Fig. 1

Rhythmic occupancy of RNAPII and temporal relationship with mRNA accumulation in rice. a Sampling time points of a diurnal light and dark cycle under field conditions. Red font indicates the sample collection time, and black font indicates sunrise and sunset. b Distribution of RNAPII occupancy along genes over a six-point time course in mature leaves of rice. The gene body was converted into percentiles to standardize genes with different lengths. Regions 3 kb upstream and downstream of the gene are shown. c Phase distribution of rhythmic RNAPII occupancy represented as a rose plot. The values inside the circle represent the coordinates, the numbers outside the circle indicate the sidereal hours. d Peak expression phase distribution of rhythmically expressed genes. The phase of each transcript rhythm is represented as a rose plot. e Heat map representation of rhythmic RNAPII occupancy and transcript levels. Each rhythmic RNAPII occupancy and the corresponding rhythmically expressed gene are represented as a horizontal line and ordered vertically by the rhythmic RNAPII occupancy phase in sidereal hours. f Density plot of RNAPII occupancy and mRNA accumulation phase. The orange dashed line indicates the average phase of RNAPII occupancy, and the green dashed line indicates the average phase of mRNA accumulation. g Features of RNAPII binding peaks and gene transcription at the indicated time point and the OsLHY locus. Each RNAPII occupancy and RNA-seq track represents the normalized read coverage (wiggle plot) at a single time point. Of the RNA-seq track, the red and black wiggle plots represent forward- and reverse-strand RNA-seq reads, respectively. Six time points (each time point is a replicate of two successive days) every 4 h over a circadian cycle are shown beginning at 00:00 and ending at 20:00