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| Status |
Public on Mar 07, 2019 |
| Title |
Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice |
| Organism |
Oryza sativa |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
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| Summary |
We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generallyspread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. Inaddition, integrative analyses of R-loop data with existing RNA-seq, chromatin-immunoprecipitation (ChIP-seq), deoxyribonucleaseI-seq (DNase-seq) and whole-genome bisulfite sequencing (BS-seq) data revealed interrelationships and intricate connectionsamong R-loops, gene expression and epigenetic signatures. Experimental validation provided evidence that the demethylationof both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants thatreveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptionalregulation.
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| Overall design |
Examination of two tissues in rice including seedlings and calli
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| Contributor(s) |
Fang Y, Zhang W |
| Citation(s) |
31262943 |
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| Submission date |
Mar 16, 2018 |
| Last update date |
Jul 05, 2019 |
| Contact name |
Fang Yuan |
| E-mail(s) |
yuanfa@mtu.edu
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| Organization name |
NanJing Argricultural University
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| Street address |
No.1, Weigang Street, Xuanwu District, Nanjing
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platforms (2) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA438658 |
| SRA |
SRP135873 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111944_Calli_all_cR-loops.macs2_peaks-q10.bed.gz |
946.0 Kb |
(ftp)(http) |
BED |
| GSE111944_Calli_all_wR-loops.macs2_peaks-q10.bed.gz |
970.3 Kb |
(ftp)(http) |
BED |
| GSE111944_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of BED, TXT) |
| GSE111944_Seedlings_all_cR-loops.macs2_peaks-q10.bed.gz |
965.2 Kb |
(ftp)(http) |
BED |
| GSE111944_Seedlings_all_wR-loops.macs2_peaks-q10.bed.gz |
970.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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