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Series GSE87351 Query DataSets for GSE87351
Status Public on Jan 25, 2017
Title ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis [AGO10SDN]
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary The degradation of small RNAs in plants and animals is associated with small RNA 3’ truncation and 3’ uridylation and thus relies on exonucleases and nucleotidyl transferases. Argonaute proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. Arabidopsis ARGONAUTE10 (AGO10) maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we report that AGO10 reduces miR165/6 accumulation by enhancing its degradation. This is contrary to the stabilizing effect of all known argonaute proteins on their associated small RNAs. We show that SMALL RNA DEGRADING NUCLEASES (SDNs) are responsible for miRNA 3’ truncation in general and AGO10 promotes the degradation of miR165/6 by SDNs. Our work identifies the exonucleases responsible for miRNA 3’ truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, demonstrates that spatially regulated miRNA degradation underlies stem cell maintenance in plants.
 
Overall design Immunoprecipitation of AGO1- and AGO10-RISCs followed by treatment with SDN/SDN-D283A exonucleases (two biological replicates and two treatments for a total of 8 samples).
Immunoprecipitation of AGO1- and AGO10-RISCs followed by Mock treatment that included buffer only (i.e., no SDN) (two biological replicates, a total of 4 samples).
 
Contributor(s) Ji L, Yu Y, Le BH, Chen X
Citation(s) 28231321
Submission date Sep 26, 2016
Last update date May 15, 2019
Contact name Xuemei Chen
E-mail(s) xuemei.chen@ucr.edu
Organization name University of California, Riverside
Department Botany and Plant Sciences
Lab Genomics Building 4237
Street address 3401 Watkins Drive
City Riverside
State/province CA
ZIP/Postal code 92521
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (12)
GSM2328675 AGO1IP-SDN-br1
GSM2328676 AGO1IP-SDN-br2
GSM2328677 AGO1IP-SDN-D283A-br1
This SubSeries is part of SuperSeries:
GSE87355 ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis
Relations
BioProject PRJNA344474
SRA SRP090467

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE87351_RAW.tar 126.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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