Fig. 4

CHH methylation shapes key gene transcription for root initiation. A Analysis of correlations between gene transcription and CHH methylation of TE within the corresponding promoters. 14,312 genes were identified with transcription variation (see the “Methods” section) during root initiation, while 33.46% (4,789/14,312) were significantly correlated with CHH methylation dynamics. B and C IGV screenshots showing the CHH methylation dynamics within the promoter regions of indicated genes during crown and lateral root initiation. Histograms show corresponding transcription levels. Two biological replications are represented. D Knock-out of bZIP65 decreases lateral root numbers in rice without affecting crown roots. Upper panel, schematic diagrams show the CRISPR target (arrow) and the mutants generated by using CRISPR-Cas9 system. Two frameshift homozygous lines are shown. Lower panel, statistics of crown and lateral root numbers compared to wild type (WT). Double asterisks indicate significant differences, P-value < 0.01 (Student’s t-test). ns, no significant difference. N = 15, 22, and 10 for CR, 27, 11, and 13 for LR