A1 Refereed original research article in a scientific journal
Quantifying RNA synthesis at rate-limiting steps of transcription using nascent RNA-sequencing data
Authors: Rabenius Adelina, Chandrakumaran Sajitha, Sistonen Lea, Vihervaara Anniina
Publisher: Cell Press
Publication year: 2022
Journal: STAR protocols
Journal name in source: STAR Protocols
Article number: 101036
Volume: 3
Issue: 1
eISSN: 2666-1667
DOI: https://doi.org/10.1016/j.xpro.2021.101036
Web address : https://doi.org/10.1016/j.xpro.2021.101036
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/175006010
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.
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