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| Status |
Public on Jul 11, 2016 |
| Title |
On the Origin and Evolutionary Consequences of Gene Body DNA Methylation |
| Organisms |
Arabidopsis thaliana; Brassica rapa; Brassica oleracea; Arabidopsis lyrata; Eutrema salsugineum; Capsella rubella |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. salsugineum, indicating that CMT3 may be required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z and various histone modifications in E. salsugineum and Arabidopsis thaliana epiRILs turned up no evidence in support of any role for gbM in regulating transcription or affecting the composition and modifications of chromatin over evolutionary time scales.
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| Overall design |
Examination of DNA methylation, gene expression, and histone variant H2A.Z between Eutrema salsugineum, A. thaliana and methylation/histone modification mutants.
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| Contributor(s) |
Schmitz RJ |
| Citation(s) |
27457936, 31356150 |
| |
| Submission date |
Nov 17, 2015 |
| Last update date |
Aug 06, 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 (10)
|
| GPL11022 |
Illumina Genome Analyzer II (Arabidopsis lyrata) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL19447 |
Illumina HiSeq 2000 (Arabidopsis lyrata) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
| GPL19953 |
Illumina HiSeq 2000 (Capsella rubella) |
| GPL21147 |
Illumina HiSeq 2500 (Eutrema salsugineum) |
| GPL21148 |
Illumina HiSeq 2500 (Brassica rapa) |
| GPL21149 |
Illumina HiSeq 2500 (Brassica oleracea) |
| GPL21150 |
Illumina NextSeq 500 (Eutrema salsugineum) |
| GPL21151 |
Illumina Genome Analyzer II (Capsella rubella) |
|
| Samples (44)
|
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| Relations |
| BioProject |
PRJNA302602 |
| SRA |
SRP066358 |
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