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| Status |
Public on Jun 07, 2016 |
| Title |
MTHFD1 controls DNA methylation in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
In order to further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. We identified the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me, and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1.
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| Overall design |
2 BS-seq datasets for genome-wide analysis of differential DNA methylation, 18 BS-seq datasets for global DNA-methylation analysis, and 3 RNA-seq datasets for differential gene expression analysis.
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| Contributor(s) |
Groth M, Jacobsen SE |
| Citation(s) |
27291711 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM060398 |
Genetics of DNA Methylation Patterning of Arabidopsis: GENETICS OF DNA METHYLATION PATTERNING IN ARABIDOPSIS: Genetics of DNA Methlyation Patterning of Arabidopsis |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
JACOBSEN |
| R01 GM072764 |
Mechanisms of Transcriptional Repression in Arabidopsis: Function of TOPLESS in Arabidopsis Embryonic Polarity |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
LONG |
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| Submission date |
Feb 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Groth |
| E-mail(s) |
grothm@ucla.edu
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| Organization name |
University of California Los Angeles
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| Department |
Molecular, Cell and Developmental Biology
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| Street address |
610 Charles E. Young Drive East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (23)
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| GSM2062687 |
WT whole genome bisulfite sequencing |
| GSM2062688 |
mthfd1-1 whole genome bisulfite sequencing |
| GSM2062689 |
WT mock, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062690 |
WT mock, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062691 |
mthfd1-1 mock, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062692 |
mthfd1-1 mock, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062693 |
WT 5-CHO-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062694 |
WT 5-CHO-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062695 |
mthfd1-1 5-CHO-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062696 |
mthfd1-1 5-CHO-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062697 |
WT Met., rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062698 |
WT Met, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062699 |
mthfd1-1 Met, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062700 |
mthfd1-1 Met, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062701 |
WT SMZ bisulfite sequencing for analysis of global DNA methylation |
| GSM2062702 |
mthfd1-1 SMZ bisulfite sequencing for analysis of global DNA methylation |
| GSM2062703 |
WT 5-CH3-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062704 |
WT 5-CH3-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062705 |
mthfd1-1 5-CH3-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062706 |
mthfd1-1 5-CH3-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation |
| GSM2062707 |
mthfd1-1 a mRNA sequencing |
| GSM2062708 |
mthfd1-1 b mRNA sequencing |
| GSM2062709 |
WT mRNA sequencing |
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| Relations |
| BioProject |
PRJNA312219 |
| SRA |
SRP070187 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77966_RAW.tar |
3.4 Gb |
(http)(custom) |
TAR (of FPKM_TRACKING, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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