Dr. HAN Fangpu's group from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences reports the genome-wide mapping of R-loops in maize in an article published online in Genome Research.
R-loops are nucleic acid structures composed of an RNA–DNA hybrid and a displaced single-stranded DNA. Twenty years after the discovery of R-loops, Crouch and colleagues showed that R-loops could form in vivo during transcription in bacterial cells, and were considered to be mere ‘by-products’ of transcription. Since then and especially in the past decade, R-loop biology has gained more attention, as these nucleic acid structures are found in a variety of organisms, ranging from bacteria to mammals, and are implicated in gene expression and chromatin structure, as well as in replication blocks and genome instability.
In the present study, the researchers presented genome-wide R-loop maps of maize leaf and identified more than 700,000 R-loop peaks. They found that sense R-loops were mainly enriched in promoters and transcription termination sites, and relatively less enriched in gene bodies, while antisense R-loops were mainly detected in transcription start sites.
In addition, the researchers revealed that the greatest R-loop enrichment in proximity to the centromeres and within pericentromeric heterochromatin at the chromosome scale 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, indicating that CENH3 nucleosomes may provide a permissible environment for R-loops. Furthermore, the researchers applied the single-molecule imaging technique of atomic force microscopy for visualizing R-loop formation in centromeric retrotransposon.
These findings shed light on the fundamental character of R-loops in the maize genome and reveal the potential role of R-loops in centromeres.
IMAGE: Contribution of CRM1 and CRM2 to R-loop formation in the maize centromere (Image by IGDB)
Contact:
Dr. HAN Fangpu
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
