Protocol for quantitative analysis of RNA 3'-end processing induced by disassociated subunits using chromatin-associated RNA-seq data

Jie Huang; Lijun Bao; Junyi Zhu; Xiong Ji

doi:10.1016/j.xpro.2023.102356

Protocol for quantitative analysis of RNA 3'-end processing induced by disassociated subunits using chromatin-associated RNA-seq data

STAR Protoc. 2023 Sep 15;4(3):102356. doi: 10.1016/j.xpro.2023.102356. Epub 2023 Jun 15.

Authors

Jie Huang¹, Lijun Bao², Junyi Zhu², Xiong Ji³

Affiliations

¹ Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: [email protected].
² Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
³ Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: [email protected].

Abstract

Sequencing chromatin-associated RNA using libraries from the chromatin fraction makes it possible to characterize RNA processing driven by disassociated subunits. Here, we present an experimental strategy and computational pipeline for processing chromatin-associated RNA-seq data to detect and quantify readthrough transcripts. We describe steps for constructing degron mouse embryonic stem cells, detecting readthrough genes, data processing, and data analysis. This protocol can be adapted to various biological scenarios and other types of nascent RNA-seq, such as TT-seq. For complete details on the use and execution of this protocol, please refer to Li et al. (2023).¹.

Keywords: Bioinformatics; Gene Expression; Genomics.

MeSH terms

Animals
Chromatin* / genetics
High-Throughput Nucleotide Sequencing* / methods
Mice
RNA / genetics
RNA Processing, Post-Transcriptional
RNA, Small Nuclear
RNA-Seq

Substances

Chromatin
RNA
RNA, Small Nuclear