Introduction

RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, IRNA-SEQ: , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.

Publications

  1. iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data.
    Cite this
    Madsen JG, Schmidt SF, Larsen BD, Loft A, Nielsen R, Mandrup S, 2015-03-01 - Nucleic acids research

Credits

  1. Jesper Grud Skat Madsen
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  2. Søren Fisker Schmidt
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  3. Bjørk Ditlev Larsen
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  4. Anne Loft
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  5. Ronni Nielsen
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  6. Susanne Mandrup
    Investigator

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

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Summary
AccessionBT001423
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionDenmark
Submitted BySusanne Mandrup