Abstract
DNA methylation is a conserved epigenetic marker in plants and animals. In Arabidopsis, DNA methylation can be established through an RNA-directed DNA methylation (RdDM) pathway. By screening for suppressors of ros1, we identified STA1, a PRP6-like splicing factor, as a new RdDM regulator. Whole-genome bisulfite sequencing suggested that STA1 and the RdDM pathway share a large number of common targets in the Arabidopsis genome. Small RNA deep sequencing demonstrated that STA1 is predominantly involved in the accumulation of the siRNAs that depend on both Pol IV and Pol V. Moreover, the sta1 mutation partially reduces the levels of Pol V-dependent RNA transcripts. Immunolocalization assay indicated that STA1 signals are exclusively present in the Cajal body and overlap with AGO4 in most nuclei. STA1 signals are also partially overlap with NRPE1. Localization of STA1 to AGO4 and NRPE1 signals is probably related to the function of STA1 in the RdDM pathway. Based on these results, we propose that STA1 acts downstream of siRNA biogenesis and facilitates the production of Pol V-dependent RNA transcripts in the RdDM pathway.
Highlights
Inactivation of transposons, retrotransposons and other DNA repeats is required for genome stability and integrity in plants as well as in fungi and animals [1,2,3,4]
The components in the RNA-directed DNA methylation (RdDM) pathway are responsible for the silencing of RD29A-LUC, whereas the DNA replication-related proteins are only required for the silencing of 35S-NPTII [47]
The results indicate that sta1 reduces DNA methylation of both RD29A promoters at CHG and CHH sites (Figure 1C and D; Supplementary Table S2)
Summary
Inactivation of transposons, retrotransposons and other DNA repeats is required for genome stability and integrity in plants as well as in fungi and animals [1,2,3,4]. In the RdDM pathway, multi-subunit DNA-dependent RNA polymerases IV and V (Pol IV and Pol V) are responsible for generating 24-nt small interfering RNAs (siRNA) and nascent scaffold RNAs, respectively [8,9,10,11,12,13,14]. After snRNPs exit the Cajal body, they are transported and assembled into spliceosome complexes on pre-mRNAs for splicing [30]. We identified a PRP6-like splicing factor, STA1, by screening for suppressors of ros and found that STA1 is required for RdDM and transcriptional gene silencing. STA1 colocalizes with AGO4 in the Cajal body and partially colocalizes with the largest subunit of Pol V, NRPE1 in the nucleoplasm Based on these results, we propose that STA1 functions together with AGO4 and NRPE1 and has a critical role downstream of siRNA biogenesis in the RdDM pathway
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