Key functional regions in the histone variant H2A.Z C-terminal docking domain

The incorporation of histone variants into nucleosomes represents one way of altering the chromatin structure to accommodate diverse functions. Histone variant H2A.Z has specific roles in gene regulation, heterochromatin boundary formation, and genomic integrity. The precise features required for H2A.Z to function and specify an identity different from canonical H2A remain to be fully explored. Analysis of the C-terminal docking domain of H2A.Z in Saccharomyces cerevisiae using epistatic miniarray profile (E-MAP) uncovered nuanced requirements of the H2A.Z C-terminal region for cell growth when additional genes were compromised. Moreover, the H2A.Z(1-114) truncation, lacking the last 20 amino acids of the protein, did not support regular H2A.Z functions, such as resistance to genotoxic stress, restriction of heterochromatin in its native context, GAL1 gene activation, and chromatin anchoring. The corresponding region of H2A could fully rescue the strong defects caused by loss of this functionally essential region in the C terminus of H2A.Z. Despite the dramatic reduction in function, the H2A.Z(1-114) truncation still bound the H2A.Z deposition complex SWR1-C, the histone chaperone Chz1, and histone H2B. These data are consistent with a model in which retaining the variant in chromatin after its deposition by SWR1-C is a crucial determinant of its function.     

Clues about the ancestral roles of plant MADS-box genes from a functional analysis of moss homologues

Classic MIKC-type MADS-box genes (MIKC ^c genes) are indispensable elements in the genetic programming of pattern formation, including the segmental organisation of angiosperm flowers, in seed plants. Since little is known about the functions of MIKC ^c genes in non-seed plants, a functional analysis of moss MIKC ^c homologues was performed using the genetically amenable, simple model plant, Physcomitrella patens. Expression of moss homologues was knocked down using an antisense RNA approach or abolished by generating transformants with gene knockouts. The knocked down (“antisense”) transformants displayed a multifaceted mutant phenotype comprising delayed gametangia formation, diminished sporophyte yield and, in the most extremely affected cases, abnormal sporophyte development and altered leaf morphogenesis. Knocked out transformants were phenotypically normal. Analysis of in situ MIKC ^c gene expression using transgenic strains containing MIKC ^c promoter–GUS fusions showed that these genes are generally expressed ubiquitously in vegetative and reproductive tissues. We conclude that MIKC ^c genes play significant roles in morphogenetic programming of the moss. Functional redundancy characterises some members of the gene group. Our findings provide clues concerning the ancestral roles of some MIKC ^c genes that may be represented in the genomes of diverse extant plant taxa. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions

The use of the budding yeast Saccharomyces cerevisiae as a simple eukaryotic model system for the study of chromatin assembly and regulation has allowed rapid discovery of genes that influence this complex process. The functions of many of the proteins encoded by these genes have not yet been fully characterized. Here, we describe a high-throughput methodology that can be used to illuminate gene function and discuss its application to a set of genes involved in the creation, maintenance and remodeling of chromatin structure. Our technique, termed E-MAPs, involves the generation of quantitative genetic interaction maps that reveal the function and organization of cellular proteins and networks.     

The next frontier of systems biology: higher-order and interspecies interactions

Systems approaches are not so different in essence from classical genetic and biochemical approaches, and in the future may become adopted so widely that the term 'systems biology' itself will become obsolete.     

A Combination of Three Mutations, dcd, pyrH, and cdd, Establishes Thymidine (Deoxyuridine) Auxotrophy in thyA+ Strains of Salmonella typhimurium

The dum gene of Salmonella typhimurium was originally identified as a gene involved in dUMP synthesis (C. F. Beck et al., J. Bacteriol. 129:305–316, 1977). In the genetic background used in their selection, the joint acquisition of a dcd (dCTP deaminase) and a dum mutation established a condition of thymidine (deoxyuridine) auxotrophy. In this study, we show that dum is identical to pyrH, the gene encoding UMP kinase. The level of UMP kinase activity in the dum mutant was found to be only 30% of that observed for the dum⁺ strain. Thymidine prototrophy was restored to the original dum dcd mutant (KP1361) either by transduction using a pyrH⁺ donor or by complementation with either of two pyrH⁺-carrying plasmids. Thymidine auxotrophy could be reconstructed in the dum⁺ derivative (KP1389) by the introduction of a mutant pyrH allele. To define the minimal mutational complement necessary to produce thymidine auxotrophy in thyA⁺ strains, a dcd::Km null mutation was constructed. In the wild-type background, dcd::Km alone or in combination with a pyrH (dum) mutation did not result in a thymidine requirement. A third mutation, cdd (cytidine-deoxycytidine deaminase), was required together with the dcd and pyrH mutations to impart thymidine auxotrophy.     

Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing

Low levels of histone covalent modifications are associated with gene silencing at telomeres and other regions in the yeast S. cerevisiae. Although the histone deacetylase Sir2 maintains low acetylation, mechanisms responsible for low H2B ubiquitylation and low H3 methylation are unknown. Here, we show that the ubiquitin protease Ubp10 targets H2B for deubiquitylation, helping to localize Sir2 to the telomere. Ubp10 exhibits reciprocal Sir2-dependent preferential localization proximal to telomeres, where Ubp10 serves to maintain low H2B Lys123 ubiquitylation in this region and, through previously characterized crosstalk, maintains low H3 Lys4 and Lys79 methylation in a slightly broader region. Ubp10 is also localized to the rDNA locus, a second silenced domain, where it similarly maintains low histone methylation. We compare Ubp10 to Ubp8, the SAGA-associated H2B deubiquitylase involved in gene activation, and show that telomeric and gene-silencing functions are specific to Ubp10. Our results suggest that these H2B-deubiquitylating enzymes have distinct genomic functions.