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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...

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Autores principales: Smargon, Aaron A., Madrigal, Assael A., Yee, Brian A., Dong, Kevin D., Mueller, Jasmine R., Yeo, Gene W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
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.
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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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