Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays

Whole genome tiling arrays provide a high resolution platform for profiling of genetic, epigenetic, and gene expression polymorphisms. In this study we surveyed natural genomic variation in cytosine methylation among Arabidopsis thaliana wild accessions Columbia (Col) and Vancouver (Van) by comparing hybridization intensity difference between genomic DNA digested with either methylation-sensitive (HpaII) or -insensitive (MspI) restriction enzyme. Single Feature Polymorphisms (SFPs) were assayed on a full set of 1,683,620 unique features of Arabidopsis Tiling Array 1.0F (Affymetrix), while constitutive and polymorphic CG methylation were assayed on a subset of 54,519 features, which contain a 5′CCGG3′ restriction site. 138,552 SFPs (1% FDR) were identified across enzyme treatments, which preferentially accumulated in pericentromeric regions. Our study also demonstrates that at least 8% of all analyzed CCGG sites were constitutively methylated across the two strains, while about 10% of all analyzed CCGG sites were differentially methylated between the two strains. Within euchromatin arms, both constitutive and polymorphic CG methylation accumulated in central regions of genes but under-represented toward the 5′ and 3′ ends of the coding sequences. Nevertheless, polymorphic methylation occurred much more frequently in gene ends than constitutive methylation. Inheritance of methylation polymorphisms in reciprocal F1 hybrids was predominantly additive, with F1 plants generally showing levels of methylation intermediate between the parents. By comparing gene expression profiles, using matched tissue samples, we found that magnitude of methylation polymorphism immediately upstream or downstream of the gene was inversely correlated with the degree of expression variation for that gene. In contrast, methylation polymorphism within genic region showed weak positive correlation with expression variation. Our results demonstrated extensive genetic and epigenetic polymorphisms between Arabidopsis accessions and suggested a possible relationship between natural CG methylation variation and gene expression variation

SETDB1 Is Involved in Postembryonic DNA Methylation and Gene Silencing in Drosophila

DNA methylation is fundamental for the stability and activity of genomes. Drosophila melanogaster and vertebrates establish a global DNA methylation pattern of their genome during early embryogenesis. Large-scale analyses of DNA methylation patterns have uncovered revealed that DNA methylation patterns are dynamic rather than static and change in a gene-specific fashion during development and in diseased cells. However, the factors and mechanisms involved in dynamic, postembryonic DNA methylation remain unclear. Methylation of lysine 9 in histone H3 (H3-K9) by members of the Su(var)3–9 family of histone methyltransferases (HMTs) triggers embryonic DNA methylation in Arthropods and Chordates. Here, we demonstrate that Drosophila SETDB1 (dSETDB1) can mediate DNA methylation and silencing of genes and retrotransposons. We found that dSETDB1 tri-methylates H3-K9 and binds methylated CpA motifs. Tri-methylation of H3-K9 by dSETDB1 mediates recruitment of DNA methyltransferase 2 (Dnmt2) and Su(var)205, the Drosophila ortholog of mammalian “Heterochromatin Protein 1”, to target genes for dSETDB1. By enlisting Dnmt2 and Su(var)205, dSETDB1 triggers DNA methylation and silencing of genes and retrotransposons in Drosophila cells. DSETDB1 is involved in postembryonic DNA methylation and silencing of Rt1b{} retrotransposons and the tumor suppressor gene retinoblastoma family protein 1 (Rb) in imaginal discs. Collectively, our findings implicate dSETDB1 in postembryonic DNA methylation, provide a model for silencing of the tumor suppressor Rb, and uncover a role for cell type-specific DNA methylation in Drosophila development

The biotic and abiotic legacy of a large infrequent flood disturbance in the Sabie River, South Africa

Large infrequent disturbances (LIDs) leave heterogeneous, patchy legacies because the event may have different severities in different locations, or may influence ecosystem components differently. Biotic and abiotic legacies form the template upon which subsequent ecological processes take place and thus, LIDs can have a long-lasting influence on ecosystems. This study determined the geomorphological (channel type), landscape state (mosaic of physical and riparian vegetation patches) and riparian vegetation legacies of an extreme flood in the Sabie River. The linear proportions of geomorphological channel types were altered by the flood because of complex patterns of sediment erosion and deposition related to bed slope and channel width. Biotic landscape states (tree, shrub, reed, herbaceous vegetation) were stripped to expose the underlying physical template. The persistence and arrangement of landscape states varied amongst channel types because of the interaction between flood flows and the geomorphological attributes of each channel type. Overall, some riparian species decreased in density because of removal by the flood, and some increased in density because of post-flood recruitment or re-establishment. The flood also changed the location of many species in relation to their characteristic pre-flood elevation within the channel. In accordance with the expectations of LIDs, the effects of the flood were not uniform. Instead, the flood left a legacy of juxtaposed biotic and abiotic components that varied spatially amongst channel types and at different elevations within the channel

The effects of extreme floods on the biophysical heterogeneity of river landscapes

Studies of large infrequent disturbances, such as the Mount St Helens volcanic eruption, the 1988 Yellowstone National Park fires, and Hurricane Hugo, show that such events leave a heterogeneous imprint on a landscape, and that this imprint subsequently influences ecological response. But what imprint does a large infrequent flood disturbance leave on a river landscape, and how does the imprint influence river ecosystem response to disturbance? We used a landscape ecological framework to examine the associations between the imprint of an extreme flood and the response of woody riparian vegetation in the Sabie River (Kruger National Park, South Africa) landscape. We found that the flood left a heterogeneous imprint, consisting of remnant vegetated patches, remnant physical patches, and newly created physical patches. The structure and composition of riparian vegetation assemblages subsequently differed among these patches. Heterogeneity of the river landscape mosaic may result in multiple trajectories of ecological response to the flood, with important consequences for biodiversity conservation in Kruger National Park