Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA341504 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [small RNA-seq]
| PRJNA341505 | ENA
Project description:The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings
| PRJNA341502 | ENA
Project description:XRN 5′-3′ exoribonucleases play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of the Arabidopsis wild type and mutants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 but not nuclear XRN2 activity largely altered Arabidopsis mRNA decay profiles. In addition to the primary XRN4 substrates derived from decapping and microRNA-directed slicing, terminating ribosome- and exon junction complex-protected fragments produced from XRN4-mediated cytoplasmic decay also represent the most abundant decay intermediates of Arabidopsis mRNAs. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that polyadenylation cleavage frequently occurs after an adenosine. An increase in decay intermediates with 5′ ends upstream of a consensus motif in the xrn4 mutant suggests an endonucleolytic cleavage mechanism targeting the 3′ untranslated region of many Arabidopsis mRNAs. However, analysis of decay fragments stabilized in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence might rarely result in major decay intermediates. Together, the results of this study reveal major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.
2022-09-06 | GSE205190 | GEO
Project description:Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. Most mRNAs decayed by multiple pathways, few mRNAs degraded exclusively by mRNA decapping or SOV, and specific codon usage was linked to decay rates. Unexpected faster decay of transcripts in some genotypes was found to be independent of siRNAs; instead the data suggested an RNA buffering-like phenomenon in Arabidopsis, and that VCS (decapping) is essential for both this process and the decay of very unstable mRNAs.
2018-01-26 | GSE86359 | GEO
Project description:Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. Most mRNAs decayed by multiple pathways, few mRNAs degraded exclusively by mRNA decapping or SOV, and specific codon usage was linked to decay rates. Unexpected faster decay of transcripts in some genotypes was found to be independent of siRNAs; instead the data suggested an RNA buffering-like phenomenon in Arabidopsis, and that VCS (decapping) is essential for both this process and the decay of very unstable mRNAs.
2018-01-26 | GSE86360 | GEO
Project description:Photoperiod is a circannual signal measured by biological systems to align growth and reproduction with the seasons. To understand the effect of photoperiod of gene expression in Arabidopsis thaliana in the absence of exogenous sugar under constant light intensity, we performed time course mRNA-seq analysis on 13-day old seedlings across three photoperiods with triplicates to identify photoperiod-regulated genes.
2023-08-15 | GSE221846 | GEO
Project description:To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome
2023-04-25 | GSE193247 | GEO
Project description:RNA-seq of Arabidopsis thaliana seedlings overexpressing the transcription factor TCP14
| PRJNA354407 | ENA
Project description:RNA-seq of Arabidopsis thaliana seedlings treated with MeJA or BTH
| PRJNA354369 | ENA
Project description:Wild type and atdamt1 seedlings were heat treated for 2.5 hours, control and treated seedlings were collected to extract total RNA for mRNA-seq. We then performed gene expression profiling analysis using data obtained from mRNA-seq.
2023-11-20 | GSE237262 | GEO