Array-Based Nuclear Run-On Analysis

  • Jinshui Fan
  • Yu-Chi Chen
  • Tonya Watkins
  • Chi V. Dang
  • Myriam Gorospe
  • Chris CheadleEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 809)


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.

Key words

Nascent RNA Nuclear run-on Biotin Microarray Posttranscriptional regulation 


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Jinshui Fan
    • 1
  • Yu-Chi Chen
    • 1
  • Tonya Watkins
    • 2
  • Chi V. Dang
    • 3
  • Myriam Gorospe
    • 4
  • Chris Cheadle
    • 1
    Email author
  1. 1.Lowe Family Genomics Core, Division of Allergy and Clinical Immunology, Department of MedicineThe Johns Hopkins University School of MedicineBaltimoreUSA
  2. 2.MS Lowe Family Genomics Core, Division of Allergy and Clinical Immunology, Department of MedicineThe Johns Hopkins University School of MedicineBaltimoreUSA
  3. 3.Division of Hematology, Departments of Medicine, Cell Biology, Oncology, and PathologyThe Johns Hopkins University School of MedicineBaltimoreUSA
  4. 4.Laboratory of Cellular and Molecular BiologyNational Institute on Aging-Intramural Research Program, NIHBaltimoreUSA

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