Genome-wide mapping reveals R-loops associated with centromeric repeats in maize

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 id...

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Bibliographic Details
Published in:Genome research 2021-08, Vol.31 (8), p.1409-1418
Main Authors: Liu, Yang, Liu, Qian, Su, Handong, Liu, Kunpeng, Xiao, Xue, Li, Wei, Sun, Qianwen, Birchler, James A, Han, Fangpu
Format: Article
Language:English
Subjects:
Atomic force microscopy
Centromere - genetics
Centromeres
Chromatin
Chromosome Mapping
Chromosomes
Gene expression
Gene mapping
Genomes
Genomic instability
Heterochromatin
Histones
Histones - genetics
Histones - metabolism
Localization
R-Loop Structures
R-loops
Single-stranded DNA
Transcription termination
Zea mays
Zea mays - genetics
Zea mays - metabolism
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Summary: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 ( ) 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 and 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.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.275270.121