Elphege Nora Lab at UCSF

Our laboratory seeks to understand how chromosome structure relates to genome functions
Tweets by Elphege

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

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?

https://t.co/l7bwPsTSkd

(1)

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@elphegenoralab.bsky.social

[Development @Dev_journal]

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:

https://t.co/gJVKlpFJHe

[Marty Yang @MartyYang]

Ecstatic to share the first story from my post-doc, co-led with Megan Ostrowski, out now in final form (https://t.co/aQFCQcstio)!

[Jane Skok @jane_skok]

Thrilled to share our new preprint, 'A genome wide code to define cell-type specific CTCF binding and chromatin organization'.
https://t.co/tzzEfysBHi

[Lluis Quintana-Murci @QuintanaMurci]

‘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. https://t.co/Ffc2cDGvwC

[Nicolas Altemose @NAltemose]

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. https://t.co/rH3plvRIpA

[Julien Richard Albert @jrichardalbert]

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.

[Michael Alexanian @m_alexanian]

🎉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: https://t.co/pBFuKIzxWq
A thread 🧵/1

https://t.co/LPB5TLE05z

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@RBioceutics Note the role of CTCF in cohesin loop extrusion is not shared by BORIS (also called CTCFL)

e.g. https://t.co/JyI8o7T2bX

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

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! 👏

[Geoff Fudenberg @gfudenberg]

Happy to share work with Hadi, Yao & @Maxime_Tortora characterizing the impact of dynamic CTCF barriers for cohesin loop extrusion
https://t.co/iiaiJg2ZeB

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@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

https://t.co/gPXBAPaRJ4

[Jesse Dixon @Jesse_R_Dixon]

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.
https://t.co/Rhg5WltjIq

[Xingjie Ren @Xingjie_Ren]

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. https://t.co/sZjg1qkRSo 1/20

[Edda Schulz @EddaGSchulz]

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

https://t.co/DaJ8G2puDm

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

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

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

Our department of Biochemistry and Biophysics at the University of California San Francisco is recruiting tenure-track faculty

https://t.co/fUVkMAfxml

We welcome all areas of biology across models - from single molecules to organisms and ecosystems.

Deadline Oct 15 2024
Pls RT

[EPIC_Unit@pasteur @pablonavarroLAB]

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 👇!
https://t.co/b7SQPvr7bo

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@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...

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@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

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

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?

https://t.co/l7bwPsTSkd

(1)

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

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

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@hitenmadhani Happy to test any of your hypotheses Hiten!

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@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)

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

@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

https://t.co/P3Z59PSuFJ