Array-based nuclear run-on analysis

Jinshui Fan, Yu Chi Chen, Tonya Watkins, Chi V. Dang, Myriam Gorospe, Chris Cheadle

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

There is extensive evidence that posttranscriptional mechanisms of gene regulation, such as mRNA turnover, critically affect the patterns of expressed mRNAs. Conventional microarray analysis measures steady-state messenger RNA (mRNA) levels, which represents the dynamic balance between new transcription and mRNA degradation. Accordingly, only de novo transcription can accurately reflect the temporal and spatial events of transcriptional regulation. In this chapter, we describe a recently reported method to study transcription systematically. It involves the genome-wide labeling of nascent transcripts using nonradioactive modified nucleotides, their isolation for amplification, and their hybridization and analysis using commercial microarrays.

Original languageEnglish (US)
Title of host publicationTranscriptional Regulation
Subtitle of host publicationMethods and Protocols
EditorsAles Vancura
Pages505-517
Number of pages13
DOIs
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
Volume809
ISSN (Print)1064-3745

Keywords

  • Biotin
  • Microarray
  • Nascent RNA
  • Nuclear run-on
  • Posttranscriptional regulation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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