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

Adelina Rabenius, Sajitha Chandrakumaran, Lea Sistonen, Anniina Vihervaara

Research output: Contribution to journalArticleScientificpeer-review

4 Citations (Scopus)
23 Downloads (Pure)

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).

Original languageEnglish
Article number101036
Number of pages23
JournalSTAR protocols
Volume3
Issue number1
DOIs
Publication statusPublished - 18 Mar 2022
MoE publication typeA1 Journal article-refereed

Keywords

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

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