Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu1,2,7,
- Qian Liu1,2,7,
- Handong Su1,3,7,
- Kunpeng Liu4,
- Xue Xiao5,
- Wei Li5,
- Qianwen Sun4,
- James A. Birchler6 and
- Fangpu Han1,2
- 1State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- 2University of Chinese Academy of Sciences, Beijing 100049, China;
- 3College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- 4Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- 5National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
- 6Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211-7400, USA
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↵7 These authors contributed equally to this work.
Abstract
R-loops are stable chromatin structures comprising a DNA:RNA hybrid and a displaced single-stranded DNA. R-loops have been implicated in gene expression and chromatin structure, as well as in replication blocks and genome instability. Here, we conducted a genome-wide identification of R-loops and identified more than 700,000 R-loop peaks in the maize (Zea mays) genome. We found that sense R-loops were mainly enriched in promoters and transcription termination sites and relatively less enriched in gene bodies, which is different from the main gene-body localization of sense R-loops in Arabidopsis and Oryza sativa. At the chromosome scale, maize R-loops were enriched in pericentromeric heterochromatin regions, and a significant portion of R-loops were derived from transposable elements. In centromeres, R-loops preferentially formed within the binding regions of the centromere-specific histone CENH3, and centromeric retrotransposons were strongly associated with R-loop formation. Furthermore, centromeric retrotransposon R-loops were observed by applying the single-molecule imaging technique of atomic force microscopy. These findings elucidate the fundamental character of R-loops in the maize genome and reveal the potential role of R-loops in centromeres.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275270.121.
- Received January 20, 2021.
- Accepted June 29, 2021.
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