Nuclear RNA Isolation and Sequencing

  • Navroop K. Dhaliwal
  • Jennifer A. MitchellEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)


Most transcriptome studies involve sequencing and quantification of steady-state mRNA by isolating and sequencing poly (A) RNA. Although this type of sequencing data is informative to determine steady-state mRNA levels it does not provide information on transcriptional output and thus may not always reflect changes in transcriptional regulation of gene expression. Furthermore, sequencing poly (A) RNA may miss transcribed regions of the genome not usually modified by polyadenylation which includes many long noncoding RNAs. Here, we describe nuclear-RNA sequencing (nucRNA-seq) which investigates the transcriptional landscape through sequencing and quantification of nuclear RNAs which are both unspliced and spliced transcripts for protein-coding genes and nuclear-retained long noncoding RNAs.

Key words

Transcriptome profiling LncRNA Nuclear RNA Cellular fractionation Massively parallel sequencing 



This work was supported by the Canadian Institutes of Health Research, the Canada Foundation for Innovation, and the Ontario Ministry of Research and Innovation (operating and infrastructure grants held by J.A.M.). Studentship funding held by N.K.D. was provided by Ontario Graduate Scholarships.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada

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