ArticleThe Plant cell2007
Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana.
Article in The Plant cell, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
What it found
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Who cites it
168 citing papers in PubMed, 330 citations in OpenAlex.
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- Unfolding of RNA secondary structure impairs RNA stability to fine-tune phosphate starvation responses in rice roots.Plant communications · 2026Article
- Comprehensive analysis of the role of ASC1 and APE2 introns on cellular fitness, transcription, and post-transcriptional dynamics.The FEBS journal · 2026Article
- Co-transcriptional splicing changes combine with reduced productive transcription initiation for cold-induced repression of FLC.Nucleic acids research · 2026Article
- Decay drives RNA abundance regulation using three distinct regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Introns increase gene expression in Caenorhabditis elegans by a mechanism that must be at least partly different than in plants.Scientific reports · 2025Article
- Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics.The New phytologist · 2025Article
- Chemically-induced cellular stress signals are transmitted to alternative splicing via UsnRNA levels to alter gene expression in Arabidopsis thaliana.Plant molecular biology · 2025Article
- Unveiling RNA structure-mediated regulations of RNA stability in wheat.Nature communications · 2024Article
- Widespread position-dependent transcriptional regulatory sequences in plants.Nature genetics · 2024Article
- Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis.The Plant cell · 2024Article
- Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover.Nucleic acids research · 2024Article
- Article
- Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.The Plant cell · 2024Article
- Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation.The Plant journal : for cell and molecular biology · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- A spatiotemporally resolved atlas of mRNA decay in thebioRxiv : the preprint server for biology · 2024Article
108 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to >24 h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns; (2) various sequence elements in the 3' untranslated region are enriched among short- and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay; and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.
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