RNA Splicing Factors and RNA-Directed DNA Methylation

Abstract

RNA-directed histone and/or DNA modification is a conserved mechanism for the establishment of epigenetic marks from yeasts and plants to mammals. The heterochromation formation in yeast is mediated by RNAi-directed silencing mechanism, while the establishment of DNA methylation in plants is through the RNA-directed DNA methylation (RdDM) pathway. Recently, splicing factors are reported to be involved in both RNAi-directed heterochromatin formation in yeast and the RdDM pathway in plants. In yeast, splicing factors may provide a platform for facilitating the siRNA generation through an interaction with RDRC and thereby affect the heterochromatin formation, whereas in plants, various splicing factors seem to act at different steps in the RdDM pathway.

Figure 1

A model for the involvement of splicing factors in different steps of the RNA-directed DNA methylation (RdDM) pathway. With the assistance of CLSY1, Pol IV is recruited to transcribe transposons and repeat loci through an interaction with DTF1/SHH1, which recognizes unmethylated K4 and methylated K9 modifications of histone H3. Coupling of Pol IV and RNA-DEPENDENT RNA POLYMERASE2 (RDR2) is required for copying Pol IV-generated transcripts into dsRNAs by RDR2. The splicing factor SR45 might be recruited by the Pol IV-RDR2 complex and facilitates the siRNA generation. The dsRNAs were diced into 24-nt siRNAs by DICER-LIKE 3 (DCL3), followed by HEN1 methylating the siRNAs at their 3'ends. One strand of the siRNAs is loaded into AGO4 and the siRNA‑bound AGO4 is recruited by Pol V transcript through base-pairing between the siRNA and nascent transcript. The interaction of AGO4 with KTF1 and Pol V is required for the stable association of AGO4 with the Pol V transcripts. DDR complex, which is consisted of DRD1, DMS3 and RDM1 proteins, facilitates Pol V transcription. The interaction of RDM1 with AGO4 and DRM2 may be involved in recruiting DRM2 to Pol V-target loci for catalyzing DNA methylation. The splicing factors STA1 and ZOP1 might be recruited by AGO4-containing effector complex, Pol V or Pol V transcripts and act at a late step in RdDM, while the splicing factor RDM16 might be simply recruited by Pol V or Pol V transcripts to function in RdDM.