iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data

Nucleic Acids Res. 2015 Mar 31;43(6):e40. doi: 10.1093/nar/gku1365. Epub 2015 Jan 6.


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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Chromatin Immunoprecipitation / methods
  • Chromatin Immunoprecipitation / statistics & numerical data
  • Gene Expression Profiling / methods*
  • Gene Expression Profiling / statistics & numerical data
  • Gene Expression Regulation
  • Genome, Human
  • Humans
  • Introns
  • Sequence Analysis, RNA / methods*
  • Sequence Analysis, RNA / statistics & numerical data