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Open Access Research article

Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs

Beata Werne Solnestam1, Henrik Stranneheim1, Jimmie Hällman1, Max Käller1, Emma Lundberg2, Joakim Lundeberg1* and Pelin Akan1

Author Affiliations

1 KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65, Solna, Sweden

2 KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Proteomics, SE-171 65, Solna, Sweden

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BMC Genomics 2012, 13:574  doi:10.1186/1471-2164-13-574

Published: 30 October 2012

Abstract

Background

The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing.

Results

For all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level.

Conclusions

We conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.

Keywords:
Differential detection; Gene expression; Nuclear retention; miRNA regulation; RNA-Seq