Nucleotide resolution sequencing of N4-acetylcytidine in RNA

Methods Enzymol. 2019:621:31-51. doi: 10.1016/bs.mie.2019.02.022. Epub 2019 Mar 12.

Abstract

Posttranscriptional modifications of RNA represent an emerging class of regulatory elements in human biology. Improved methods for studying how these elements are controlled and where they occur has the potential to transform our understanding of gene expression in development and disease. Here we describe a chemical method for nucleotide resolution sequencing of N4-acetylcytidine (ac4C), a highly conserved modified nucleobase whose formation is catalyzed by the essential cytidine acetyltransferase enzyme NAT10. This approach enables the sensitive, PCR-amplifiable detection of individual ac4C sites from nanograms of unfractionated cellular RNA. The sensitive and quantitative nature of this assay provides a powerful tool to understand how cytidine acetylation is targeted, profile RNA acetyltransferase dynamics, and validate the sites and stoichiometry of ac4C in novel RNA species.

Keywords: Epigenetics; Epitranscriptome; Kre33; Modifications; NAT10; Nucleotide resolution sequencing of N4-acetylcytidine in RNA: acetylation; RNA; Sequencing; TmcA N4-acetylcytidine.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Acetylation
  • Animals
  • Cell Line
  • Cytidine / analogs & derivatives*
  • Cytidine / analysis
  • Cytidine / genetics
  • Cytidine / metabolism
  • Humans
  • N-Terminal Acetyltransferases / metabolism
  • Polymerase Chain Reaction / methods
  • RNA / chemistry*
  • RNA / genetics
  • RNA / metabolism
  • RNA Processing, Post-Transcriptional
  • Sequence Analysis, RNA / methods*

Substances

  • N-acetylcytidine
  • Cytidine
  • RNA
  • N-Terminal Acetyltransferases
  • NAT10 protein, human