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.


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


  • RNA