Massively Parallel Analysis of Regulatory RNA Sequences

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


The stability of RNA transcripts is regulated by signals within their sequences, but the identity of those signals still remain elusive in many biological systems. Recently introduced massively parallel tools for the analysis of regulatory RNA sequences provide the ability to detect functional cis-regulatory sequences of post-transcriptional RNA regulation at a much larger scale and resolution than before. Their application formulates the underlying sequence-based rules and predicts the impact of genetic variations. Here, we describe the application of UTR-Seq, as a strategy to uncover cis-regulatory signals of RNA stability during early zebrafish embryogenesis. The method combines massively parallel reporter assays (MPRA) with computational regression models. It surveys the effect of tens of thousands of regulatory sequences on RNA stability and analyzes the results via regression models to identify sequence signals that impact RNA stability and to predict the in vivo effect of sequence variations.

Original languageAmerican English
Title of host publicationMethods in Molecular Biology
Number of pages11
StatePublished - 2021

Publication series

NameMethods in Molecular Biology


  • Cis-regulation
  • Massively parallel reporter assays
  • Post-transcriptional regulation
  • RNA stability
  • UTR-Seq
  • Zebrafish embryogenesis

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics


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