Multiplex and Combinatorial Genome Editing: Mechanisms, Kinetics, and Structural Basis of CRISPR-Cas Systems.

This Research Topic is part of a set of companion collections; authors are welcome to submit to either this collection or text , depending on which best aligns with their expertise and the focus of their work.CRISPR-Cas systems have expanded genome engineering beyond single-site editing to enable multiplex and combinatorial perturbations, where multiple genomic loci can be targeted simultaneously or in defined combinations. These approaches are central to probing genetic interactions, engineering complex phenotypes, and advancing synthetic and therapeutic applications. However, key determinants of performance—efficiency, specificity, scalability, and outcome distribution—are governed by underlying mechanisms. When multiple targets are engaged, CRISPR effectors operate within competing kinetic pathways shaped by guide RNA architecture, target accessibility, enzyme availability, and structural constraints.From target search across multiple loci to coordinated binding, cleavage, and repair, multiplex CRISPR activity involves interconnected steps influenced by kinetic competition and system-level interactions. Differences in binding rates, cleavage probabilities, and repair outcomes can lead to uneven editing, target bias, and combinatorial variability. Understanding these processes in terms of rate constants, structural transitions, and interaction networks is essential for rationally improving multiplex editing strategies and achieving predictable, high-fidelity outcomes.This Research Topic will bring together studies that dissect multiplex and combinatorial genome editing through the lens of mechanism, kinetics, and structural basis. We welcome contributions spanning quantitative biochemistry, structural biology, single-molecule and high-throughput approaches, and computational modeling that reveal how CRISPR systems coordinate multiple editing events. Particular interest includes work linking mechanistic insights to functional outcomes, such as editing efficiency across targets, guide competition, off-target effects in multiplex settings, and control of combinatorial perturbations.We encourage submissions that address, but are not limited to, the following themes:1. Kinetic frameworks for multiplex CRISPR activity, including target competition, binding hierarchies, and enzyme turnover2. Structural determinants of multiplex capability, including conformational constraints and engineered CRISPR architectures3. Guide RNA design and multiplexing strategies, including arrays, expression systems, and orthogonal Cas platforms4. Mechanistic interplay between CRISPR activity and DNA repair pathways in multi-target contexts5. Quantitative and computational models of combinatorial editing outcomes and variability6. High-throughput and single-cell approaches to map multiplex perturbations and genetic interactions7. Engineering approaches to improve specificity, scalability, and control in multiplex systems8. Applications of combinatorial genome editing in functional genomics, synthetic biology, and therapeutic developmentArticle types include Original Research, Methods, Reviews, and Mini-Reviews, with a particular emphasis on Original Research articles that deliver quantitative and mechanistic insights into multiplex and combinatorial genome editing. Topic editors: Kirtikumar Kondhare, Tianzi Wei Source: https://www.frontiersin.org/research-topics/79745/multiplex-and-combinatorial-genome-editing-mechanisms-kinetics-and-structural-basis-of-crispr-cas-systems