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| Status |
Public on May 02, 2017 |
| Title |
Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit |
| Organism |
Solanum lycopersicum |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
DNA methylation is a conserved epigenetic mark important for genome integrity, development and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5mC DNA glycosylases/lyases (i.e. DNA demethylases). The role of DNA demethylases in transposon regulation, pathogen responses, and gene imprinting and other developmental processes have been studied extensively in the model plant Arabidopsis thaliana. Recent studies suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlROS1/SlDML1/2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes. These genes include not only hundreds of ripening induced genes but also many ripening repressed genes. Our results show that SlROS1 is critical for tomato fruit ripening, and suggest that active DNA demethylation is required for both the activation of ripening induced genes and inhibition of ripening repressed genes.
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| Overall design |
MethylC-Seq: 6 samples examined, wild type (WT) 25dpa (day after anthesis), WT 46dpa, and WT 60dpa, sldml2-1 25dpa , sldml2-1 46dpa (two replicates), sldml2-2 60dpa (2 replicates);
mRNA-Seq: 3 samples examined, WT 25dpa, WT 46dpa and sldml2-1 46dpa (2 replicates)
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| Contributor(s) |
Tang K, Wang Y, Lang Z, Zhu J |
| Citation(s) |
28507144 |
| Submission date |
Feb 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
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| Organization name |
Purdue University
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| Department |
Department of Horticulture and Landscape Architecture
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| Street address |
625 Agriculture Mall Dr.
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platforms (1) |
| GPL19694 |
Illumina HiSeq 2500 (Solanum lycopersicum) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA374747 |
| SRA |
SRP099790 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE94903_RAW.tar |
6.4 Gb |
(http)(custom) |
TAR (of BEDGRAPH, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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