中国科学院动物研究所赵方庆团队使用PROFIT-seq实现实时和可编程的转录组测序。该项研究成果于2024年10月23日在线发表在《自然—细胞生物学》杂志上。

研究人员描述了一种可编程全长异构体转录组测序方法（PROFIT-seq），该方法在保持对整个转录组无偏量化的同时富集靶向转录本。PROFIT-seq通过组合逆转录捕获聚腺苷化、非聚腺苷化和环状RNA，并结合可编程控制系统，在测序过程中选择性富集靶向转录本。

该方法实现了数据有效产出的3倍以上增加，并将检测特定病原体或关键突变所需的时间减少了75%。研究人员将PROFIT-seq应用于结直肠息肉的研究，并揭示了宿主免疫反应与细菌感染之间的复杂关系。PROFIT-seq为靶向转录本的精确高效测序提供了有力工具，同时保留了整体转录组的量化，在临床诊断和靶向富集场景中具有广泛应用。

据悉，真核转录组的高度多样性和复杂性使得有效检测特定感兴趣的转录本变得困难。当前的靶向RNA测序方法通常需要复杂的测序前富集步骤，这可能会影响整个转录组的全面表征。

附：英文原文

Title: Real-time and programmable transcriptome sequencing with PROFIT-seq

Author: Zhang, Jinyang, Hou, Lingling, Ma, Lianjun, Cai, Zhengyi, Ye, Shujun, Liu, Yang, Ji, Peifeng, Zuo, Zhenqiang, Zhao, Fangqing

Issue&Volume: 2024-10-23

Abstract: The high diversity and complexity of the eukaryotic transcriptome make it difficult to effectively detect specific transcripts of interest. Current targeted RNA sequencing methods often require complex pre-sequencing enrichment steps, which can compromise the comprehensive characterization of the entire transcriptome. Here we describe programmable full-length isoform transcriptome sequencing (PROFIT-seq), a method that enriches target transcripts while maintaining unbiased quantification of the whole transcriptome. PROFIT-seq employs combinatorial reverse transcription to capture polyadenylated, non-polyadenylated and circular RNAs, coupled with a programmable control system that selectively enriches target transcripts during sequencing. This approach achieves over 3-fold increase in effective data yield and reduces the time required for detecting specific pathogens or key mutations by 75%. We applied PROFIT-seq to study colorectal polyp development, revealing the intricate relationship between host immune responses and bacterial infection. PROFIT-seq offers a powerful tool for accurate and efficient sequencing of target transcripts while preserving overall transcriptome quantification, with broad applications in clinical diagnostics and targeted enrichment scenarios.

DOI: 10.1038/s41556-024-01537-1

Source: https://www.nature.com/articles/s41556-024-01537-1