Elphege Nora Lab at UCSF
@ElphegeNoraLab
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Our laboratory seeks to understand how chromosome structure relates to genome functions Tweets by Elphege
San Francisco, CA
Joined December 2018
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)
biorxiv.org
Enhancers are critical genetic elements controlling transcription from promoters, but the mechanisms by which they convey regulatory information across large genomic distances remain elusive. Here,...
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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
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Ecstatic to share the first story from my post-doc, co-led with Megan Ostrowski, out now in final form ( https://t.co/aQFCQcstio)!
cell.com
By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for...
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Thrilled to share our new preprint, 'A genome wide code to define cell-type specific CTCF binding and chromatin organization'. https://t.co/tzzEfysBHi
biorxiv.org
CTCF-mediated chromatin folding plays a key role in gene regulation, however the mechanisms underlying cell type-specific control are not fully elucidated. Comprehensive analyses reveal that CTCF...
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‘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: On the Genetic Traces of Human Evolution, Migration and Adaptation
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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
Eukaryotic genomes are frequently littered with large arrays of tandem repeats, called satellite DNA, which underlie the constitutive heterochromatin often found around centromeric regions. While...
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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.
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🎉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
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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.
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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
biorxiv.org
Precise transcriptional regulation is critical for cellular function and development, yet the mechanism of this process remains poorly understood for many genes. To gain a deeper understanding of the...
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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! 👏
Happy to share work with Hadi, Yao & @Maxime_Tortora characterizing the impact of dynamic CTCF barriers for cohesin loop extrusion https://t.co/iiaiJg2ZeB
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📢 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
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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
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
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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
science.org
Early embryogenesis is driven by transcription factors (TFs) that first activate the zygotic genome and then specify the lineages constituting the blastocyst. Although the TFs specifying the blasto...
Our work establishing the orphan nuclear receptor NR5A2 as an essential regulator of early mouse development is finally out! We show that NR5A2 is required for the development of a viable morula. https://t.co/1mi2hCuxqf
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@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
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@KarissaLHansen @dewit @geoff @RobertBlelloch (20) Additional authors on X: @_RiniShah @Erikacander @LucaBraccioli @bffswithbiology @RobertBlelloch
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19) This was a heroic effort by graduate student @KarissaLHansen, who created more engineered cell lines than we can count with the help of genome editor extraordinaire Annie Adachi, and many wonderful collaborators in our lab and in @deWit, @Geoff & @RobertBlelloch groups
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(18) How does the SRR2 work to boost the effect of distal enhancers? Condensate biophysics? Unknown looping factors? 🤷 How can we hunt for similar elements across the genome & across cell types? 🧪🧬❓ We would love to know – check out the paper for some discussion.
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(17) So it’s not that complicated in the end: If you rely on an enhancer, you will need cohesin extrusion beyond ~18kb. UNLESS you have a promoter-proximal regulatory element that can synergize with your distal enhancer – which happens independently of cohesin.
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(16) Why? Quite simply, you have now removed the two redundant axes that support long-range enhancer action at Sox2.
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