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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2021
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.
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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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