Quantifying RNA synthesis at rate-limiting steps of transcription using nascent RNA-sequencing data

Adelina Rabenius; Sajitha Chandrakumaran; Lea Sistonen; Anniina Vihervaara

doi:10.1016/j.xpro.2021.101036

Quantifying RNA synthesis at rate-limiting steps of transcription using nascent RNA-sequencing data

STAR Protoc. 2022 Jan 5;3(1):101036. doi: 10.1016/j.xpro.2021.101036. eCollection 2022 Mar 18.

Authors

Adelina Rabenius¹, Sajitha Chandrakumaran¹, Lea Sistonen^{2

3}, Anniina Vihervaara¹

Affiliations

¹ KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.
² Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland.
³ Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.

Abstract

Nascent RNA-sequencing tracks transcription at nucleotide resolution. The genomic distribution of engaged transcription complexes, in turn, uncovers functional genomic regions. Here, we provide analytical steps to (1) identify transcribed regulatory elements de novo genome-wide, (2) quantify engaged transcription complexes at enhancers, promoter-proximal regions, divergent transcripts, gene bodies, and termination windows, and (3) measure distribution of transcription machineries and regulatory proteins across functional genomic regions. This protocol tracks engaged transcription complexes across functional genomic regions demonstrated in human K562 erythroleukemia cells. For complete details on the use and execution of this protocol, please refer to Vihervaara et al. (2021).

Keywords: Bioinformatics; Chromatin immunoprecipitation (ChIP); Gene Expression; Genetics; Genomics; RNAseq; Systems biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Humans
Promoter Regions, Genetic
RNA* / genetics
Regulatory Sequences, Nucleic Acid*
Sequence Analysis, RNA / methods

Substances

RNA