|
Status |
Public on Jun 24, 2016 |
Title |
A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation using whole-genome bisulfite sequencing |
Organism |
Arabidopsis thaliana |
Experiment type |
Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing
|
Summary |
The non-methylable cytosine analogs, 5-azacytidine and zebularine, are widely used to disrupt DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that 5-azacytidine and zebularine-treated seedlings have nearly indistinguishable patterns of DNA methylation genome-wide and that 5-azacytidine, despite being more unstable in aqueous solution, has a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of up-regulated genes and transposable element genes, particularly CACTA-like elements, demonstrating that chemical demethylating agents have a disproportionately large effect on loci that are silenced by DNA methylation.
|
|
|
Overall design |
Bisulfite-Seq and RNA-Seq
|
|
|
Contributor(s) |
Schmitz RJ |
Citation(s) |
27402357 |
|
Submission date |
Apr 14, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Robert J Schmitz |
E-mail(s) |
schmitz@uga.edu
|
Organization name |
University of Georgia
|
Department |
Genetics
|
Street address |
B416 Davison Life Sciences
|
City |
Athens |
State/province |
GA |
ZIP/Postal code |
30602 |
Country |
USA |
|
|
Platforms (1) |
GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
|
Samples (15)
|
|
Relations |
BioProject |
PRJNA318516 |
SRA |
SRP073326 |