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| Status |
Public on Apr 13, 2015 |
| Title |
Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci).
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| Overall design |
Examination of small RNA profiles in 4 genotypes with 3 biological replicates each.
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| Contributor(s) |
Guo H, Zhang X |
| Citation(s) |
25838384 |
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| Submission date |
May 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Damon Lisch |
| Organization name |
Purdue University
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| Street address |
915 West State Street
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA248453 |
| SRA |
SRP042220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57936_processed_data_smRNA-seq.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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