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Series GSE148512 Query DataSets for GSE148512
Status Public on Apr 13, 2020
Title 22-nucleotide siRNAs mediate translational repression and trigger a silencing storm [es]
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small interfering RNAs (siRNAs) are critical for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21-, 22-, or 24- nucleotides (nt), wherein the 21- and 24-nt siRNAs mediate mRNA cleavage and DNA methylation2,3, respectively. However, the biological functions of 22-nt siRNAs remain elusive. Here we report the identification and characterization of a group of endogenous 22-nt siRNAs generated from the action of DICER-LIKE 2 (DCL2). When cytoplasmic RNA decay and DCL4 are deficient, the massive accumulation of 22-nt siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defect, and pigmentation. Notably, two genes that encode nitrate reductases, NIA1 and NIA2, produce nearly half of the total of 22-nt siRNAs. Production of 22-nt siRNA triggers explosive self-amplification that leads to a small RNA storm, and induces dramatic translational repression both gene-specifically and globally. 22-nt siRNAs are also found to preferentially accumulate upon nitrogen deficiency, which acts to restrain plant growth and promote stress responses. Thus, our research uncovers the unique properties of 22-nt siRNAs, a previously unexplored class of plant siRNAs, and highlights the length of small RNA as a major functional determinant.
 
Overall design ein5-1 ski2-3 and ein5-1 ski2-3 dcl4-2 dcl2-1 were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts were collected for small RNA extraction. Three or four biological replicates were prepared for each genotype. Library preparation and high-throughput sequencing were conducted in accordance with the manufacturers’ instructions. Total small RNA was extracted using the miRNeasy Mini Kit (Qiagen). Sequencing libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina. RNA quality and library quality were examined by a Bioanalyzer 2100 instrument (Agilent), and single-end, 50-bp deep sequencing was performed on an Illumina HiSeq 4000 platform.
 
Contributor(s) Wu H, Li B, Guo H
Citation(s) 32376953, 38637717
Submission date Apr 12, 2020
Last update date May 01, 2024
Contact name Bosheng Li
E-mail(s) libs@sustc.edu.cn
Organization name SUSTC (current, may different with previous institution )
Department MCDB
Street address SUStech Huiyuan #1 406
City Shenzhen
State/province Guangdong
ZIP/Postal code 581055
Country China
 
Platforms (1)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (8)
GSM4472991 es3_smRNA_rep1
GSM4472992 es3_smRNA_rep2
GSM4472993 es3_smRNA_rep3
This SubSeries is part of SuperSeries:
GSE136164 Plant 22-nt siRNAs mediate translational repression and stress adaptation
Relations
BioProject PRJNA624856
SRA SRP256233

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Supplementary file Size Download File type/resource
GSE148512_es3_smRNA_processed_data.xlsx 7.1 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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