In budding yeast, intragenic histone modification is linked with transcriptional elongation through the conserved regulator Paf1C. To investigate Paf1C-related function in higher eukaryotes, we analyzed the effects of loss of Paf1C on histone H3 density and patterns of H3 methylated at K4, K27, and K36 in Arabidopsis genes, and integrated this with existing gene expression data. Loss of Paf1C did not change global abundance of H3K4me3 or H3K36me2 within chromatin, but instead led to a 3′ shift in the distribution of H3K4me3 and a 5′ shift in the distribution of H3K36me2 within genes. We found that genes regulated by plant Paf1C showed strong enrichment for both H3K4me3 and H3K27me3 and also showed a high degree of tissue-specific expression. At the Paf1C- and PcG-regulated gene FLC, transcriptional silencing and loss of H3K4me3 and H3K36me2 were accompanied by expansion of H3K27me3 into the promoter and transcriptional start regions and further enrichment of H3K27me3 within the transcribed region. These results highlight both genic and global functions for plant Paf1C in histone modification and gene expression, and link transcriptional activity with cellular memory.

The Arabidopsis thaliana VERNALIZATION INDEPENDENCE (VIP) gene class has multiple functions in development, including repression of flowering through activation of the MADSbox gene FLC. Epigenetic silencing of FLC plays a substantial role in the promotion of flowering through cold (vernalization). To better understand how VIP genes influence development, we undertook a genetic and molecular study of the previously uncharacterized VIP5 and VIP6 genes. We found that loss of function of these genes also resulted in downregulation of other members of the FLC/MAF gene family, including the photoperiodic pathway regulator MAF1/FLM. We cloned VIP5 and VIP6 through mapping and transcriptional profiling. Both proteins are closely related to distinct components of budding yeast Paf1C, a transcription factor that assists in establishment and maintenance of transcription-promotive chromatin modifications such as ubiquitination of H2B by Bre1/Rad6 and methylation of histone H3 lysine-4 by the trithorax-related histone methylase Set1. Genetic analysis and coimmunoprecipitation experiments suggest that VIP5 and VIP6 function in the same mechanism as the previously described VIP3 and VIP4. Our findings suggest that an evolutionarily conserved transcriptional mechanism plays an essential role in the maintenance of gene expression in higher eukaryotes and has a central function in flowering.

Despite its economic and environmental significance, understanding the molecular biology of secondary growth (i.e. wood formation) in tree species has been lagging behind that of primary growth, primarily due to the inherent difficulties of tree biology. In recent years, Arabidopsis has been shown to express all of the major components of secondary growth. Arabidopsis was induced to undergo secondary growth and the transcriptome profile changes were surveyed during secondary growth using 8.3 K Arabidopsis Genome Arrays. Twenty per cent of the approximately 8300 genes surveyed in this study were differentially regulated in the stems treated for wood formation. Genes of unknown function made up the largest category of the differentially expressed genes, followed by transcription regulation-related genes. Examination of the expression patterns of the genes involved in the sequential events of secondary growth (i.e. cell division, cell expansion, cell wall biosynthesis, lignification, and programmed cell death) identified several key candidate genes for the genetic regulation of secondary growth. In order to gain further insight into the transcriptional regulation of secondary growth, the expression patterns of the genes encoding transcription factors were documented in relation to secondary growth. A computational biology approach was used to identify regulatory cis-elements from the promoter regions of the genes that were up-regulated in wood-forming stems. The expression patterns of many previously unknown genes were established and various existing insights confirmed. The findings described in this report should add new information that can lead to a greater understanding of the secondary xylem formation process.

Chloroplast-localized sigma factor (SIG) proteins promote specificity of the plastid-encoded RNA polymerase. SIG2 function appears to be necessary for light-grown Arabidopsis thaliana plants. Specific photoreceptors or light-dependent factors that impact the light-induced accumulation of SIG2 have not been reported. A molecular link between phytochromes and nuclear-encoded SIG2, which impacts photomorphogenesis specifically under red (R) and far-red (FR) light, is described here. Both phyA and phyB promote SIG2 transcript accumulation. Disruption of SIG2 results in R- and FR-specific defects in the inhibition of hypocotyl elongation and cotyledon expansion, although no impairments in these responses are detected for sig2 mutants under blue (B) or white (W) light. SIG2 also impacts root elongation under W and R, and the R-dependent expression of PIF4, encoding a phytochrome-interacting factor, and HY2, which encodes a phytochrome chromophore biosynthetic enzyme. Whereas SIG2 apparently impacts the accumulation of the phytochromobilin (PΦB) phytochrome chromophore, sig2 mutants differ significantly from PΦB mutants, primarily due to wavelength-specific defects in photomorphogenesis and disruption of a distinct subset of phytochrome-dependent responses. The molecular link between phytochromes and SIG2 is likely to be an important part of the co-ordination of gene expression to maintain stoichiometry between the nuclear-encoded phytochrome apoprotein and plastid-derived PΦB, which combine to form photoactive phytochromes, and/or light-dependent SIG2 accumulation is involved in an inductive light signalling pathway co-ordinating components between nucleus and plastids.