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Profiling of alternative polyadenylation events in Arabidopsis thaliana

ABSTRACT: Profiling of alternative polyadenylation events in Arabidopsis thaliana

PROVIDER: PRJNA814211 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18276458_1.fastq.gz	Fastqsanger.gz
	SRR18276458_2.fastq.gz	Fastqsanger.gz
	SRR18276459_1.fastq.gz	Fastqsanger.gz
	SRR18276459_2.fastq.gz	Fastqsanger.gz
	SRR18276460_1.fastq.gz	Fastqsanger.gz

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Profiling of alternative polyadenylation events in Arabidopsis thaliana

Project description:Use 3ʹ region extraction and deep sequencing (3'READS) and bioinformatics techniques to profile alternative polyadenylation and gene regulation in plant Arabidopsis thaliana exposed to light and darkness

2022-12-31 | GSE198202 | GEO

Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

Project description:Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

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Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress

Arginine methylation regulates widespread alternative polyadenylation

Project description:Alternative polyadenylation (APA) has recently been recognized as a universal mechanism for gene regulation, but it remains unclear how APA is controlled. Here we report that the Arabidopsis thaliana Protein Arginine Methyltransferase 10 (AtPRMT10) regulates global APA with its protein partner HLP1, a conserved hnRNP A/B protein. HLP1 binds preferentially to A-rich and U-rich cis-elements around polyadenylation sites, thereby linking AtPRMT10 to the control of APA through protein-protein interactions. AtPRMT10 mutations cause significant proximal-to-distal poly(A) site shifts largely overlapping with those in hlp1-1 mutants. Proximal polyadenylation is maintained by AtPRMT10-directed methylation and is mediated in part by methylation of HLP1 at specific arginine residues. Our findings demonstrate that arginine methylation of an RNA-binding protein adds a novel layer of regulation to widespread alternative polyadenylation.

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Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

2016-03-14 | GSE79157 | GEO

Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

Project description:Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA. Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.

2020-01-14 | GSE137732 | GEO

Study of genome-wide alternative polyadenylation in A. thaliana

Project description:Study of genome-wide alternative polyadenylation in A. thaliana

| PRJEB2761 | ENA

Study of genome-wide alternative polyadenylation in A. thaliana

Project description:Study of genome-wide alternative polyadenylation in A. thaliana

| PRJEB6 | ENA

Mouse alternative polyadenylation

Project description:Divergence of alternative polyadenylation in mouse

| PRJEB15336 | ENA

AMPKα1 and α2 knockout and usage of alternative polyadenylation sites

Project description:Role of alternative polyadenylation in muscle development remains largely undetermined. Our WTTS-seq approach to capture 3'-end of RNAs clearly revealed alternaitve polyadenylation events responsible for reduced muscle mass in AMPK α1, but increased muscle mass in AMPK α2 knockout mice.

2018-05-09 | GSE107212 | GEO

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