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Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
Published on: May 17, 2014
A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of
1Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. liang.chen@usc.edu
Nucleic Acids Research
|December 9, 2009
Summary
Cell-specific differences in nucleocytoplasmic compartmentalization of transcript isoforms were observed. Cytosolic isoforms show distinct structural and conservation features compared to nuclear ones.
Area of Science:
- Molecular Biology
- Genomics
- Cell Biology
Background:
- Traditional transcriptome analyses often overlook nucleocytoplasmic differences.
- This oversight neglects post-transcriptional regulations impacting protein expression.
- Recent advancements enable genome-wide study of nuclear vs. cytosolic transcriptomes.
Purpose of the Study:
- To compare nuclear and cytosolic transcriptomes in HepG2 and HeLa cells.
- To investigate cell-specific characteristics of nucleocytoplasmic compartmentalization.
- To identify features associated with differential transcript isoform distribution.
Main Methods:
- Comparative transcriptome analysis of nuclear and cytosolic fractions.
- Utilized HepG2 and HeLa cell lines for study.
- Analyzed transcript isoform features, including introns, exons, and RNA folds.
Main Results:
- Significant cell-specific differences in transcript isoform compartmentalization were found.
- Differential distribution occurs at the isoform level, not the gene level.
- Cytosolic isoforms exhibit more introns, longer introns, unique 3' exons, and higher conservation.
- MicroRNA impact on distribution is minimal, while nonsense-mediated decay favors nuclear isoforms.
Conclusions:
- Nucleocytoplasmic compartmentalization is a cell-specific trait.
- Transcript isoform features dictate their subcellular localization.
- Nonsense-mediated decay plays a role in nuclear enrichment of certain isoforms.
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