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| Status |
Public on Feb 14, 2020 |
| Title |
Plant 22-nt siRNAs mediate translational repression and stress adaptation |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| 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.
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| Overall design |
Col-0, ein5-1 dcl4-2 and ein5-1 dcl4-2 dcl2-1were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old plant were collected at 15:00 for AGO1-associated small RNA isolation. Two biological replicates were prepared for each genotype. Library preparation and high-throughput sequencing were conducted in accordance with the manufacturers’ instructions. Total RNA was extracted using the Trizol and precipitated by ethonal. 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 paired-end, 150-bp deep sequencing was performed on an Illumina Nova6000 platform.
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| Contributor(s) |
Wu H, Li B, Guo H |
| Citation(s) |
32376953, 38637717 |
| Submission date |
Aug 19, 2019 |
| Last update date |
May 01, 2024 |
| Contact name |
Bosheng Li |
| E-mail(s) |
libs@sustc.edu.cn
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| Organization name |
SUSTC (current, may different with previous institution )
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| Department |
MCDB
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| Street address |
SUStech Huiyuan #1 406
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
581055 |
| Country |
China |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (6)
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| GSM4038527 |
Col-0 AGO1 IP aerial part_rep1 (AGO1-associated small RNAs) |
| GSM4038528 |
Col-0 AGO1 IP aerial part_rep2 (AGO1-associated small RNAs) |
| GSM4038529 |
ein5 dcl4 AGO1 IP aerial part_rep1 (AGO1-associated small RNAs) |
| GSM4038530 |
ein5 dcl4 AGO1 IP aerial part_rep2 (AGO1-associated small RNAs) |
| GSM4038531 |
ein5 dcl4 dcl2 AGO1 IP aerial part_rep1 (AGO1-associated small RNAs) |
| GSM4038532 |
ein5 dcl4 dcl2 AGO1 IP aerial part_rep2 (AGO1-associated small RNAs) |
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| This SubSeries is part of SuperSeries: |
| GSE136164 |
Plant 22-nt siRNAs mediate translational repression and stress adaptation |
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| Relations |
| BioProject |
PRJNA560787 |
| SRA |
SRP218724 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135962_AGO1_IP_processed_data.xlsx |
2.8 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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