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| Status |
Public on May 31, 2017 |
| Title |
Genome-wide maps of R-loops in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Other
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| Summary |
Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. R-loops are prevalent in regions with multiple chromatin modifications, and are negatively correlated with CG DNA hypermethylation. R-loops are strongly enriched in gene promoters and gene bodies, highly associated with noncoding RNA and repetitive genomic regions, and correlated with activated and repressed gene loci. In summary, our analysis reveals that R-loop is a common feature of the Arabidopsis genome, and suggests diverse roles for R-loops in genome organization and gene regulation, thereby providing novel insights into plant nuclear genome formation and function.
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| Overall design |
DRIP in 12-day-old Arabidopsis seedlings
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| Contributor(s) |
Xu W, Sun Q |
| Citation(s) |
28848233 |
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| Submission date |
Mar 07, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
li kuan |
| E-mail(s) |
likuan@cibr.ac.cn
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| Organization name |
Tsinghua University
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| Street address |
zhongguancun
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (1) |
| GPL23157 |
HiSeq X Ten (Arabidopsis thaliana) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA378348 |
| SRA |
SRP101480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95765_RAW.tar |
346.7 Mb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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