Graham McVicker

Excited to announce our preprint describing SUPERB-SEQ 🦸, a new method to measure Cas9 edits and their effects on gene expression in single cells. Developed by @micklorenzini, myself, and @GrahamMcVicker biorxiv.org/content/10.110…

Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively dlvr.it/TFL7y4

Happy to share that the paper on enhancer interactions led by @zrcjessica and I from my time in the @GrahamMcVicker lab is now published in Cell Genomics! cell.com/cell-genomics/… A thread on some of the new analyses below: (1/n)

Our paper is out today in Nature Neuroscience! Here, we analyzed single-nucleus RNA-seq and ATAC-seq data generated from the amygdalae of outbred rats displaying divergent addiction-like behaviors following protracted abstinence (4wks) from cocaine.

This suggests that, if they do exist, epistatic-like interactions between enhancers must be uncommon, weak, or specific to certain conditions/cell types.

This made it possible for us to interrogate interactions between 3,808 enhancer pairs. We found that the effects of individual enhancers combine multiplicatively to regulate gene expression. Beyond this, we found no evidence for interactions between enhancers.

We are excited to share our preprint describing our analysis of enhancer interactions led by @zrcjessica and @somet3000! biorxiv.org/content/10.110…

We also added luciferase reporter assays, which support a regulatory function for the SNP rs725861. This SNP lies in a distal enhancer-like sequence 1 Mb downstream of GATA3 and is one of several candidate variants associated with allergic diseases.

This allowed us to improve the resolution of the identified regulatory elements and evaluate their function in primary T cells.

Our paper “Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases” is now online at AJHG (open access): cell.com/ajhg/fulltext/…

🚨 ONLINE @AJHGNews 📰 Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases 👩🏾‍🤝‍👨🏻 @GrahamMcVicker & team 👇 bit.ly/40mmluN

@UPennGCB @CAMBUpenn @PennMedicine @pennbgs @casey6r0wn So sorry to hear this tragic news. I don't have much to say beyond what others have already said. Casey was great person and generous contributor to our field. When I visited Penn he was such a wonderful host. 💔💔💔

It is with great sadness that we share the news that Dr. Casey Brown passed away on Saturday, March 18. He was a friend, colleague, and mentor to so many in the GCB and CAMB communities, as well as the scientific community as a whole, and will be deeply missed.

UCSD graduate students are integral to research at the Salk Institute. A group of Salk faculty have signed a letter supporting their effort to obtain fair compensation that allows them to live near the university. docs.google.com/document/d/1hV…

@genomeknows Good luck Max! Looking forward to hearing more about what you are up to next!

Quietly... today was my last day in academe, I did the thing, but ultimately left for all the reasons we already know. I loved my colleagues and students, but I'm very excited to start in biotech on Monday! I'll report back what I find. Wish me luck

Small deletions spanning one risk variant decrease GATA3 expression in Th2 cells suggesting a mechanism for this variant in allergic diseases. Our study demonstrates the power of integrating GWAS signals with deletion mapping and identifies key regulatory sequences for GATA3.

As an alternative approach, we mapped regulatory elements for GATA3 using a high-throughput tiling deletion screen. We identify 23 regulatory sequences, including one 1Mb downstream that contains risk variants for allergic diseases.

The latest paper from my lab is now out on bioRxiv! “Deletion mapping of regulatory elements for GATA3 reveals a distal T helper 2 cell enhancer involved in allergic diseases” biorxiv.org/content/10.110…