# The editable landscape of the yeast genome reveals hotspots of structural variant formation

## TL;DR

This study maps regions in the yeast genome where CRISPR editing is more likely to cause unintended changes and introduces a tool to predict and reduce these risks.

## Contribution

The study provides a genome-wide map of CRISPR editing hotspots and introduces SCORE, a predictive model for structural variant risk.

## Key findings

- Unintended edits, including structural variants, are enriched in specific genomic contexts.
- The SCORE model identified 562 SV hotspots covering 4.8% of the genome.
- Donor repair strategies reduced SVs in moderate-risk regions but not high-risk ones.

## Abstract

It is unclear how CRISPR editing outcomes vary across the genome and whether undesirable events such as structural variants (SVs) are predictable or preventable. To define a genome-wide map of editability, we performed whole-genome sequencing on 1875 budding yeast clones edited across 16 chromosomes by CRISPR-Cas9 and donor-templated repair. We found that unintended edits, including short indels and SVs, were enriched in specific genomic and sequence contexts. We developed a predictive model, SCORE (System for CRISPR Outcome and Risk Evaluation), which revealed 4.8% of the genome as SV prone, consisting of 562 SV hotspots. Donor repair-enhancing strategies suppressed SV formation in regions with moderate, but not high, predicted risk. Applying SCORE to the Sc2.0 synthetic yeast genome revealed a markedly altered SV landscape due to the removal of endogenous repetitive elements and the insertion of loxP sites. Our study provides the genome-scale map of SV hotspots after CRISPR editing and predictive and experimental tools to mitigate their formation.

Some parts of the genome are intrinsically difficult to edit, necessitating systematic approaches to elucidate their patterns.