Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing

Genome Biology

Hanlee P. Ji¹  Billy T. Lau¹  Heon Seok Kim¹  Susan M. Grimes¹  Anna C. Hooker¹ 

[1] Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, CA-94305, Stanford, USA;

关键词: Single-cell long-read CRISPR screen;    Single-cell CRISPR screen;    Single-cell long-read sequencing;    Single-cell sequencing;    Alternative splicing;    Transcript isoform;   

DOI  :  10.1186/s13059-021-02554-1

来源: Springer

【 摘 要 】

We developed a single-cell approach to detect CRISPR-modified mRNA transcript structures. This method assesses how genetic variants at splicing sites and splicing factors contribute to alternative mRNA isoforms. We determine how alternative splicing is regulated by editing target exon-intron segments or splicing factors by CRISPR-Cas9 and their consequences on transcriptome profile. Our method combines long-read sequencing to characterize the transcript structure and short-read sequencing to match the single-cell gene expression profiles and gRNA sequence and therefore provides targeted genomic edits and transcript isoform structure detection at single-cell resolution.

【 授权许可】

CC BY