A1 Refereed original research article in a scientific journal

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




AuthorsRabenius Adelina, Chandrakumaran Sajitha, Sistonen Lea, Vihervaara Anniina

PublisherCell Press

Publication year2022

JournalSTAR protocols

Journal name in sourceSTAR Protocols

Article number101036

Volume3

Issue1

eISSN2666-1667

DOIhttps://doi.org/10.1016/j.xpro.2021.101036

Web address https://doi.org/10.1016/j.xpro.2021.101036

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/175006010


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.


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Last updated on 2025-27-03 at 21:55