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Crosstalk between CRISPR-Cas9 and the human transcriptome
CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8891275/ https://www.ncbi.nlm.nih.gov/pubmed/35236841 http://dx.doi.org/10.1038/s41467-022-28719-5 |
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author | Smargon, Aaron A. Madrigal, Assael A. Yee, Brian A. Dong, Kevin D. Mueller, Jasmine R. Yeo, Gene W. |
author_facet | Smargon, Aaron A. Madrigal, Assael A. Yee, Brian A. Dong, Kevin D. Mueller, Jasmine R. Yeo, Gene W. |
author_sort | Smargon, Aaron A. |
collection | PubMed |
description | CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a cellular and RNA impact likely inherent to CRISPR-Cas systems. |
format | Online Article Text |
id | pubmed-8891275 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-88912752022-03-17 Crosstalk between CRISPR-Cas9 and the human transcriptome Smargon, Aaron A. Madrigal, Assael A. Yee, Brian A. Dong, Kevin D. Mueller, Jasmine R. Yeo, Gene W. Nat Commun Article CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a cellular and RNA impact likely inherent to CRISPR-Cas systems. Nature Publishing Group UK 2022-03-02 /pmc/articles/PMC8891275/ /pubmed/35236841 http://dx.doi.org/10.1038/s41467-022-28719-5 Text en © The Author(s) 2022 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Smargon, Aaron A. Madrigal, Assael A. Yee, Brian A. Dong, Kevin D. Mueller, Jasmine R. Yeo, Gene W. Crosstalk between CRISPR-Cas9 and the human transcriptome |
title | Crosstalk between CRISPR-Cas9 and the human transcriptome |
title_full | Crosstalk between CRISPR-Cas9 and the human transcriptome |
title_fullStr | Crosstalk between CRISPR-Cas9 and the human transcriptome |
title_full_unstemmed | Crosstalk between CRISPR-Cas9 and the human transcriptome |
title_short | Crosstalk between CRISPR-Cas9 and the human transcriptome |
title_sort | crosstalk between crispr-cas9 and the human transcriptome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8891275/ https://www.ncbi.nlm.nih.gov/pubmed/35236841 http://dx.doi.org/10.1038/s41467-022-28719-5 |
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