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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Updated: Mar 20, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences.

C E Brule1, K M Dean1, E J Grayhack1

  • 1Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States.

Methods in Enzymology
|June 1, 2016
PubMed
Summary

RNA-ID is a sensitive method for discovering gene regulatory sequences in yeast. This system uses fluorescence assays to analyze regulatory elements affecting gene expression, aiding biological research.

Keywords:
Flow cytometryRNA-IDTranslationYeast

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • Gene expression regulation is fundamental to biological processes.
  • Identifying regulatory sequences is crucial for understanding gene function.
  • Existing methods may lack efficiency or sensitivity in regulatory sequence discovery.

Purpose of the Study:

  • To describe the RNA-ID system for identifying and analyzing cis-regulatory sequences.
  • To detail the methodology for constructing and assaying RNA-ID reporter variants.
  • To present applications and modifications of the RNA-ID system for various research needs.

Main Methods:

  • Utilizes a dual-fluorescence reporter system with green fluorescent protein (GFP) and red fluorescent protein (RFP) in Saccharomyces cerevisiae.
  • Employs fluorescence-based assays and flow cytometry for sensitive detection of regulatory sequence activity.
  • Describes methods for analyzing single regulatory sequences and screening libraries of strains.

Main Results:

  • The RNA-ID system provides an efficient and sensitive approach to discover and investigate regulatory sequences.
  • Detailed methodology covers reporter construction, single-sequence analysis, and library screening.
  • The system is adaptable for various applications in studying gene regulation.

Conclusions:

  • RNA-ID is a valuable tool for the comprehensive study of cis-regulatory sequences in yeast.
  • The described methodology facilitates detailed analysis and high-throughput screening of regulatory elements.
  • This system advances the understanding of gene expression regulation in biological systems.