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Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath
Current pooled CRISPR screens for cis-regulatory elements (CREs), based on transcriptional output changes, are typically limited to characterizing CREs of only one gene. Here, we describe CRISPRpath, a scalable screening strategy for parallelly characterizing CREs of genes linked to the same biologi...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Association for the Advancement of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443183/ https://www.ncbi.nlm.nih.gov/pubmed/34524848 http://dx.doi.org/10.1126/sciadv.abi4360 |
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author | Ren, Xingjie Wang, Mengchi Li, Bingkun Jamieson, Kirsty Zheng, Lina Jones, Ian R. Li, Bin Takagi, Maya Asami Lee, Jerry Maliskova, Lenka Tam, Tsz Wai Yu, Miao Hu, Rong Lee, Lindsay Abnousi, Armen Li, Gang Li, Yun Hu, Ming Ren, Bing Wang, Wei Shen, Yin |
author_facet | Ren, Xingjie Wang, Mengchi Li, Bingkun Jamieson, Kirsty Zheng, Lina Jones, Ian R. Li, Bin Takagi, Maya Asami Lee, Jerry Maliskova, Lenka Tam, Tsz Wai Yu, Miao Hu, Rong Lee, Lindsay Abnousi, Armen Li, Gang Li, Yun Hu, Ming Ren, Bing Wang, Wei Shen, Yin |
author_sort | Ren, Xingjie |
collection | PubMed |
description | Current pooled CRISPR screens for cis-regulatory elements (CREs), based on transcriptional output changes, are typically limited to characterizing CREs of only one gene. Here, we describe CRISPRpath, a scalable screening strategy for parallelly characterizing CREs of genes linked to the same biological pathway and converging phenotypes. We demonstrate the ability of CRISPRpath for simultaneously identifying functional enhancers of six genes in the 6-thioguanine–induced DNA mismatch repair pathway using both CRISPR interference (CRISPRi) and CRISPR nuclease (CRISPRn) approaches. Sixty percent of the identified enhancers are known promoters with distinct epigenomic features compared to other active promoters, including increased chromatin accessibility and interactivity. Furthermore, by imposing different levels of selection pressure, CRISPRpath can distinguish enhancers exerting strong impact on gene expression from those exerting weak impact. Our results offer a nuanced view of cis-regulation and demonstrate that CRISPRpath can be leveraged for understanding the complex gene regulatory program beyond transcriptional output at scale. |
format | Online Article Text |
id | pubmed-8443183 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Association for the Advancement of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-84431832021-09-24 Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath Ren, Xingjie Wang, Mengchi Li, Bingkun Jamieson, Kirsty Zheng, Lina Jones, Ian R. Li, Bin Takagi, Maya Asami Lee, Jerry Maliskova, Lenka Tam, Tsz Wai Yu, Miao Hu, Rong Lee, Lindsay Abnousi, Armen Li, Gang Li, Yun Hu, Ming Ren, Bing Wang, Wei Shen, Yin Sci Adv Biomedicine and Life Sciences Current pooled CRISPR screens for cis-regulatory elements (CREs), based on transcriptional output changes, are typically limited to characterizing CREs of only one gene. Here, we describe CRISPRpath, a scalable screening strategy for parallelly characterizing CREs of genes linked to the same biological pathway and converging phenotypes. We demonstrate the ability of CRISPRpath for simultaneously identifying functional enhancers of six genes in the 6-thioguanine–induced DNA mismatch repair pathway using both CRISPR interference (CRISPRi) and CRISPR nuclease (CRISPRn) approaches. Sixty percent of the identified enhancers are known promoters with distinct epigenomic features compared to other active promoters, including increased chromatin accessibility and interactivity. Furthermore, by imposing different levels of selection pressure, CRISPRpath can distinguish enhancers exerting strong impact on gene expression from those exerting weak impact. Our results offer a nuanced view of cis-regulation and demonstrate that CRISPRpath can be leveraged for understanding the complex gene regulatory program beyond transcriptional output at scale. American Association for the Advancement of Science 2021-09-15 /pmc/articles/PMC8443183/ /pubmed/34524848 http://dx.doi.org/10.1126/sciadv.abi4360 Text en Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (https://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited. |
spellingShingle | Biomedicine and Life Sciences Ren, Xingjie Wang, Mengchi Li, Bingkun Jamieson, Kirsty Zheng, Lina Jones, Ian R. Li, Bin Takagi, Maya Asami Lee, Jerry Maliskova, Lenka Tam, Tsz Wai Yu, Miao Hu, Rong Lee, Lindsay Abnousi, Armen Li, Gang Li, Yun Hu, Ming Ren, Bing Wang, Wei Shen, Yin Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath |
title | Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath |
title_full | Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath |
title_fullStr | Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath |
title_full_unstemmed | Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath |
title_short | Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath |
title_sort | parallel characterization of cis-regulatory elements for multiple genes using crisprpath |
topic | Biomedicine and Life Sciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443183/ https://www.ncbi.nlm.nih.gov/pubmed/34524848 http://dx.doi.org/10.1126/sciadv.abi4360 |
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