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

• 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).

Ämnesord

NATURVETENSKAP  -- Biologi -- Utvecklingsbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Developmental Biology (hsv//eng)

Nyckelord

Bioinformatics

Chromatin immunoprecipitation (ChIP)

Gene Expression

Genetics

Genomics

RNAseq

Systems biology

RNA

human

nucleotide sequence

procedures

promoter region

regulatory sequence

sequence analysis

Base Sequence

Humans

Promoter Regions

Genetic

Regulatory Sequences

Nucleic Acid

Sequence Analysis

RNA

Publikations- och innehållstyp

ref (ämneskategori)

art (ämneskategori)