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Arabidopsis thaliana

ABSTRACT: Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis.

PROVIDER: PRJNA387601 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5588570_1.fastq.gz	Fastqsanger.gz
	SRR5588570_2.fastq.gz	Fastqsanger.gz
	SRR5588580_1.fastq.gz	Fastqsanger.gz
	SRR5588580_2.fastq.gz	Fastqsanger.gz
	SRR5588571_1.fastq.gz	Fastqsanger.gz

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Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis.

Project description:Alternative splicing (AS) plays key roles in plant development and responses to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from alternative splicing) in plant accessions and its contributions to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0, and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing (RNA-seq). We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that SNPs influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.

2018-11-08 | GSE99226 | GEO

Predominant cis-contribution in mouse AS evolution

Project description:Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing

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Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

Project description:Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis.

2020-03-03 | GSE146189 | GEO

RNA-seq analysis of alternative splicing events in duplicated genes of Arabidopsis thaliana indicates considerable qualitative and quantitative divergence

Project description:Divergence of alternative splicing in duplicated genes is investigated Three replicates of RNA-seq for Arabidopsis first true leaf tissue

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RNA-seq analysis of alternative splicing between two Arabidopsis accessions and its inheritance in hybrid

Project description:To uncover the possible regulatory mechanism in regulatory alternative splicing in plants evolution, we used RNA-seq to compare the transcriptomes in Arabidopsis ecotypes Col and C24. We found different class of AS types have different regulatory mechanisms in Arabidopsis and divergence of alternative splicing in different class is varied in evolution. Sequence variation analysis had found evolution divergent AS events significantly altered their sequences compared to conserved events and the variation is AS class specific.

2018-04-23 | GSE62478 | GEO

Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

Project description:Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation.

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Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

Project description:We investigated the cis-regulatory divergences in alternative splicing and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid mouse. By obtaining more than 240 million read pairs on average in each sample from 5 organs and ESC as well as published data in liver, we comprehensively analyzed the allelic splicing patterns across tissues in hybrid mice. We find that tissue-dependent regulation causing large splicing differences is highly conserved and likely functional, while splicing divergence mainly affects genes under relaxed selective constraints. Although cis-divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform could tolerate more mutations, which explains the paradoxical sequence conservation pattern in their exonic versus intronic splicing site flanking regions. Finally, we demonstrated that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attributed such buffering effect to trans-regulatory splicing efficiency.

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Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

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Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana

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