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Methods Mol Biol. 2012;809:505-17. doi: 10.1007/978-1-61779-376-9_33.

Array-based nuclear run-on analysis.

Author information

1
Lowe Family Genomics Core, Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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.

PMID:
22113297
PMCID:
PMC3504798
DOI:
10.1007/978-1-61779-376-9_33
[Indexed for MEDLINE]
Free PMC Article

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