ArticlePloS one2013
Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 86 citations in OpenAlex.
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- PROTEIN PHOSPHATASE 2A B'η drives spliceosome subunit dephosphorylation to mediate alternative splicing following heat stress.The Plant cell · 2025Article
- Transcriptome analysis of two isolates of the tomato pathogen Cladosporium fulvum, uncovers genome-wide patterns of alternative splicing during a host infection cycle.PLoS pathogens · 2024Article
- Determination of Differential Alternative Splicing Under Stress Conditions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Alternative splicing of theForestry research · 2024Article
- Do not panic: An intron-centric guide to alternative splicing.The Plant cell · 2023Review
- Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation.BMC plant biology · 2022Article
- OsTBP2.1, a TATA-Binding Protein, Alters the Ratio ofInternational journal of molecular sciences · 2022Article
- ABA Mediates Plant Development and Abiotic Stress via Alternative Splicing.International journal of molecular sciences · 2022Review
- Article
- Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis.Frontiers in plant science · 2022Article
- Dynamic changes in the transcriptome landscape ofFrontiers in plant science · 2022Article
- Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.Nucleic acids research · 2021Article
- First Come, First Served: Sui Generis Features of the First Intron.Plants (Basel, Switzerland) · 2020Review
- Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant.BMC genomics · 2020Article
- Alternative Splicing and DNA Damage Response in Plants.Frontiers in plant science · 2020Review
- Genome-wide identification and expression analysis of the SR gene family in longan (Dimocarpus longan Lour.).PloS one · 2020Article
- DEAD-Box RNA Helicase 42 Plays a Critical Role in Pre-mRNA Splicing under Cold Stress.Plant physiology · 2020Article
- Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress.Frontiers in plant science · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.
Indexed as
Identifiers
What OpenQuestion holds
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.