Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and significant economic losses 1,2 . Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguard future food production 3 .Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE 1 and 2 (MAGO1 and MAGO2) associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to control the activity of

Chromatin-mediated transcriptional states are central to gene regulation in development and environmental response, with co-transcriptional processes involved in their establishment. Quantitative regulation of Arabidopsis FLOWERING LOCUS C (FLC) is key to determining reproductive strategy. Low FLC expression underpins rapid-cycling and is established through a transcription-coupled chromatin mechanism. Proximal termination of antisense transcripts is linked to histone 3 lysine 4 demethylation of adjacent chromatin that leads to stable Polycomb Repressive Complex 2 (PRC2) silencing. However, how the termination-induced chromatin environment influences the switch to PRC2 silencing is still unclear. Here, we combine molecular approaches with theory to develop a dynamic mathematical model that incorporates sense/antisense transcription, alternative termination sites, and the interplay of these processes with varying levels of activating (H3K4me1)/silencing (H3K27me3) histone modifications. The model captures different feedback mechanisms between co-transcriptional 3′ processing and chromatin modifications, detailing how proximal co-transcriptional polyadenylation/termination can set the subsequent level of productive transcription via removal of H3K4 monomethylation across the locus. Since transcription universally antagonizes Polycomb silencing, this dictates the degree of antagonism to H3K27me3, thus determining the rate at which Polycomb repression is established. These principles are likely to be central to regulating transcriptional output at many targets and generally relevant for Polycomb silencing in many genomes.

RNA-mediated chromatin silencing plays important roles in development and environmental response in many organisms. However, it is still unclear how the RNA, and/or the transcriptional processes producing them, trigger chromatin silencing. Through the study of developmental timing in plants we have found co-transcriptional RNA processing modulates a chromatin regulatory mechanism controlling quantitative expression of Arabidopsis FLOWERING LOCUS C (FLC). Here, we show that the phosphatase module of the mRNA 3′ processing CPSF complex is central to this mechanism. The phosphatase module components APRF1 (yeast Swd2/human WDR82), TOPP4 (Glc7/PP1) and LD (which we show is functionally equivalent to Ref2/PNUTS) all function genetically downstream of the CPSF-mediated cleavage and polyadenylation and are necessary for chromatin modification that results in FLC transcriptional silencing. LD has been previously shown to stoichiometrically co-associate in vivo with the histone demethylase FLD. We show both proteins result in removal of H3K4 monomethylation in the central section of the FLC locus. This links transcription termination to delivery of chromatin modifications that then influence subsequent transcription. Thus, physical association of the CPSF phosphatase module with chromatin modifiers generates a transcription-coupled silencing mechanism. The conservation of the factors involved suggest this mechanism may be generally relevant to transcription-mediated chromatin silencing.

Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and significant economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguard future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE 1 and 2 (MAGO1 and MAGO2) associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to control the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how MAGO2 activity and its interaction with retrotransposon RNA targets are modulated through the dynamic phosphorylation of a set of highly conserved surface-located serine residues. Our results demonstrate that an Argonaute-dependent RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions by controlling the mutagenic activity of transposons in male germ cells.