Significance: Long noncoding RNAs (lncRNAs) play important roles in chromatin regulation in higher eukaryotes. Studies analysing how lncRNAs influence Polycomb silencing suggested they specifically bind and recruit Polycomb Repressive Complex 2 (PRC2) to defined targets. However, the promiscuous binding of PRC2 to RNA has raised questions as to the mechanism by which lncRNA contributes to Polycomb silencing. We investigate the function of a set of cold-induced antisense transcripts in the Polycomb-dependent epigenetic silencing of a floral repressor gene in Arabidopsis . Through analysis of a transgene, in which antisense transcripts are no longer cold-induced, we show that these antisense transcripts are required for coordinated switching of opposing chromatin states. This mechanism links transcriptional shutdown by cold to long-term epigenetic silencing.

The phytopathogenic bacterium Xanthomonas axonopodis pv. citri is responsible for the canker disease affecting citrus plants throughout the world. Here, we have evaluated the role of bacterial attachment and biofilm formation in leaf colonization during canker development on lemon leaves. Crystal violet staining and confocal laser scanning microscopy analysis of X. axonopodis pv. citri strains expressing the green fluorescent protein were used to evaluate attachment and biofilm formation on abiotic and biotic (leaf) surfaces. Wild-type X. axonopodis pv. citri attached to and formed a complex, structured biofilm on glass in minimal medium containing glucose. Similar attachment and structured biofilm formation also were seen on lemon leaves. An X. axonopodis pv. citri gumB mutant strain, defective in production of the extracellular polysaccharide xanthan, did not form a structured biofilm on either abiotic or biotic surfaces. In addition, the X. axonopodis pv. citri gumB showed reduced growth and survival on leaf surfaces and reduced disease symptoms. These findings suggest an important role for formation of biofilms in the epiphytic survival of X. axonopodis pv. citri prior to development of canker disease.

The determinants that specify the genomic targets of Polycomb silencing complexes are still unclear. Polycomb silencing of Arabidopsis FLOWERING LOCUS C ( FLC ) accelerates flowering and involves a cold-dependent epigenetic switch. Here we identify a single point mutation at an intragenic nucleation site within FLC that prevents this epigenetic switch from taking place. The mutation blocks nucleation of plant homeodomain–Polycomb repressive complex 2 (PHD-PRC2) and indicates a role for the transcriptional repressor VAL1 in the silencing mechanism. VAL1 localizes to the nucleation region in vivo, promoting histone deacetylation and FLC transcriptional silencing, and interacts with components of the conserved apoptosis- and splicing-associated protein (ASAP) complex. Sequence-specific targeting of transcriptional repressors thus recruits the machinery for PHD-PRC2 nucleation and epigenetic silencing.

Significance: How organisms monitor external environmental signals and integrate these measurements into their development is a fundamental question. Here, we investigate this issue in the context of vernalization, the perception and memory of long-term cold temperature exposure in plants. We use a combination of mathematical modeling coupled with experiments on plants exposed to an interrupted cold temperature regime. We find that cold temperature exposure is likely to be registered in an all-or-nothing (digital) manner at the relevant gene FLOWERING LOCUS C . Such a mechanism allows for integration of noisy, interrupted temperature signals and for subsequent switching into a stable, digital epigenetic memory state. This analysis is a key step toward uncovering the biochemical elements behind long-term cold temperature monitoring.

The requirement for vernalization, a need for prolonged cold to trigger flowering, aligns reproductive development with favorable spring conditions. In Arabidopsis thaliana vernalization depends on the cold-induced epigenetic silencing of the floral repressor locus FLC. Extensive natural variation in vernalization response is associated with A. thaliana accessions collected from different geographical regions. Here, we analyse natural variation for vernalization temperature requirement in accessions, including those from the northern limit of the A. thaliana range. Vernalization required temperatures above 0°C and was still relatively effective at 14°C in all the accessions. The different accessions had characteristic vernalization temperature profiles. One Northern Swedish accession showed maximum vernalization at 8°C, both at the level of flowering time and FLC chromatin silencing. Historical temperature records predicted all accessions would vernalize in autumn in N. Sweden, a prediction we validated in field transplantation experiments. The vernalization response of the different accessions was monitored over three intervals in the field and found to match that when the average field temperature was given as a constant condition. The vernalization temperature range of 0–14°C meant all accessions fully vernalized before snowfall in N. Sweden. These findings have important implications for understanding the molecular basis of adaptation and for predicting the consequences of climate change on flowering time.