Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-2473
PROVIDER: PRJNA91189 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs. Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs. Keywords: small RNA sequences generated by 454 sequencing
2006-09-08 | GSE5343 | GEO
Project description:Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome
| PRJNA125847 | ENA
Project description:Analysis of small RNA population in Arabidopsis drb2 and drb4 mutants
| PRJNA138567 | ENA
Project description:In Arabidopsis thaliana, four different DICER-LIKE (DCL) proteins have distinct, but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from longer, non-coding precursor RNAs. To analyze the impact of different components of the small RNA (sRNA) biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in sRNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. We discovered distinct effects of dcl1, hyl1 and se mutations on the transcriptome, as well as a number of common genes affected in dcl1 and dcl2 dcl3 dcl4 triple mutants. Our results furthermore suggest that the DCL1 is not only involved in miRNA action, but can also contribute to silencing of certain transposons, apparently through an effect on DNA methylation. Together, our findings contribute to the knowledge of both specialization and overlap between different RNA silencing pathways.
2010-05-08 | GSE21685 | GEO
Project description:small RNA, PATH and mRNA libraries were made to characterize Col and various small RNA biogenesis mutants.
2015-09-13 | GSE61439 | GEO
Project description:RNA and small RNA sequencing analysis in the silencing suppressors mutants
| PRJNA528254 | ENA
Project description:Small RNAs in Arabidopsis hyl1 and hyl1 suppressor mutants
| PRJNA141021 | ENA
Project description:small RNA, PATH and mRNA libraries were made to characterize Col and various small RNA biogenesis mutants. Genome-wide RNA profiling was done by Illumina TruSeq sample preparation kits followed by high-throughput sequencing with Illumina HiSeq 2500 platform.
2015-09-13 | E-GEOD-61439 | biostudies-arrayexpress
Project description:small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant [small RNA-seq]
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Project description:Transcriptome and small RNA-Seq analysis of PTGS-defective Arabidopsis mutants
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