Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain.

H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily conserved nucleosome-binding globular domain, GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species studied so far, linker histones are highly heterogenous, with numerous nonallelic variants cooccurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established. This contrasts markedly with the rather limited knowledge concerning the phylogeny and structural and functional roles of an unusually diverse group of GH1-containing proteins in plants. The dearth of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead to misunderstandings regarding their identity and possible relationships, thereby hampering plant chromatin research. Based on published data and our in silico and high-throughput analyses, we propose a systematization and coherent nomenclature of GH1-containing proteins of Arabidopsis (Arabidopsis thaliana [L.] Heynh) that will be useful for both the identification and structural and functional characterization of homologous proteins from other plant species

Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression

ATP-dependent chromatin remodeling complexes are important regulators of gene expression in Eukaryotes. In plants, SWI/SNF-type complexes have been shown critical for transcriptional control of key developmental processes, growth and stress responses. To gain insight into mechanisms underlying these roles, we performed whole genome mapping of the SWI/SNF catalytic subunit BRM in Arabidopsis thaliana, combined with transcript profiling experiments. Our data showthatBRM occupies thousands of sites in Arabidopsis genome, most of which located within or close to genes. Among identified direct BRM transcriptional targets almost equal numbers were up- and downregulated upon BRM depletion, suggesting that BRM can act as both activator and repressor of gene expression. Interestingly, in addition to genes showing canonical pattern of BRM enrichment near transcription start site, many other genes showed a transcription termination sitecentred BRM occupancy profile. We found that BRMbound 3� gene regions have promoter-like features, including presence of TATA boxes and high H3K4me3 levels, and possess high antisense transcriptional activity which is subjected to both activation and repression by SWI/SNF complex. Our data suggest that binding to gene terminators and controlling transcription of non-coding RNAs is another way through which SWI/SNF complex regulates expression of its targets

Variation - sources, types and role in evolution

Genetic variation among individuals within a population concerns both quantitative and discrete traits and manifests at a variety of organizational levels, from whole organisms down to chemical constituents of cells. The results of DNA sequencing revealed even more variation than was detected by earlier comparisons of proteins by gel electrophoresis. The observation of unexpectedly high levels of genetic variation in both coding and the non-coding regions of DNA led to development of the neutral theory which holds that most variation at the molecular level does not affect fitness and can be accounted for by stochastic processes. A relatively constant rate of molecular evolution - the molecular clock - provided it is properly calibrated, became a useful method of estimating the time of events in evolutionary history. While mutations are the ultimate source of genetic variation, the major source of differences among sexually reproducing individuals in populations results from meiotic crossing over, recombination of chromosomes and random fertilization. Since recently, high throughput sequencing methods provide new insights into the evolution of genomes revealing major contributions from gene and whole genome duplications, large deletions and horizontal transfer of genes. The uncovering of the mechanisms responsible for epigenetic phenomena in plants and animals and the observations of transgenerational epigenetic inheritance (i.e. inheritance not dependent on changes in the sequence of DNA) opens the way to study the importance of multigenerational epigenetics for evolution and adaptation

Biology in postgenomic phase

The current postgenomic phase in biology is characterized by the occurrence of numerous novel research areas. Within the next twenty years or so, some of them will probably develop into well defined sub-disciplines, the other will disappear or transform into something completely new. Of the emerging directions, three seem particularly promising. They are: comparative genomics, deep analysis of the genomes and a search for the new ways of describing organisms. The recent exemplary achievments obtained by researchers pursuing these directions were the elucidation of the role of segmental DNA duplications in the evolution of mammals, the discovery of the regulatory functions and the widespread occurrence in the genomes of the tiny RNA molecules, the microRNA, and the finding that such processes as karyokinesis or nuclear-cytoplasmic transport are controlled by the fields of interactions resulting form gradients of regulatory molecules

Suppression of Histone H1 Genes in Arabidopsis Results in Heritable Developmental Defects and Stochastic Changes in DNA Methylation

Histone H1 is an abundant component of eukaryotic chromatin that is thought to stabilize higher-order chromatin structures. However, the complete knock-out of H1 genes in several lower eukaryotes has no discernible effect on their appearance or viability. In higher eukaryotes, the presence of many mutually compensating isoforms of this protein has made assessment of the global function of H1 more difficult. We have used double-stranded RNA (dsRNA) silencing to suppress all the H1 genes of Arabidopsis thaliana. Plants with a >90% reduction in H1 expression exhibited a spectrum of aberrant developmental phenotypes, some of them resembling those observed in DNA hypomethylation mutants. In subsequent generations these defects segregated independently of the anti-H1 dsRNA construct. Downregulation of H1 genes did not cause substantial genome-wide DNA hypo- or hypermethylation. However, it was correlated with minor but statistically significant changes in the methylation patterns of repetitive and single-copy sequences, occurring in a stochastic manner. These findings reveal an important and previously unrecognized link between linker histones and specific patterns of DNA methylation