Fig. 1: Histone modification landscapes profiled by eChIP-Seq in rice.

a Schematic diagram of the eChIP and regular ChIP methods. Both methods start fixing tissues with formaldehyde, followed by grinding tissues to fine powder, homogenate lysis, chromatin sonication, IP (immunoprecipitation) with antibodies, ChIP DNA purification, library preparation, and sequencing. For eChIP, the lysed homogenate is directly sonicated for IP. In regular ChIP, the homogenate is first filtered through a mesh, and the isolated nuclei are then sonicated for IP. Steps 3a, 3b and 3c in regular ChIP are replaced by step 3 in eChIP. More details are shown in “Methods”. b Genome browser screenshot showing eChIP-Seq data for a young leaf of MH63. c Density distribution of the lengths of histone mark-modified and RNAPII-occupied regions in young leaf of rice. d Distribution of gene expression from the young leaf. The genes were divided into different categories based on the H3K4me3 peak positions relative to TSS and ATG of genes. TSS transcription start sites. Peak numbers of each categories are shown. e Distribution of TE genes and non-TE genes, marked with or without H3K9me2, in the young leaf of rice. f Expression levels of genes with promoters marked by different histone modifications and RNAPII. Numbers of genes in promoter categories are shown. Short line means that there is no certain histone modification or RNAPII occupancy. Boxplots in (d) and (f) include a median with quartiles and outliers above the top whisker. The statistical analysis was performed using two-side Wilcoxon test. The numbers indicate the sample size used in the analysis. g Breadth of expression (number of tissues that a gene is expressed in) of genes modified by different histone marks and RNAPII. Source Data underlying Fig. 1f, g are provided as a Source Data file.