Additional file 1: of Position-specific intron retention is mediated by the histone methyltransferase SDG725

Figure S1. The quantification of H3K36 methylation in 725Ri-1. and WT plants. Figure S2. Differential gene expression between 725Ri-1. and WT rice. Figure S3. Accumulative plot of up-regulated (725Ri-1._IRI_up) and down-regulated (725Ri-1._IRI_down) IR events with different intron length coverage. Figure S4. Distribution of up-regulated (red.) and down-regulated (blue.) intron retention (IR) events between 725Ri-1. and wild-type (WT) rice (a) and between 708Ri-1. and WT (b). Figure S5. Schematic diagram illustrating the way to transform the H3K36 methylation changes between the 725Ri-1. and wild-type plants at individual gene level. Figure S6. Box plot for levels of H3K36 methylations at IRI-up or IRI-down introns. Figure S7. qPCR validation of quality of cellular fractionation in wild-type rice. Figure S8. Box plot for expression level of transcripts with premature termination codon. Figure S9. Box plot of gene expression before and after cycloheximide (CHX) treatment in either wild-type or 725Ri-1. rice. Figure S10. H3K36 methylations associate with gene expression levels. Figure S11. Distribution of up-regulated (red.) and down-regulated (blue.) intron retention (IR) events in genes with no obvious changes (≤ 2-fold) in total levels of H3K36me2 (a) or H3K36me3 (b). Figure S12. Box plot for intron length in two groups of introns by distinct methods in calculating the degree of intron retention. Figure S13. Box plot for GC percentage in two groups of introns. Figure S14. Box plot for maximum entropy score of 5′ splice site (a) and 3′ splice site (b) in two groups of introns. Figure S15. Comparison of H3K36me2/me3 distribution across gene body between rice (a) and Arabidopsis (b). (DOCX 2596 kb)