H3K36 methylation and intron retention in SDG725Ri rice

Knockdown of SDG725, a Histone H3 lysine 36 (H3K36)-specific methyltransferase in rice, leads to alterations of intron retention in more than 4,700 genes. Intron retention events are globally increased at the 5′ region but decreased at the 3′ region of gene body in the SDG725-knockdown mutant. Chromatin Immunoprecipitation sequencing (ChIP-seq) analyses reveal that SDG725 depletion results in a genome-wide increase of the H3K36 mono-methylation (H3K36me1) but unexpectedly, promoter-proximal shifts of H3K36 di- and tri-methylation (H3K36me2 and H3K36me3). Consistent with the results in animals, the levels of H3K36me1/me2/me3 in rice positively correlate with gene expression levels, whereas shifts of H3K36me2/me3 coincide with position-specific alterations of intron retention. We find that either H3K36me2 or H3K36me3 alone contributes to the positional change of intron retention caused by SDG725-knockdown, although intron retention shift is more significant when both H3K36me2 and H3K36me3 modifications are simultaneously shifted.