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

BMC Genomics

Research Article

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

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

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

DOI  :  10.1186/1471-2164-13-574

 received in 2012-07-11, accepted in 2012-10-22,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsFor 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.ConclusionsWe 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.

【 授权许可】

Unknown   
© Solnestam et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.