Fig. 4: CRISPR/Cas9-based dissection of HAN2-downstream Copia LTR in gene repression.

a Expression levels of HAN2 in WT and HAN2^-LTR plants. Data are shown as mean ± SD (n = 3 biological replicates, with 3 seedlings per replicate). b Chilling tolerance phenotype of WT and HAN2^-LTR plants. Seedlings were incubated at 4 °C for 5 days and then transferred to normal temperature for a 7 day recovery. Left and right panels show WT and HAN2^-LTR plants before and after chilling treatment, respectively. c Survival rates of WT and HAN2^-LTR plants after recovery. Data are shown as mean ± SD (n = 3 biological replicates, with 8 seedlings per replicate). d Expression levels of HAN2 in tropical japonica rice varieties with or without the Copia LTR insertion. Data are shown as mean ± SD (n = 6 biological replicates). e Survival rates of tropical japonica rice with or without the Copia LTR insertion after chilling treatment. Data are shown as mean ± SD (n = 7 biological replicates). f Chromatin modification patterns and transcriptional activity across the HAN2 gene body. g Distribution of ChIP-qPCR fragments within the HAN2 gene. P1, P2–P13 represent DNA fragments spanning different exons; LTR indicates the Copia LTR. h, i ChIP-qPCR assays showing enrichment of H3K4me3 (h) and H3K36me3 (i) at the HAN2 locus in WT and HAN2^-LTR plants. Data are shown as mean ± SD (n = 3 biological replicates). Statistical significance in (a, c–e, and h, i) was evaluated using a two-tailed Student’s t-test; P-values are indicated. Source data are provided as a Source Data file.