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| Status |
Public on Apr 25, 2018 |
| Title |
Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Epigenetic markers such as histone acetylation and DNA methylation determine chromatin organization. In eukaryotic cells, metabolites from organelles or the cytosol affect epigenetic modifications. However, the relationships between metabolites and epigenetic modifications are not well understood in plants. We found that peroxisomal acyl-CoA oxidase 4 (ACX4), an enzyme in the fatty acid β-oxidation pathway, is required for suppressing the silencing of some endogenous loci as well as Pro35S:NPTII in the ProRD29A:LUC/C24 transgenic line. The acx4 mutation reduces nuclear histone acetylation and increases DNA methylation at the NOS terminator of Pro35S:NPTII, and at some endogenous genomic loci, which are also targeted by the demethylation enzyme REPRESSOR OF SILENCING 1 (ROS1). Furthermore, mutations in multifunctional protein 2 (MFP2) and 3-ketoacyl-CoA thiolase-2 (KAT2/PED1/PKT3), two enzymes in the last two steps of the β-oxidation pathway, lead to similar patterns of DNA hypermethylation as in acx4. Thus, metabolites from fatty acid β-oxidation in peroxisomes are closely linked to nuclear epigenetic modifications, which may affect diverse cellular processes in plants.
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| Overall design |
Examine DNA methylation,and RNA expression changes by whole-genome bisulfite sequencing; RNA sequencing in A. thaliana wild type and acx4,Col-0,ros1-4,acx4-1,mfp2-2,kat2-3 mutants
Examine histone acetylation changes by whole-genome sequencing; H3K9Ac-, H3K14Ac-, H3K18Ac-, H3K23Ac-ChIP-seq in A. thaliana wild type and acx4 mutant.
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| Contributor(s) |
Wang L, Wang C, Liu X, Cheng J, Li S, Zhu J, Gong Z |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Apr 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yusheng Zhao |
| E-mail(s) |
gonglab-8@cau.edu.cn
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| Organization name |
China agricultural university
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| Street address |
Yuanmingyuan Road #2, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
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| Platforms (2) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
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| Samples (35)
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| Relations |
| BioProject |
PRJNA384268 |
| SRA |
SRP105230 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98214_10_RDC0062-acx4-4_H3K18Ac-input.bw |
97.0 Mb |
(ftp)(http) |
BW |
| GSE98214_11_RDC0065-WT_H3K18Ac.bw |
102.8 Mb |
(ftp)(http) |
BW |
| GSE98214_12_RDC0066-acx4-4_H3K18Ac.bw |
117.1 Mb |
(ftp)(http) |
BW |
| GSE98214_13_RDC0051-WT_H3K23Ac-input.bw |
94.8 Mb |
(ftp)(http) |
BW |
| GSE98214_14_RDC0052-acx4-4_H3K23Ac-input.bw |
94.5 Mb |
(ftp)(http) |
BW |
| GSE98214_15_RDC0053-WT_H3K23Ac.bw |
111.3 Mb |
(ftp)(http) |
BW |
| GSE98214_16_RDC0054-acx4-4_H3K23Ac.bw |
118.4 Mb |
(ftp)(http) |
BW |
| GSE98214_1_RDC0059-WT_H3K9Ac-input.bw |
94.9 Mb |
(ftp)(http) |
BW |
| GSE98214_2_RDC0060-acx4-4_H3K9Ac-input.bw |
89.4 Mb |
(ftp)(http) |
BW |
| GSE98214_3_RDC0049-WT_H3K9Ac.bw |
96.0 Mb |
(ftp)(http) |
BW |
| GSE98214_4_RDC0050-acx4-4_H3K9Ac.bw |
101.3 Mb |
(ftp)(http) |
BW |
| GSE98214_5_RDC0061-WT_H3K14Ac-input.bw |
111.3 Mb |
(ftp)(http) |
BW |
| GSE98214_6_RDC0062-acx4-4_H3K14Ac-input.bw |
97.0 Mb |
(ftp)(http) |
BW |
| GSE98214_7_RDC0063-WT_H3K14Ac.bw |
110.1 Mb |
(ftp)(http) |
BW |
| GSE98214_8_RDC0064-acx4-4-H3K14Ac.bw |
124.2 Mb |
(ftp)(http) |
BW |
| GSE98214_9_RDC0061-WT_H3K18Ac-input.bw |
111.3 Mb |
(ftp)(http) |
BW |
| GSE98214_ACX4-1.bedGraph.gz |
207.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_CHG_acx4.bedGraph.gz |
24.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_CHH_acx4.bedGraph.gz |
112.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_Col-0.bedGraph.gz |
181.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_CpG_acx4.bedGraph.gz |
21.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_KAT2-3.bedGraph.gz |
204.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_MFP2-2.bedGraph.gz |
206.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE98214_genes_and_TEs_up_and_down_regulated_in_acx4.xls.gz |
274.9 Kb |
(ftp)(http) |
XLS |
| GSE98214_ros1-4.bedGraph.gz |
165.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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