Kuban, M. | Search bioRxiv

bioRxiv2025

Context-dependent effects of mutations on complex splicing decisions

Alternative pre-mRNA splicing is an essential step in human gene regulation, and mutation-induced aberrant splicing is frequently found in diseases and therapy resistance. Splicing regulation is highly dependent on sequence and cellular context, posing a challenge to predict outcomes of splicing-related disease mutations. Here, we use kinetic modeling to derive the underlying quantitative principles, describing splice site competition and downstream effects on a wide spectrum of splice isoforms. Employing statistical learning on a large-scale mutagenesis dataset for CD19 mRNA splicing, our model quantitatively describes the generation of 93 RNA isoforms. It takes into account various splicing events such as cassette exon skipping, intron retention, and extensive alternative 3 and 5 splice site usage, which are implicated in CART therapy resistance in leukemia. Beyond CD19, by analyzing genome-wide RNA sequencing data and large-scale screening of synthetic splicing decisions, we find that splice site distance is an important parameter controlling the switch from canonical to alternative/cryptic splice site usage, as mutations located in between two nearby splice sites show a pronounced directionality, regulating up- and downstream effectors in opposite direction. Taken together, our work demonstrates that a quantitative description of splice site competition provides insights into context-dependent, complex isoform changes and cryptic splice site activation in health and disease.

systems biology↗

bioRxiv2024

CRISPR gene and transcriptome engineering (CRISPRgate) improves loss-of-function genetic screening approaches

The CRISPR/Cas9 technology has revolutionized genotype-to-phenotype assignments through large-scale loss-of-function (LOF) screens. However, limitations like editing inefficiencies and unperturbed genes cause significant noise in data collection. To address this, we introduce CRISPR Gene and Transcriptome Engineering (CRISPRgate), which uses two specific sgRNAs to simultaneously repress and cleave the target gene within the same cell, increasing LOF efficiencies and reproducibility. CRISPRgate outperforms conventional CRISPRko, CRISPRi, or CRISPRoff systems in suppressing challenging targets and regulators of cell proliferation. Additionally, it efficiently suppresses modulators of EMT and impairs neuronal differentiation in a human iPSC model. In a multiplexed chromatin-focused phenotypic LOF screen, CRISPRgate exhibits improved depletion efficiency, reduced sgRNA performance variance, and accelerated gene depletion compared to individual CRISPRi or CRISPRko, ensuring consistency in phenotypic effects and identifying more significant gene hits. By combining CRISPRko and CRISPRi, CRISPRgate increases LOF rates without increasing genotoxic stress, facilitating library size reduction for advanced LOF screens. MotivationThe CRISPR technology (CRISPRko/CRISPRi) enables the specific depletion of target genes with fewer off-target effects, facilitating precise investigations of gene function. Despite its benefits, CRISPR applications have limitations. Residual active protein expression mediated by in-frame DNA repair or alternative splicing1-8 as well as strong epigenetic regulation and difficulties in sgRNA design to the transcription start site (TSS)9-12 hinder the full potential of loss-of-function studies using CRISPRko or CRISPRi. We aimed to achieve robust target gene reduction in order to improve the reproducibility of the CRISPR technology by integrating the widely used CRISPRko and CRISPRi approaches into a single application.

biochemistry↗