define cell-type specific CTCF binding and chromatin organization'. biorxiv.org/content/10.110…

‘Human Peoples’ is out @PenguinBooks A genetic journey through how migrations, admixture (among humans and with Neanderthals and Denisovans), and adaptations to environmental pressures (climate, nutrition, pathogens) shaped our physiology and health today. amazon.co.uk/Human-Peoples-…

I’m excited to share the first preprint out of the Altemose Lab! This stems from a heroic effort by Dr. Matt Franklin @matt_franklin_ (who's on the job market!), who made surprising discoveries regarding some of the most mysterious regions of the genome. biorxiv.org/content/10.110…

In short, we investigated the impact of DNA methylation (5-methyl-CpG) on 1. CTCF promoter-enhancer looping and 2. Polycomb-associated H3K27me3. To our surprise, we found both regulatory mechanisms converge to modulate the expression of Zdbf2, @maxvcg ‘s favourite gene.

🎉Excited to finally share that our new work (previously @biorxivpreprint) is now online at @Nature! A fantastic team effort with amazing collaborators. You can read the paper by using the following link: rdcu.be/dXQs7 A thread 🧵/1 nature.com/articles/s4158…

@RBioceutics Note the role of CTCF in cohesin loop extrusion is not shared by BORIS (also called CTCFL) e.g. genomebiology.biomedcentral.com/articles/10.11…

@RBioceutics I am not sure where the field stands regarding oncogenesis, but there are good cases for BORIS overexpression contributing to the resistance of certain cancers to drug therapies nature.com/articles/s4158…

CTCF, just like any transcription factor, binds its target sites on and off. Turns out considering this dynamic is essential to explain chromosome folding patterns from Hi-C and microscopy, and how they rearrange upon tampering with cohesin. What an exciting manuscript! 👏

It’s a bit belated, but I am happy to share the latest work from our group, led by a very talented post doc in the lab, Tessa Popay @tessapopay with great support from the 4D Nucleome consortium, Rita Allen, and the Pew Biomedical Scholars. biorxiv.org/content/10.110…

We @YinShenLab are excited to share our work on the functional characterization of enhancers of neuropsychiatric risk genes in human iPSC-induced excitatory neurons using CRISPR tiling deletion screening. biorxiv.org/content/10.110… 1/20

📢 New preprint from the lab! CRISPR-screening wizard 🧙 🧬 @TSchwammle figured out how different signals 🚦 are integrated at the Xist locus. See his tweetorial below. biorxiv.org/cgi/content/sh…

1 week left to apply to the open-rank faculty search for the UCSF dept. of Biochemistry & Biophysics All area of fundamental biology are welcome Reach out if you have any questions

After a massive team effort leaded by the incomparable @NicolaFestuccia I am really happy to share our freshly published @ScienceMagazine ms where we elevate Nr5a2 to the top of gene regulation in the morula. 🔥🔥🔥 Take a look at Nicola's description 👇! science.org/doi/10.1126/sc…

@vitaliikl We are definitely thinking along the same lines! We thought disabling extrusion would reveal all the functional enhancer-promoter links - that's why we did the experiment in the first place. But plot twist, it's more complicated...

@ElphegeNoraLab I think that means that we need creative ways to combine more scalable experiments with large computational models that use findings from papers like yours as inductive biases. The question is which experiments could help.

Amazing study. Disrupting these kinds of nuclear function mechanisms and measuring with the most relevant modalities is IMO a big part of what you need to make progress with genome-to-transcription phenotype AI/ML models. Without papers like this we won’t find out how it works.

@KarissaLHansen @dewit @geoff @RobertBlelloch @_RiniShah @Erikacander @LucaBraccioli @bffswithbiology (21) Oops, wrong X handle 😅 - meant to tag the one and only Geoff Fudenberg @gfudenberg for key contributions to the transcriptomic analyses and stimulating ideas

@KarissaLHansen @dewit @geoff @RobertBlelloch (20) Additional authors on X: @_RiniShah @Erikacander @LucaBraccioli @bffswithbiology @RobertBlelloch

First preprint from the lab 🚨 How can enhancers regulate target promoters across vast genomic distances, and what is the role of cohesin loop extrusion in the process? biorxiv.org/content/10.110… (1)

@hitenmadhani Happy to test any of your hypotheses Hiten!

@vitaliikl We are of course working very hard to crack how SRR2 works at Sox2 to see if we could find similar sequences elsewhere. But my guess is that the mechanism will be quite degenerate, involving generic TFs & co-activators (I don't expect a new CTCF-like factor to pop up)

@vitaliikl Very promising algorithms using Hi-C (e.g. ABC, ENCODE-rE2G...) are making great strides towards this. But we are not yet at point to have trustworthy lists of enhancer-promoter dependencies across just any cell types and any organisms biorxiv.org/content/10.110…