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| Status |
Public on Jul 09, 2018 |
| Title |
Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. To further investigate the downstream targets of REF6 represented H3K27me3 demethylase, we performed RNA-seq using single, double mutant and triple mutant. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions.
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| Overall design |
Expression profiling by RNA-seq in different genetic backgrounds of Arabidopsis.
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| Contributor(s) |
Chen D, Yan W, Kaufmann K |
| Citation(s) |
30104650 |
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dijun Chen |
| E-mail(s) |
chendijun2012@gmail.com
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| Phone |
030-2093 49744
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| Organization name |
Humboldt University
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| Department |
Plant Cell and Molecular Biology
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| Lab |
Prof. Kaufmann
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| Street address |
Philippstr. 13 (House 22)
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| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
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| Platforms (1) |
| GPL24270 |
NextSeq 550 (Arabidopsis thaliana) |
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| Samples (15)
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| GSM2857921 |
elf6-3ref6Cjmj13G, rep1 |
| GSM2857922 |
elf6-3ref6Cjmj13G, rep2 |
| GSM2857923 |
elf6-3ref6Cjmj13G, rep3 |
| GSM2857924 |
elf6-3ref6C, rep1 |
| GSM2857925 |
elf6-3ref6C, rep2 |
| GSM2857926 |
elf6-3ref6C, rep3 |
| GSM2857927 |
ref6-3, rep1 |
| GSM2857928 |
ref6-3, rep2 |
| GSM2857929 |
ref6-3, rep3 |
| GSM2857930 |
ref6C, rep1 |
| GSM2857931 |
ref6C, rep2 |
| GSM2857932 |
ref6C, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE106944 |
Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds |
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| Relations |
| BioProject |
PRJNA418578 |
| SRA |
SRP125057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106943_RNAseq.xlsx |
12.6 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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