|
| Status |
Public on Nov 23, 2024 |
| Title |
Epigenetic characterization of carbon dots functions in rice |
| Organism |
Oryza sativa Japonica Group |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
Nanoparticles (NPs) can serve as efficient carriers for delivery of genetic materials in plants. They can regulate normal growth and development, and responses to stresses in plants. However, epigenetic mechanisms underlying NPs or carbon dots (CDs) affecting plant growth and development are still largely unknown. Here we showed that CDs reprogrammed gene transcription associated with some biological processes such as stress responses and photosynthesis. Moreover, CDs resulted in subtle but significant DNA hypermethylation, especially for CHG and CHH hypermethylation, which is possibly caused by CDs induced up-regulation of OsCMTs. Interestingly, we found that CDs stabilized i-motif in the promoter regions of OsCMTs1/2, therefore resulting in CHG and CHH hypermethylation. Thus, our study for the first time reveals possible mechanisms underlying impacts of CDs on cytosine context-dependent DNA methylation on a genome-wide scale, which may regulate genes responsible for CDs-induced phenotypic changes in plants. It will be helpful for considering future application of CDs in improving crop agronomic traits.
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| |
|
| Overall design |
Bisulfite-Seq: 2 samples examined, CD (Carbon dot treatment, 2 replicates), CK (Control, 2 replicates); RNA-Seq: 2 samples examined, CD (Carbondot treatment, 2 replicates), CK (Control, 2 replicates)
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| |
|
| Contributor(s) |
Luo Z |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 23, 2021 |
| Last update date |
Nov 23, 2024 |
| Contact name |
zhenyu luo |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agricultural University
|
| Department |
College of Agricuture
|
| Lab |
Zhanglab
|
| Street address |
Xuanwu
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL27860 |
Illumina NovaSeq 6000 (Oryza sativa Japonica Group) |
|
| Samples (8)
|
|
| Relations |
| BioProject |
PRJNA782997 |
| SRA |
SRP347463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189428_CD_BS-seq_merge.CGmap.gz |
400.0 Mb |
(ftp)(http) |
CGMAP |
| GSE189428_CD_BS-seq_merge.bw |
274.5 Mb |
(ftp)(http) |
BW |
| GSE189428_CD_BS-seq_merge_CG.bw |
50.5 Mb |
(ftp)(http) |
BW |
| GSE189428_CD_BS-seq_merge_CHG.bw |
51.2 Mb |
(ftp)(http) |
BW |
| GSE189428_CD_BS-seq_merge_CHH.bw |
177.0 Mb |
(ftp)(http) |
BW |
| GSE189428_CK_BS-seq_merge.CGmap.gz |
445.5 Mb |
(ftp)(http) |
CGMAP |
| GSE189428_CK_BS-seq_merge.bw |
300.4 Mb |
(ftp)(http) |
BW |
| GSE189428_CK_BS-seq_merge_CG.bw |
53.8 Mb |
(ftp)(http) |
BW |
| GSE189428_CK_BS-seq_merge_CHG.bw |
54.4 Mb |
(ftp)(http) |
BW |
| GSE189428_CK_BS-seq_merge_CHH.bw |
194.7 Mb |
(ftp)(http) |
BW |
| GSE189428_RAW.tar |
108.7 Mb |
(http)(custom) |
TAR (of BW) |
| GSE189428_RNA-seq_expression_TPM.xls.gz |
2.0 Mb |
(ftp)(http) |
XLS |
| GSE189428_RNA-seq_read_counts.xls.gz |
4.0 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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