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Gutierrez, Alan

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Gutierrez

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Gutierrez, Alan

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    Direct Characterization of Cis-Regulatory Elements and Functional Dissection of Complex Genetic Associations Using HCR–FlowFISH
    (Springer Science and Business Media LLC, 2021-07-29) Reilly, Steven; Gosai, Sager J.; Gutierrez, Alan; Mackay-Smith, Ava; Ulirsch, Jacob; Kanai, Masahiro; Mouri, Kousuke; Berenzy, Daniel; Kales, Susan; Butler, Gina M.; Gladden-Young, Adrianne; Bhuiyan, Redwan M.; Stitzel, Michael L.; Finucane, Hilary K.; Sabeti, Pardis; Tewhey, Ryan
    Abstract: Effective interpretation of genome function and genetic variation requires a shift from epigenetic mapping of cis-regulatory elements (CREs) to characterization of endogenous function. We developed HCR-FlowFISH, a broadly applicable approach to characterize CRISPR-perturbed CREs via accurate quantification of native transcripts, alongside CASA (CRISPR Activity Screen Analysis), a hierarchical Bayesian model to quantify CRE activity. Across >325,000 perturbations, we provide evidence that CREs can regulate multiple genes, skip over the nearest gene, and can display activating and/or silencing effects. At the cholesterol-level associated FADS locus, we combine endogenous screens with reporter assays to exhaustively characterize multiple genome-wide association signals, functionally nominating causal variants and identifying their target genes.