ArticlePLoS genetics2017
Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells.
Article in PLoS genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
- The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis.Nature cell biology · 2026Article
- Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.Molecular systems biology · 2024Article
- Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle.Nature communications · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Nuclear export is a limiting factor in eukaryotic mRNA metabolism.PLoS computational biology · 2024Article
- Rapid nuclear deadenylation of mammalian messenger RNA.iScience · 2023Article
- PRD-2 mediates clock-regulated perinuclear localization of clock gene RNAs within the circadian cycle ofProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver.PLoS genetics · 2022Article
- A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis.Developmental cell · 2022Article
- Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages.Genome research · 2022Article
- Seeking a Role for Translational Control by Alternative Polyadenylation inMicroorganisms · 2021Review
- An APEX2 proximity ligation method for mapping interactions with the nuclear lamina.The Journal of cell biology · 2021Article
- Mammalian gene expression variability is explained by underlying cell state.Molecular systems biology · 2020Article
- Using TTNature protocols · 2020Article
- Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo.Plant reproduction · 2019Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states. We found prominent correlations between mRNA decay rate and transcript size, while nuclear export rates are linked to the size of the 3'UTR. Transcription, export and decay rates are each associated with distinct spectra of RBPs. Specific classes of genes, such as those encoding cytoplasmic ribosomal proteins, exhibit characteristic combinations of rate constants, suggesting modular control. Binding of splicing factors is associated with faster rates of export, and our data suggest coordinated regulation of nuclear export of specific functional classes of genes. Finally, correlations between rate constants suggest global coordination between the three processes. Our approach provides insights into the genome-wide nucleocytoplasmic kinetics of mRNA and should be generally applicable to other cell systems.
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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.