The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs

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.

A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast

“…Both Saf1 and Saf5 were found to associate principally with components of the U5 snRNP and the NineTeen Complex (NTC), suggesting that these factors are likely to be associated with the catalytically activated form of the spliceosome. Connections between RNAi and splicing factors have recently been reported in several systems, including plants [49][50][51][52][53], worms [54][55][56] and flies [57]. In fission yeast, we have shown previously that conditional mutants of a subset of essential splicing factors disrupt heterochromatin even under permissive conditions, independently of any apparent effects on splicing.…”

Emerging roles of RNA processing factors in regulating long non-coding RNAs

“…9 While it is unclear how Pol V lncRNAs may be involved in the reinforcement of siRNA production, STA1 appears to be a connection between Pol V-dependent lncRNAs and siRNAs, because STA1-dependent siRNAs are almost exclusively Pol V-dependent. 36 Pol IV-dependent siRNA accumulation was also impaired in Arabidopsis mutants defective in several other RNA splicing factors, including ZOP1, SR45, MAC3A, MAC3B, MOS4, MOS12, and MOS14. 38,39 ZOP1 physically associates with STA1 and, similar to STA1, is present in Cajal bodies where AGO4 is also localized.…”

“…1). 35,36 The rdm16 and sta1 mutants do not display altered mRNA accumulation or pre-mRNA splicing of known RdDM factors. 35,36 Thus the effects of RDM16 and STA1 on Pol V lncRNA homeostasis are possibly direct, although the underlying mechanisms remain unclear.…”

“…35,36 Nuclear immunostaining studies revealed that RDM16 is distributed throughout the nucleoplasm while STA1 is mainly present in nucleolus-associated Cajal bodies. 35,36 Protein localization in Cajal bodies has been observed for some siRNA-producing RdDM factors, including RDR2, DCL3, and AGO4. 31,37 Consistent with their nuclear localization patterns, STA1 but not RDM16 was found to be required for siRNA accumulation.…”

STABILIZED1 Modulates Pre-mRNA Splicing for Thermotolerance

“…In conclusion, heat-inducible STA1-dependent posttranscriptional regulation of the stress-responsive gene expression plays a role in the establishment of the acquired heat stress tolerance in Arabidopsis. More recently STA1 has been reported to play a role in miRNA biogenesis and RNA-directed DNA methylation based on analyses of relevant molecular and cellular phenotypes of sta1-1 (Ben Chaabane et al, 2013;Dou et al, 2013). Moreover, heat stress seemingly alters splicing of miRNA, perhaps linking STA1 activity to miRNA splicing (Yan et al, 2012).…”