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Series GSE82040 Query DataSets for GSE82040
Status Public on Dec 23, 2016
Title Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis [RNA-Seq]
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The endoplasmic reticulum (ER) was implicated as the site of microRNA (miRNA)-mediated translation repression in plants. Here, we examined the ER- and rough ER-associated small RNAome, transcriptome and translatome. We found that almost all cellular transcripts were present on membrane-bound polysomes (MBPs), and miRNAs were enriched in membranes and on MBPs. miRNAs were recruited to membranes by their effector protein AGO1, whereas AGO1 associated with membranes and, partly ribosomes, in an RNA-independent manner. Most strikingly, 22 ntmiRNA isoformsand a set of 22 ntsiRNAs, were enriched in the membrane fraction and onMBPs, where they trigger phasedsecondary siRNAproduction from target transcripts. Loss of membrane association of the 22 nt small RNAs resulted in the loss of phasing in secondary siRNA production.These findings point to the ER as a hub that hosts and organizes endogenous small RNAs in plants.
 
Overall design Examination of mRNA in 4 cell fractions of Col-0 seedlings with 3 biological replicates
 
Contributor(s) Chen X
Citation(s) 27938667
Submission date May 30, 2016
Last update date May 15, 2019
Contact name Chenjiang You
E-mail(s) chenjiang.you@ucr.edu, youchenjiang2003@hotmail.com
Organization name Fudan University
Street address 2005 Songhu Rd
City Shanghai
State/province Shanghai
ZIP/Postal code 200438
Country China
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (12)
GSM2181692 mRNA_Col_Cytosol_1
GSM2181693 mRNA_Col_Cytosol_2
GSM2181694 mRNA_Col_Cytosol_3
This SubSeries is part of SuperSeries:
GSE82041 Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis
Relations
BioProject PRJNA323731
SRA SRP075885

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
GSE82040_RAW.tar 2.2 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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