Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation

Methods Mol Biol. 2021:2324:115-129. doi: 10.1007/978-1-0716-1503-4_8.

Abstract

Pseudogenes may regulate expression of their parental genes as well as other protein-coding genes through various mechanisms. One such mechanism is the ability to act as competitive endogenous RNA (ceRNA) and participate in microRNA-mediated cross-regulation. Here, we outline how to predict the targets of pseudogene ceRNAs bioinformatically and how to validate them experimentally.

Keywords: 3′UTR; Prediction; Pseudogene; Validation; ceRNA.

Publication types

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

MeSH terms

  • 3' Untranslated Regions
  • Animals
  • Cell Line
  • Computational Biology / methods*
  • Gene Silencing
  • Genomics / methods
  • Humans
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Pseudogenes / genetics*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Small Interfering
  • Regulatory Sequences, Ribonucleic Acid / genetics*
  • Transfection

Substances

  • 3' Untranslated Regions
  • MicroRNAs
  • RNA, Messenger
  • RNA, Small Interfering
  • Regulatory Sequences, Ribonucleic Acid