Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq

STAR Protoc. 2021 Mar 18;2(1):100366. doi: 10.1016/j.xpro.2021.100366. eCollection 2021 Mar 19.

Abstract

Double-stranded RNAs (dsRNAs) are abundantly present in cells, playing multiple regulatory functions. dsRNAs of viral origin activate innate immune responses. Since RNA editing and modifications affect the structure and recognition of RNAs, their alteration can result in the accumulation of aberrant endogenous dsRNAs inducing a deleterious innate immune response. Here, we present a complete protocol for the measurement of dsRNAs in a live mouse tissue using dsRNA immunoprecipitation and sequencing (dsRIP-Seq). This protocol focuses on tissue isolation, dsRNA immunoprecipitation and downstream computational analysis. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020).

Keywords: Cell Biology; Immunology; Model Organisms; RNA-seq; Sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / genetics
  • Adenosine Deaminase / genetics
  • Animals
  • Fetus / cytology
  • Gene Expression / genetics
  • Gene Expression Profiling / methods*
  • Immunity, Innate / genetics
  • Immunity, Innate / physiology
  • Immunoprecipitation / methods*
  • Liver / cytology
  • Mice
  • RNA / analysis*
  • RNA / chemistry
  • RNA / genetics
  • RNA Editing / genetics
  • RNA, Double-Stranded / genetics
  • Transcriptome / genetics

Substances

  • RNA, Double-Stranded
  • RNA
  • Adenosine Deaminase
  • Adenosine