Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

ABSTRACT: Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

PROVIDER: PRJNA715469 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13999500.fastq.gz	Fastqsanger.gz
	SRR13999462.fastq.gz	Fastqsanger.gz
	SRR13999463.fastq.gz	Fastqsanger.gz
	SRR13999464.fastq.gz	Fastqsanger.gz
	SRR13999465.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 39

Similar Datasets

Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

Project description:Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.

2022-02-02 | GSE169171 | GEO

Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana.

| S-EPMC8795450 | biostudies-literature

Endo-siRNAs repress expression of SINE1B during in vitro maturation of porcine oocyte

Project description:We performed small RNA-seq on Dicer KD and control porcine oocyte, and report endo-siRNAs corresponding to SINE1B are significantly down-regulated by Dicer knockdown and are essential for in vitro maturation of porcine oocyte

2018-12-04 | GSE123274 | GEO

Endo-siRNAs repress expression of SINE1B during in vitro maturation of porcine oocyte

Project description:Endo-siRNAs repress expression of SINE1B during in vitro maturation of porcine oocyte

| PRJNA507998 | ENA

LncRNA and mRNA changes during postnatal islet maturation

Project description:LncRNA and mRNA changes during postnatal islet maturation

| PRJNA418442 | ENA

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (small RNA-seq)

Project description:Utilizing whole-genome sRNA-seq to analyze transposon derived siRNAs in DNA methylation mutants, and RNAi mutants, compared to wildtype.

2014-03-18 | GSE52951 | GEO

A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

Project description:DNA methylation directed by 24-nucleotide (nt) small interfering RNAs (siRNAs) plays critical roles in gene regulation and transposon silencing in Arabidopsis. Twenty-four-nt siRNAs are known to be processed from double-stranded RNAs by Dicer-like 3 (DCL3) and loaded into the effector Argonaute 4 (AGO4). Here we report a distinct class of siRNAs independent of DCLs (sidRNAs). sidRNAs are present as ladders of ~20 to 60nt in length, often having same 5' ends but differing in 3' ends by 1-nt steps. We further show that sidRNAs are associated with AGO4 and capable of directing DNA methylation. Finally we show that sidRNA production depends on AGO4 and distributive 3'-5' exonucleases. Our findings suggest an alternative route for siRNA biogenesis: precursor transcripts are bound by AGO4 and subsequently subjected to 3'-5' exonucleolytic trimming for maturation. We propose that sidRNAs generated through this route are the initial triggers of de novo DNA methylation. Small RNAs were profiled in Arabidopsis wild type (Col-0), dcl1/2/3/4 and other mutants by Illumina high-throughput sequencing, to identify siRNAs independent of DCLs (sidRNAs) and dissect their biogenesis pathway. DNA methylation was profiled in various mutants by whole-genome bisulfite sequencing to establish a role for sidRNAs in DNA methylation

2015-12-17 | E-GEOD-74398 | biostudies-arrayexpress

Polysome-bound mRNA during oocyte maturation

Project description:Oocyte maturation, fertilization, and early embryonic development occur in the absence of gene transcription. Therefore, it is critical to understand at a global level the post-transcriptional events that are driving these transitions. Here, we have used a systems approach by combining polysome mRNA profiling and bioinformatics to identify RNA binding motifs in mRNAs that either enter or exit the polysome pool during mouse oocyte maturation. Association of mRNA with the polysomes correlates with active translation.

2012-01-14 | GSE35106 | GEO

mRNA profiling of Trihelix transcription factor ASIL mutants

Project description:mRNA profiling of Trihelix transcription factor ASIL mutants

| PRJNA684319 | ENA

Expression data from NKYS transfected with siRNAs or plasmids

Project description:The siRNA transfection includes JAK3 and EZH2 siRNAs. The plasmid transfection includes EZH2 WT and its mutants. We used gene expression data from JAK3 siRNA to test whether it affected epigenetic regulation, and used EZH2 mutants to study how it affected EZH2 canonical function.

2016-07-26 | GSE75680 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data