ArticleBMC genomics2012
Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Transcriptional and functional profiles of muscarinic receptor-expressing neurons in primate lateral prefrontal and anterior cingulate cortices.Communications biology · 2026Article
- ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics.Nature communications · 2025Article
- Widespread posttranscriptional regulation of cotransmission.Science advances · 2023Article
- Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells.Scientific reports · 2023Article
- Review
- Widespread post-transcriptional regulation of co-transmission.bioRxiv : the preprint server for biology · 2023Article
- Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function.Science (New York, N.Y.) · 2022Article
- Dissecting the transcriptome in cardiovascular disease.Cardiovascular research · 2022Review
- Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.Cell reports · 2021Article
- INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison.International journal of molecular sciences · 2021Article
- Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.Scientific reports · 2021Article
- Heterogeneous glutamatergic receptor mRNA expression across phrenic motor neurons in rats.Journal of neurochemistry · 2020Article
- Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation.Genome research · 2020Article
- Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Isolation and genome-wide characterization of cellular DNA:RNA triplex structures.Nucleic acids research · 2019Article
- Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo.Plant reproduction · 2019Article
- The Cyclin-Dependent Kinase 5 Inhibitor Peptide Inhibits Herpes Simplex Virus Type 1 Replication.Scientific reports · 2019Article
- Adolescent social isolation affects parvalbumin expression in the medial prefrontal cortex in the MAM-E17 model of schizophrenia.Metabolic brain disease · 2019Article
- Physiological and Epigenetic Features of Yoyo Dieting and Weight Control.Frontiers in genetics · 2019Review
- Nuclear Compartmentalization Contributes to Stage-Specific Gene Expression Control inFrontiers in cell and developmental biology · 2017Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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