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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Updated: May 24, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Hazuki Takahashi1, Timo Lassmann, Mitsuyoshi Murata

  • 1RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan.

Nature Protocols
|February 25, 2012
PubMed
Summary
This summary is machine-generated.

This study optimizes Cap-analysis gene expression (CAGE) for accurate RNA expression measurement. The enhanced protocol provides single-nucleotide resolution of transcriptional start sites, aiding gene regulatory network construction.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Cap-analysis gene expression (CAGE) is a high-throughput method for measuring RNA expression.
  • CAGE enables precise mapping of RNA initiation sites and transcriptional start sites (TSS).
  • Understanding TSS is crucial for studying gene regulatory mechanisms and transcriptional networks.

Purpose of the Study:

  • To provide an optimized protocol for constructing CAGE libraries.
  • To improve the efficiency and accessibility of CAGE technology.
  • To facilitate the study of gene expression regulation at single-nucleotide resolution.

Main Methods:

  • Development of an optimized protocol for CAGE library preparation.
  • Utilizing 27-nt-long tags corresponding to the 5' ends of capped RNAs.
  • Incorporation of filtration-based steps for streamlined library construction, completed in 4 days.

Main Results:

  • An optimized 4-day protocol for CAGE library construction.
  • Generation of 27-nt CAGE tags with single-nucleotide resolution.
  • Demonstrated compatibility of CAGE tags with Illumina sequencing and other platforms.

Conclusions:

  • The optimized CAGE protocol is efficient and accessible.
  • This method enhances the study of RNA expression and gene regulation.
  • The protocol facilitates the construction of transcriptional networks through precise TSS mapping.