Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation

Youjin Hu (), Jiawei Zhong, Yuhua Xiao, Zheng Xing, Katherine Sheu, Shuxin Fan, Qin An, Yuanhui Qiu, Yingfeng Zheng, Xialin Liu, Guoping Fan and Yizhi Liu ()
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Youjin Hu: Sun Yat-Sen University
Jiawei Zhong: Sun Yat-Sen University
Yuhua Xiao: Sun Yat-Sen University
Zheng Xing: UCLA
Katherine Sheu: UCLA
Shuxin Fan: Sun Yat-Sen University
Qin An: UCLA
Yuanhui Qiu: Sun Yat-Sen University
Yingfeng Zheng: Sun Yat-Sen University
Xialin Liu: Sun Yat-Sen University
Guoping Fan: UCLA
Yizhi Liu: Sun Yat-Sen University

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract The differences in transcription start sites (TSS) and transcription end sites (TES) among gene isoforms can affect the stability, localization, and translation efficiency of mRNA. Gene isoforms allow a single gene diverse functions across different cell types, and isoform dynamics allow different functions over time. However, methods to efficiently identify and quantify RNA isoforms genome-wide in single cells are still lacking. Here, we introduce single cell RNA Cap And Tail sequencing (scRCAT-seq), a method to demarcate the boundaries of isoforms based on short-read sequencing, with higher efficiency and lower cost than existing long-read sequencing methods. In conjunction with machine learning algorithms, scRCAT-seq demarcates RNA transcripts with unprecedented accuracy. We identified hundreds of previously uncharacterized transcripts and thousands of alternative transcripts for known genes, revealed cell-type specific isoforms for various cell types across different species, and generated a cell atlas of isoform dynamics during the development of retinal cones.

Date: 2020
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DOI: 10.1038/s41467-020-18976-7

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