A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens

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Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships...

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Autores principales: Guna, Alina, Page, Katharine R., Replogle, Joseph M., Esantsi, Theodore K., Wang, Maxine L., Weissman, Jonathan S., Voorhees, Rebecca M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614335/
https://www.ncbi.nlm.nih.gov/pubmed/37904134
http://dx.doi.org/10.1186/s12864-023-09754-y
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author Guna, Alina
Page, Katharine R.
Replogle, Joseph M.
Esantsi, Theodore K.
Wang, Maxine L.
Weissman, Jonathan S.
Voorhees, Rebecca M.
author_facet Guna, Alina
Page, Katharine R.
Replogle, Joseph M.
Esantsi, Theodore K.
Wang, Maxine L.
Weissman, Jonathan S.
Voorhees, Rebecca M.
author_sort Guna, Alina
collection PubMed
description Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09754-y.
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spelling pubmed-106143352023-10-31 A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens Guna, Alina Page, Katharine R. Replogle, Joseph M. Esantsi, Theodore K. Wang, Maxine L. Weissman, Jonathan S. Voorhees, Rebecca M. BMC Genomics Research Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09754-y. BioMed Central 2023-10-30 /pmc/articles/PMC10614335/ /pubmed/37904134 http://dx.doi.org/10.1186/s12864-023-09754-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Guna, Alina
Page, Katharine R.
Replogle, Joseph M.
Esantsi, Theodore K.
Wang, Maxine L.
Weissman, Jonathan S.
Voorhees, Rebecca M.
A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens
title A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens
title_full A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens
title_fullStr A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens
title_full_unstemmed A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens
title_short A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens
title_sort dual sgrna library design to probe genetic modifiers using genome-wide crispri screens
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614335/
https://www.ncbi.nlm.nih.gov/pubmed/37904134
http://dx.doi.org/10.1186/s12864-023-09754-y
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