Fussing, B. | bioRxiv Science

bioRxiv2025

BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments

CRISPR base editors enable scalable targeted DNA mutagenesis and are a powerful tool for the interpretation of gene function, the study of variants of unknown significance, and disease modelling. Existing guide RNA (gRNA) design tools focus on engineering a small number of targeted variants in a given gene or lack comprehensive functional annotation of target sequences. Here we developed BEstimate, a flexible computational pipeline that systematically specifies base editor gRNA target sites, generates gRNA off-target predictions, and rich functional, structural and clinical annotations of targeted edits. BEstimate accommodates custom gRNA design against variant alleles, improving editing accuracy and facilitating the programmed reversion of disease variants. BEstimate is a freely available, versatile tool for designing gRNA libraries and analysing base editor screens.

bioinformatics↗

bioRxiv2024

A genome-scale single cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines

Population-scale resources of genetic, molecular, and cellular information form the basis for understanding human genomes, charting the heritable basis of disease, and tracing the effects of mutations. Pooled perturbation assays applied to cellular models, probing the effect of many perturbations coupled with an scRNA-seq readout (Perturb-seq), are especially potent references for interpreting disease-linked mutations or gene expression changes. However, the utility of existing maps has been limited by the comprehensiveness of perturbations possible, and the relevance of their cell line context. Here, we present the first genome-scale CRISPR interference (CRISPRi) perturbation map with single-cell RNA sequencing readout across many human genetic backgrounds in human pluripotent cells. To do so, we establish large-scale CRISPRi screening in human induced pluripotent stem cells from healthy donors, using over 20,000 guide RNAs to target 7,226 genes across 34 cell lines from 26 genetic backgrounds, and gather expression data from nearly 2 million cells. We comprehensively map trans expression changes induced by the target knockdowns, which complement co-expression patterns in unperturbed cells and facilitate the functional annotation of target genes to biological processes and complexes. Consistency of targeting protein complex members point to protein complexes as a nexus for aggregating transcriptional variation, revealing novel interaction partners. We characterise variation in perturbation effects across donors, with expression quantitative trait loci linked to higher genetic modulation of perturbation effects but overall low replication of trans effects due to knockdown of their corresponding cis regulators. This study pioneers population-scale CRISPR perturbations with single cell readouts that will fuel foundation models for the future of effective modulation of cellular disease phenotypes.

genetics↗