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.

中文翻译：

---

全基因组图谱揭示了与玉米着丝粒重复相关的 R 环

R 环是稳定的染色质结构，包含 DNA:RNA 杂合体和置换的单链 DNA。R 环与基因表达和染色质结构以及复制块和基因组不稳定性有关。在这里，我们对 R 环进行了全基因组鉴定，并在玉米 ( Zea mays ) 基因组中鉴定了超过 700,000 个 R 环峰。我们发现有义R-loops主要富集在启动子和转录终止位点，而在基因体中的富集相对较少，这与拟南芥和水稻中正义R-loops的主要基因体定位不同。. 在染色体尺度上，玉米 R 环在着丝粒周围异染色质区域富集，并且很大一部分 R 环来源于转座因子。在着丝粒中，R-loops 优先在着丝粒特异性组蛋白 CENH3 的结合区域内形成，着丝粒反转录转座子与 R-loop 形成密切相关。此外，通过应用原子力显微镜的单分子成像技术观察到着丝粒反转录转座子 R 环。这些发现阐明了玉米基因组中 R 环的基本特征，并揭示了 R 环在着丝粒中的潜在作用。