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E-GEOD-57690

ABSTRACT: Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

OTHER RELATED OMICS DATASETS IN: PRJNA247731

PROVIDER: E-GEOD-57690 | ExpressionAtlas | 2019-05-14

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-57690-analysis-methods.tsv	Tabular
	E-GEOD-57690-analytics.tsv	Tabular
	E-GEOD-57690-analytics.tsv.undecorated	Tabular
	E-GEOD-57690-analytics.tsv.undecorated.unrounded	Tabular
	E-GEOD-57690-analytics.tsv.unrounded	Tabular

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Similar Datasets

Arabidopsis thaliana

Project description:Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

| PRJNA247731 | ENA

Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

Project description:The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptomewide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale coexpression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. Analysing long and short poly(A)-tail fractions from 4 paps1 mutant and 4 Ler samples.

2015-07-30 | E-GEOD-57690 | biostudies-arrayexpress

Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

2015-07-30 | GSE57690 | GEO

E-MEXP-3685

Project description:Genome-wide analysis of genes regulated by ARR22 overexpression.

2015-06-05 | E-MEXP-3685 | ExpressionAtlas

E-GEOD-16538

Project description:Genome-wide gene expression profile analysis in pulmonary sarcoidosis

2025-01-24 | E-GEOD-16538 | ExpressionAtlas

E-MEXP-2714

Project description:Genome wide analysis of glucose brassinosteroid interaction in Arabidopsis

2014-07-03 | E-MEXP-2714 | ExpressionAtlas

PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif [PAR-CLIP]

Project description:PAPD5 is one of the seven members of non-canonical poly(A) polymerases in human cells. There are previous reports about polyadenylation dependent degradation of pre-ribosomal RNAs and uridylation dependent degradation of histone mRNAs in vivo. In this study, we observed polyadenylation but not polyuridylation activity of PAPD5 with in vitro assays. We aimed to get genome-wide targets of PAPD5 and used PAR-CLIP and deep sequencing for this purpose.

2012-04-03 | GSE36987 | GEO

E-GEOD-62024

Project description:Genome-wide analysis of the prmt5 and prmt4a;4b mutant transcriptomes

2019-05-14 | E-GEOD-62024 | ExpressionAtlas

E-GEOD-63406

Project description:Genome-wide analysis of wild type and gemin2 mutant plants [cold exposure]

2019-05-14 | E-GEOD-63406 | ExpressionAtlas

The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development [small RNA]

Project description:RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null-mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in expression of pollen-differentiation genes, paps1 null mutant pollen show a strong overaccumulation of transposable-element transcripts, yet a depletion of 21- and particularly 24-nucleotide long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding transposable elements. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4 mutations. In particular, the double mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. Thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.

2019-12-31 | GSE127992 | GEO

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