Ontology highlight
ABSTRACT:
PROVIDER: PRJNA564216 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10077369_1.fastq.gz | Fastqsanger.gz | |||
| SRR10077369_2.fastq.gz | Fastqsanger.gz | |||
| SRR10077370_1.fastq.gz | Fastqsanger.gz | |||
| SRR10077370_2.fastq.gz | Fastqsanger.gz | |||
| SRR10077371_1.fastq.gz | Fastqsanger.gz |
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Project description:Plants developed a plasticity to environmental conditions, such as temperature, that allows their adaptation. A change in ambient temperature leads to changes in the transcriptome in plants, such as the production of different splicing isoforms. Here we study temperature induced alternative splicing events in Arabidopsis thaliana wild-type and two epigenetic mutants, sdg8-2 and sdg26-1 using an RNA-seq approach.
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Project description:Patterns of alternative splicing during heat stress in Arabidopsis thaliana and Boechera depauperata indicate complex and species-specific interactions between differential expression and alternative splicing.
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Project description:RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we showed that in Arabidopsis thaliana, nearly all introns undergo co-transcriptional splicing and this occurs with higher efficiency for introns in protein-coding genes than for noncoding RNAs. Co-transcriptional splicing efficiency correlates with density of 19 epigenetic modifications. Total intron number and intron position are two predominant sequence features that correlate with co-transcriptional splicing efficiency, and introns with alternative 5′ or 3′ splice sites are less efficiently spliced. Furthermore, we found that trans-acting protein mutations lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs, and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level. Our results not only uncovered widespread co-transcriptional splicing in Arabidopsis, but also uncovered features that may affect or be affected by co-transcriptional splicing efficiency.
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