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Perez-Bermejo JA, Efagene O, Matern WM, Holden JK, Kabir S, Chew GM, Andreoletti G, Catton E, Ennis CL, Garcia A, Gerstenberg TL, Hill KA, Jain A, Krassovsky K, Lalisan CD, Lord D, Quejarro BJ, Sales-Lee J, Shah M, Silva BJ, Skowronski J, Strukov YG, Thomas J, Veraz M, Vijay T, Wallace KA, Yuan Y, Grogan JL, Wienert B, Lahiri P, Treusch S, Dever DP, Soros VB, Partridge JR, Seim KL. Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair. Nat Commun 2024; 15:2625. [PMID: 38521763 PMCID: PMC10960832 DOI: 10.1038/s41467-024-46816-5] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
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Affiliation(s)
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- Graphite Bio, South San Francisco, CA, USA
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- Graphite Bio, South San Francisco, CA, USA
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Strukov YG, Belmont AS. Mitotic chromosome structure: reproducibility of folding and symmetry between sister chromatids. Biophys J 2009; 96:1617-28. [PMID: 19217877 DOI: 10.1016/j.bpj.2008.10.051] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022] Open
Abstract
Mitotic chromosome structure and pathways of mitotic condensation remain unknown. The limited amount of structural data on mitotic chromosome structure makes it impossible to distinguish between several mutually conflicting models. Here we used a Chinese hamster ovary cell line with three different lac operator-tagged vector insertions distributed over an approximately 1 microm chromosome arm region to determine positioning reproducibility, long-range correlation in large-scale chromatin folding, and sister chromatid symmetry in minimally perturbed, metaphase chromosomes. The three-dimensional positions of these lac operator-tagged spots, stained with lac repressor, were measured in isolated metaphase chromosomes relative to the central chromatid axes labeled with antibodies to topoisomerase II. Longitudinal, but not axial, positioning of spots was reproducible but showed intrinsic variability, up to approximately 300 nm, between sister chromatids. Spot positions on the same chromatid were uncorrelated, and no correlation or symmetry between the positions of corresponding spots on sister chromatids was detectable, showing the absence of highly ordered, long-range chromatin folding over tens of mega-basepairs. Our observations are in agreement with the absence of any regular, reproducible helical, last level of chromosome folding, but remain consistent with any hierarchical folding model in which irregularity in folding exists at one or multiple levels.
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Affiliation(s)
- Yuri G Strukov
- Biophysics Program, University of Illinois, Urbana-Champaign, Illinois, USA
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Abstract
INTRODUCTIONThe discovery and use of fluorescent proteins to label chromosomal proteins has yielded basic structural information as well as insights into dynamics that were previously inaccessible. This protocol describes a method for tagging specific chromosome sites using the lac operator/repressor system, wherein direct repeats of bacterial operator sequences are coupled with green fluorescent protein (GFP)-tagged proteins that recognize these sequences. Direct lac operator repeats are generated by directional cloning. Although the use of direct repeats, as opposed to inverted repeats, reduces recombination within the bacterial host at high copy number, even the direct repeats are unstable, requiring the use of special bacterial hosts and low-copy-number plasmids for cloning. The introduction of the lac operator repeats into eukaryotic cells uses traditional transformation methods. Techniques for the isolation of stable cell clones with varying transgene copy numbers are described in the protocol, as are several methods for visual screening of large numbers of stable cell clones to isolate rare clones containing labeled chromosomal regions with desired features.
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Strukov YG, Wang Y, Belmont AS. Engineered chromosome regions with altered sequence composition demonstrate hierarchical large-scale folding within metaphase chromosomes. J Cell Biol 2003; 162:23-35. [PMID: 12835314 PMCID: PMC2172725 DOI: 10.1083/jcb.200303098] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitotic chromosome structure and DNA sequence requirements for normal chromosomal condensation remain unknown. We engineered labeled chromosome regions with altered scaffold-associated region (SAR) sequence composition as a formal test of the radial loop and other chromosome models. Chinese hamster ovary cells were isolated containing high density insertions of a transgene containing lac operator repeats and a dihydrofolate reductase gene, with or without flanking SAR sequences. Lac repressor staining provided high resolution labeling with good preservation of chromosome ultrastructure. No evidence emerged for differential targeting of SAR sequences to a chromosome axis within native chromosomes. SAR sequences distributed uniformly throughout the native chromosome cross section and chromosome regions containing a high density of SAR transgene insertions showed normal diameter and folding. Ultrastructural analysis of two different transgene insertion sites, both spanning less than the full chromatin width, clearly contradicted predictions of simple radial loop models while providing strong support for hierarchical models of chromosome architecture. Specifically, an approximately 250-nm-diam folding subunit was visualized directly within fully condensed metaphase chromosomes. Our results contradict predictions of simple radial loop models and provide the first unambiguous demonstration of a hierarchical folding subunit above the level of the 30-nm fiber within normally condensed metaphase chromosomes.
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Affiliation(s)
- Yuri G. Strukov
- Biophysics Program, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Yan Wang
- Department of Cell and Structural Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - Andrew S. Belmont
- Department of Cell and Structural Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801
- Biophysics Program, University of Illinois, Urbana-Champaign, Urbana, IL 61801
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