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Series GSE124098 Query DataSets for GSE124098
Status Public on Dec 06, 2019
Title Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissue
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Arabidopsis encodes ten ARGONAUTE (AGO) effectors of RNA silencing, canonically loaded with either 21-22nt small RNAs (sRNA) to mediate post-transcriptional-gene-silencing (PTGS) or 24nt sRNAs to promote RNA-directed-DNA-methylation. Using full-locus constructs, we characterized the expression, biochemical properties, and possible modes of action of AGO3. Although AGO3 arose from a recent duplication at the AGO2 locus, their expression differs drastically, with AGO3 prevailing in aerial vascular terminations and specifically in chalazal seed integuments; accordingly, AGO3 down-regulation alters gene expression in siliques. Similar to AGO2, AGO3 binds sRNAs with a strong 5’-adenosine bias, but unlike most Arabidopsis AGOs - AGO2 included - it binds efficiently both 24nt and 21nt sRNAs. AGO3 immuno precipitation experiments in siliques revealed that these sRNAs mostly associate to genes and intergenic regions and not to canonical AGO targets, such as transposable elements. AGO3 localizes to the cytoplasm and co-fractionates with polysomes to possibly mediate PTGS via translation inhibition.
Overall design For mRNA sequencing, 2 biological samples per genotype were assessed. Samples were: ago3-3 homozygous, ago3-3 heterozygous, and Columbia 0 wilt-type samples. For sRNA sequencing, no replication was done. Three samples were analyzed: Total sRNA extracted from Arabidopsis siliques (TOTAL_smRNA), sRNA fraction which was collected from immunoprecipitated AGO3:FLAG protein (IP_AGO3), and sRNA from a control Immunoprecipitation experiment, conducted in wild-type siliques using a FLAG antibody.
Contributor(s) Jullien PE, Grob S, Marchais A, Pumplin N, Chevalier C, Otto C, Schott G, Voinnet O
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Submission date Dec 19, 2018
Last update date Dec 06, 2019
Contact name Pauline Emilie Jullien
Organization name University of Bern
Department Institute of Plant Biology
Street address Altenbergrain 21
City Bern
ZIP/Postal code 3013
Country Switzerland
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (9)
GSM3520449 ago3_HE_rep1_1
GSM3520450 ago3_HE_rep2_1
GSM3520451 ago3_HO_rep1_1
BioProject PRJNA510767
SRA SRP173915

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Supplementary file Size Download File type/resource
GSE124098_RNAseq_counts.txt.gz 390.4 Kb (ftp)(http) TXT
GSE124098_sRNA_per_500bp_fragments.txt.gz 2.3 Mb (ftp)(http) TXT
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