Fig. 4
From: Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice
RNAPII-organized chromatin spatial clusters (CSCs) change throughout the day. a Browser view of a 203-kb genomic segment with five CSCs showing RNAPII ChIA-PET data at the 08:00 (AM) and 20:00 (PM) time points. The number in brackets represents the number of connecting genes in each CSC. b Simulated 3D model of the CSCs throughout the diurnal cycle. CSCs change in an oscillatory manner with three forms: (i) an AM-specific state, (ii) a PM-specific state, and (iii) a static state (overlap). c The phase distribution of rhythmically expressed node genes in the three possible models specified in b represented as rose plots. d Expression levels of rhythmically or non-rhythmically expressed node genes in the three possible models. ***p < 0.0001. e Boxplot shows that rhythmically expressed node genes within AM CSCs tended to connect with rhythmically expressed genes, whereas non-rhythmically expressed node genes in PM CSCs tended to connect with non-rhythmically expressed genes. The red dashed line indicates the number of rhythmically expressed linked genes equally to the number of non-rhythmically expressed linked genes within a CSC. ***p < 0.0001. f, g Violin plot showing the distribution of the mean gene number in AM-specific CSCs (f) and PM-specific CSCs (g) with randomly simulated rhythmically and non-rhythmically expressed genes. h Schematic model of the chromatin organization during the circadian cycle. Representative CSCs from AM and PM circadian windows as well as their components and influence on rhythmically and non-rhythmically expressed genes transcription are shown. Red wavy lines indicate transcript abundance.