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Kim S, Yuan JB, Woods WS, Newton DA, Perez-Pinera P, Song JS. Corrigendum: Chromatin structure and context-dependent sequence features control prime editing efficiency. Front Genet 2024; 15:1391923. [PMID: 38528914 PMCID: PMC10961610 DOI: 10.3389/fgene.2024.1391923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2023.1222112.].
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Affiliation(s)
- Somang Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jimmy B. Yuan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Destry A. Newton
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Pablo Perez-Pinera
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jun S. Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Center for Theoretical Physics, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Statistics, Harvard University, Cambridge, MA, United States
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Kim S, Yuan JB, Woods WS, Newton DA, Perez-Pinera P, Song JS. Chromatin structure and context-dependent sequence features control prime editing efficiency. Front Genet 2023; 14:1222112. [PMID: 37456665 PMCID: PMC10344898 DOI: 10.3389/fgene.2023.1222112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Prime editing (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer-binding site (PBS) and reverse transcription (RT) template regions of PE guide RNA (pegRNA) yield high editing efficiency, especially for short PBS designs. The presence of G/C nucleotides was most critical immediately 5' to the protospacer adjacent motif (PAM) site for all designs. The effects of different last templated nucleotides were quantified and observed to depend on the length of both PBS and RT templates. Our models found AGG to be the preferred PAM and detected a guanine nucleotide four bases downstream of the PAM to facilitate editing, suggesting a hitherto-unrecognized interaction with Cas9. A neural network interpretation method based on nonextensive statistical mechanics further revealed multi-nucleotide preferences, indicating dependency among several bases across pegRNA. Our work clarifies previous conflicting observations and uncovers context-dependent features important for optimizing PE designs.
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Affiliation(s)
- Somang Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jimmy B. Yuan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Destry A. Newton
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Pablo Perez-Pinera
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jun S. Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Center for Theoretical Physics, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Statistics, Harvard University, Cambridge, MA, United States
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