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High throughput PRIME editing screens identify functional DNA variants in the human genome
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10370011/ https://www.ncbi.nlm.nih.gov/pubmed/37502948 http://dx.doi.org/10.1101/2023.07.12.548736 |
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author | Ren, Xingjie Yang, Han Nierenberg, Jovia L. Sun, Yifan Chen, Jiawen Beaman, Cooper Pham, Thu Nobuhara, Mai Takagi, Maya Asami Narayan, Vivek Li, Yun Ziv, Elad Shen, Yin |
author_facet | Ren, Xingjie Yang, Han Nierenberg, Jovia L. Sun, Yifan Chen, Jiawen Beaman, Cooper Pham, Thu Nobuhara, Mai Takagi, Maya Asami Narayan, Vivek Li, Yun Ziv, Elad Shen, Yin |
author_sort | Ren, Xingjie |
collection | PubMed |
description | Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated saturation mutagenesis. Next, we applied PRIME to functionally characterize 1,304 non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate PRIME capable of characterizing genetic variants at base-pair resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification. |
format | Online Article Text |
id | pubmed-10370011 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-103700112023-07-27 High throughput PRIME editing screens identify functional DNA variants in the human genome Ren, Xingjie Yang, Han Nierenberg, Jovia L. Sun, Yifan Chen, Jiawen Beaman, Cooper Pham, Thu Nobuhara, Mai Takagi, Maya Asami Narayan, Vivek Li, Yun Ziv, Elad Shen, Yin bioRxiv Article Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated saturation mutagenesis. Next, we applied PRIME to functionally characterize 1,304 non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate PRIME capable of characterizing genetic variants at base-pair resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification. Cold Spring Harbor Laboratory 2023-07-12 /pmc/articles/PMC10370011/ /pubmed/37502948 http://dx.doi.org/10.1101/2023.07.12.548736 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article Ren, Xingjie Yang, Han Nierenberg, Jovia L. Sun, Yifan Chen, Jiawen Beaman, Cooper Pham, Thu Nobuhara, Mai Takagi, Maya Asami Narayan, Vivek Li, Yun Ziv, Elad Shen, Yin High throughput PRIME editing screens identify functional DNA variants in the human genome |
title | High throughput PRIME editing screens identify functional DNA variants in the human genome |
title_full | High throughput PRIME editing screens identify functional DNA variants in the human genome |
title_fullStr | High throughput PRIME editing screens identify functional DNA variants in the human genome |
title_full_unstemmed | High throughput PRIME editing screens identify functional DNA variants in the human genome |
title_short | High throughput PRIME editing screens identify functional DNA variants in the human genome |
title_sort | high throughput prime editing screens identify functional dna variants in the human genome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10370011/ https://www.ncbi.nlm.nih.gov/pubmed/37502948 http://dx.doi.org/10.1101/2023.07.12.548736 |
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