Fig. 1

ALKBH1 demethylates 6mA in R-loops in rice. a Metaplots of 6mA levels of all genes in alkbh1 compared with wild type. b Scatterplot of 6mA levels between WT and alkbh1. DIP-seq peaks merged from all samples (n = 42,387) are shown. The x-axis and y-axis represent the normalized read number at each peak of WT and alkbh1, respectively. Blue dots represent the downregulated peaks; red dots represent the upregulated peaks; differential peaks (fold change > 1.5, P < 0.05) overlapping between two replicates were considered as significantly changed. c Metaplots of 6mA levels at R-loops [39] in alkbh1 compared with wild type. d Venn diagram showing the percentages of 6mA DIP-seq peaks that overlap with DRIP-seq peaks [39] (DNA: RNA hybrid immunoprecipitation and sequencing for R-loops). P-values were calculated by hypergeometric tests. e DRIP-seq and 6mA DIP-seq signals at a representative genomic region. Gray areas display the difference in signals between the mutant and WT