Where polyadenylation, siRNAs, and DNA methylation meet

It has become more apparent in recent years that the different aspects of gene expression – transcription initiation, transcription elongation, mRNA capping, splicing, and polyadenylation, transport of the mRNA to the cytoplasm, translation, and mRNA quality control – are rather extensively interconnected.  One corollary is that the polyadenylation complex, through various of its subunits, plays roles in various of these other processes.  This has been established for the most parts in mammalian and yeast models, but some recent work in plants is adding new and important variation to this theme.

A most recent of such studies has appeared online on PNAS.  This study, from the lab of Caroline Dean, reveals that the polyadenylation factor subunit FY (a homolog of the yeast protein Pfs2), acting in concert with the flowering regulator FCA, plays a crucial role in chromatin modifications that regulate the expression of the FLC gene.  Interestingly, this effect is not limited to just the FLC gene. Rather, other genes that are silenced by small RNA-mediated DNA methylation also require FY for this silencing.  This provocative finding seems to place FY in some sort of proximity to the small RNA-guided DNA methylation machinery, and may have some relevance to many aspects of transcription and mRNA quality control.

The abstract and citation follows. As always, enjoy.

The role of RNA metabolism in chromatin silencing is now widely recognized. We have studied the Arabidopsis RNA-binding protein FCA that down-regulates an endogenous floral repressor gene through a chromatin mechanism involving histone demethylase activity. This mechanism needs FCA to interact with an RNA 3′ processing/polyadenylation factor (FY/Pfs2p), but the subsequent events leading to chromatin changes are unknown. Here, we show that this FCA–FY interaction is required for general chromatin silencing roles where hairpin transgenes induce DNA methylation of an endogenous gene. We also show 2 conserved RNA processing factors, AtCPSF100 and AtCPSF160, but not FCA, are stably associated with FY in vivo and form a range of different-sized complexes. A hypomorphic fy allele producing a shorter protein, able to provide some FY functions but unable to interact with FCA, reduces abundance of some of the larger MW complexes. Suppressor mutants, which specifically disrupt the FY motif through which FCA interacts, also lacked these larger complexes. Our data support a model whereby FCA, perhaps after recognition of a specific RNA feature, transiently interacts with FY, an integral component of the canonical RNA 3′ processing machinery, changing the interactions of the different RNA processing components. These altered interactions would appear to be a necessary step in this RNA-mediated chromatin silencing.

(Also of interest for the more hardcore readers of this blog are the indications that FY exists in multiple complexes.  This is something that our own studies of the interaction network involving Arabidopsis polyadenylation factor subunits suggested.  This is a gratifying development.)

David Manzano, Sebastian Marquardt,  Alexandra M. E. Jones, Isabel Bäurle, Fuquan Liu and Caroline Dean. Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing . Published online before print May 13, 2009, doi: 10.1073/pnas.0903444106