Work

CryEx.v2, an enhanced protocol for the quantitative detection and visualization of cryptic splicing using human transcriptome data

Year: 2026

Type: article

Abstract: Unraveling the mechanisms that suppress cryptic splicing is essential for maintaining transcriptome stability and developing therapeutic strategies in genetic disorders such as cancer. Here, we present a protocol to identify cryptic exons in human epithelial breast cells and quantify their inclusion utilizing RNA sequencing (RNA-seq) data. We describe steps for determining precise chromosome coordinates, calculating percent-spliced-in (PSI) values, classifying exons based on isoform presence, and conducting differential splicing analysis across conditions. We also detail procedures for visualizing a representative splicing event. For complete details on the use and execution of the original and this updated protocol, please refer to Zheng et al. 1 1. Zheng, R. ∙ Dunlap, M. ∙ Bobkov, G.O.M. ... hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing Mol. Cell. 2024; 84 :2087-2103.e8 Full Text Full Text (PDF) Scopus (28) PubMed Google Scholar

Source: STAR Protocols

DOI: 10.1016/j.xpro.2026.104931

Authors: Rong Zheng, Giovanni Quinones-Valdez, Xinshu Xiao, Chonghui Cheng

Institutions: Baylor College of Medicine, University of California, Los Angeles

Language: English

Topic: RNA Research and Splicing

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,550

Funders: Cancer Prevention and Research Institute of Texas, National Institute on Aging, National Cancer Institute, National Institute of General Medical Sciences