@GrahamMcVicker

Associate Professor at @salkinstitute. Interested in human genetic variation, gene regulation, chromatin.

Joined May 2012
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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/10.1101/…

Joint single-cell profiling of CRISPR-Cas9 edits and transcriptomes reveals widespread off-target...

A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to measure Cas9 edit outcomes and their functional effects at single-cell resolution. Here we present Superb-seq,...

biorxiv.org
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Graham McVicker retweeted
Cell Genomics@CellGenomics14 Oct 2024
Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively dlvr.it/TFL7y4

Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplic...

Zhou and Guruvayurappan et al. present a statistical framework for quantifying the joint activity of multiple enhancers from single-cell CRISPR perturbation experiments. They find that pairs of...

cell.com
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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/fullt… A thread on some of the new analyses below: (1/n)

Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplic...

Zhou and Guruvayurappan et al. present a statistical framework for quantifying the joint activity of multiple enhancers from single-cell CRISPR perturbation experiments. They find that pairs of...

cell.com
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Graham McVicker retweeted
Jessica Zhou@zrcjessica5 Oct 2023
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.
Nature Neuroscience
@NatureNeuro5 Oct 2023
Single-nucleus genomics in outbred rats with divergent cocaine #addiction-like behaviors reveals changes in amygdala GABAergic inhibition New from @TeleseFrancesca and colleagues nature.com/articles/s41593-0…
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We are excited to share our preprint describing our analysis of enhancer interactions led by @zrcjessica and @somet3000! biorxiv.org/content/10.1101/…

Genome-wide analysis of CRISPR perturbations indicates that enhancers act multiplicatively and...

A single gene may be regulated by multiple enhancers, but how they work in concert to regulate transcription is poorly understood. Prior studies have mostly examined enhancers at single loci and have...

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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.
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This suggests that, if they do exist, epistatic-like interactions between enhancers must be uncommon, weak, or specific to certain conditions/cell types.
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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/S0002…

Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in...

To map regulatory elements for GATA3, we deleted genome sequences in human T cells. We discovered a regulatory sequence 1 Mb downstream of GATA3 that contains variants associated with allergic...

cell.com
Graham McVicker@GrahamMcVicker9 Jun 2022
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/10.1101/…

Deletion mapping of regulatory elements for GATA3 reveals a distal T helper 2 cell enhancer...

The GATA3 gene is essential for T cell differentiation and is surrounded by risk variants for immune traits. Interpretation of these variants is challenging because the regulatory landscape of GATA3...

biorxiv.org
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This allowed us to improve the resolution of the identified regulatory elements and evaluate their function in primary T cells.
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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.
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Graham McVicker retweeted
AJHG@AJHGNews28 Mar 2023
🚨 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
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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/1…

Letter of support for UCSD graduate students from Salk Institute faculty

Letter of Support for UCSD Graduate Students from Salk Institute Faculty December 1, 2022 Dear President Drake, Provost Brown, and Chancellor Khosla, We are writing as a group of scientists who are...

docs.google.com
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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/10.1101/…

Deletion mapping of regulatory elements for GATA3 reveals a distal T helper 2 cell enhancer...

The GATA3 gene is essential for T cell differentiation and is surrounded by risk variants for immune traits. Interpretation of these variants is challenging because the regulatory landscape of GATA3...

biorxiv.org
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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.
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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.
Graham McVicker retweeted
Dr./Prof. Keolu Fox@KeoluFox28 Dec 2021
RIP to one of the most ambitious, brilliant, creative minds I have ever known— Glad you got to see me become a professor— We’re going to miss that laugh of yours in lecture halls, laboratories, boardrooms, restaurants, bars and dinner tables around the world 🙏🏽❤️
Prof. Debbie Nickerson and I post dissertation (Genome Sciences building, Seattle, WA). Immediately after this photo we started spraying everybody with champagne like we won a championship game 🥂 🍾

ALT Prof. Debbie Nickerson and I post dissertation (Genome Sciences building, Seattle, WA). Immediately after this photo we started spraying everybody with champagne like we won a championship game 🥂 🍾

Ed Ramos@ERamosPhD28 Dec 2021
Replying to @piperbelow @uwgenome
In grad school, Debbie always provided the down-to-Earth vibe. I respected her intelligence & humanity-always putting the care of her mother first. She would channel her infectious energy to both science and trainees like my former student @KeoluFox. Rest in peace, Debbie.
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Only 2 weeks before our inaugural seminar!! 🎉 Register for Graham's seminar here: bit.ly/3sCrRZp! Streaming link included with free registration. Please share with all that are interested! #ECI
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