ArticleNucleic acids research2010
A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 25 citations in OpenAlex.
- Influence of HIV-1 Genomic RNA on the Formation of Gag Biomolecular Condensates.Journal of molecular biology · 2023Article
- Fine-grained cell-type specific association studies with human bulk brain data using a large single-nucleus RNA sequencing based reference panel.Scientific reports · 2023Article
- Adenosine Kinase on Deoxyribonucleic Acid Methylation: Adenosine Receptor-Independent Pathway inFrontiers in pharmacology · 2022Review
- NanoSINC-seq dissects the isoform diversity in subcellular compartments of single cells.Science advances · 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
- Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.Nucleic acids research · 2021Article
- Dysregulation of adenosine kinase isoforms in breast cancer.Oncotarget · 2019Article
- Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo.Plant reproduction · 2019Article
- The determinants of alternative RNA splicing in human cells.Molecular genetics and genomics : MGG · 2017Review
- Inhibition of nonsense-mediated RNA decay by ER stress.RNA (New York, N.Y.) · 2017Article
- miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif.Frontiers in molecular neuroscience · 2017Article
- Nonsense-mediated RNA decay--a switch and dial for regulating gene expression.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Article
- Role of Pnn in alternative splicing of a specific subset of lncRNAs of the corneal epithelium.Molecular vision · 2014Article
- Characterization and comparison of human nuclear and cytosolic editomes.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing.Genome research · 2013Article
- PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2.Nature neuroscience · 2012Article
- mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance.Nucleic acids research · 2011Article
- Implementation of exon arrays: alternative splicing during T-cell proliferation as determined by whole genome analysis.BMC genomics · 2010Article
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1 author at 1 institution in 1 country.
Funding
Abstract
Transcriptome analyses have typically disregarded nucleocytoplasmic differences. This approach has ignored some post-transcriptional regulations and their effect on the ultimate protein expression levels. Despite a longstanding interest in the differences between the nuclear and cytosolic transcriptomes, it is only recently that data have become available to study such differences and their associated features on a genome-wide scale. Here, we compared the nuclear and cytosolic transcriptomes of HepG2 and HeLa cells. HepG2 and HeLa cells vary significantly in the differential compartmentalization of their transcript isoforms, indicating that nucleocytoplasmic compartmentalization is a cell-specific characteristic. The differential compartmentalization is manifested at the transcript isoform level instead of the gene level because alternative isoforms of one gene can display different nucleocytoplasmic distributions. The isoforms enriched in the cytosol tend to have more introns and longer introns in their pre-mRNAs. They have more functional RNA folds and unique exons in the 3' regions. These isoforms are more conserved than the isoforms enriched in the nucleus. Surprisingly, the presence of microRNAs does not have a significant impact on the nucleocytoplasmic distribution of their target isoforms. In contrast, nonsense-mediated decay is significantly more associated with the isoforms enriched in the nucleus than those enriched in the cytosol.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.