Genetic variant at ETS1 locus increases lupus risk and affects Stat1 binding (BA2P.115)

Over the past 10 years, genetic association studies have identified over 55 systemic lupus erythematous (SLE)-risk loci. Genetic variants in ETS1 have been associated with SLE in several independent studies in populations of Asian ancestry. Several recent studies have implicated Ets1 as a critical driver of B and T cell function; indeed, mice deficient in Ets1 develop an SLE-like autoimmunity. rs1128334, in the 3’ UTR of ETS1, has been associated with the decreased expression of Ets1. We performed a fine-mapping study of over 20,000 subjects of two multi-ancestral cohorts using genotyped and imputed variants spanning the ETS1 locus. By constructing genetic models using frequentist and Bayesian association methods, we identified a set of variants that are most likely to be causal. Of the three variants that we tested, only rs6590330 differentially binds lysate from B cell lines as assessed by electrophoretic mobility shift assays and DNA affinity precipitation assays. We found that the active form of the transcription factor Stat1 binds the risk allele of rs6590330 but not the non-risk allele using mass spectrometry, a finding confirmed by Western blot analysis. rs6590330 is in strong linkage disequilibrium with rs1128334 and is predicted to also be associated with decreased Ets1 expression. We propose a model in which the risk allele of rs6590330 increases SLE risk by binding Stat1 and depressing the expression of Ets1.

A novel C2H2 transcription factor that regulates gliA expression interdependently with GliZ in Aspergillus fumigatus

Secondary metabolites are produced by numerous organisms and can either be beneficial, benign, or harmful to humans. Genes involved in the synthesis and transport of these secondary metabolites are frequently found in gene clusters, which are often coordinately regulated, being almost exclusively dependent on transcription factors that are located within the clusters themselves. Gliotoxin, which is produced by a variety of Aspergillus species, Trichoderma species, and Penicillium species, exhibits immunosuppressive properties and has therefore been the subject of research for many laboratories. There have been a few proteins shown to regulate the gliotoxin cluster, most notably GliZ, a Zn2Cys6 binuclear finger transcription factor that lies within the cluster, and LaeA, a putative methyltransferase that globally regulates secondary metabolism clusters within numerous fungal species. Using a high-copy inducer screen in A. fumigatus, our lab has identified a novel C2H2 transcription factor, which plays an important role in regulating the gliotoxin biosynthetic cluster. This transcription factor, named GipA, induces gliotoxin production when present in extra copies. Furthermore, loss of gipA reduces gliotoxin production significantly. Through protein binding microarray and mutagenesis, we have identified a DNA binding site recognized by GipA that is in extremely close proximity to a potential GliZ DNA binding site in the 5' untranslated region of gliA, which encodes an efflux pump within the gliotoxin cluster. Not surprisingly, GliZ and GipA appear to work in an interdependent fashion to positively control gliA expression.

The UCSC Genome Browser Database: update 2006

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity (available at http://bio.cse.psu.edu/ since May 2001). Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs include a stacked set of percent identity plots, called a MultiPip, comparing the reference sequence with subsequent sequences, and a nucleotide-level multiple alignment. New tools are provided to search MultiPipMaker output for conserved matches to a user-specified pattern and for conserved matches to position weight matrices that describe transcription factor binding sites (singly and in clusters). We illustrate the use of MultiPipMaker to identify candidate regulatory regions in WNT2 and then demonstrate by transfection assays that they are functional. Analysis of the alignments also confirms the phylogenetic inference that horses are more closely related to cats than to cows.

Volatile Constituents of Artemisia vestita Oil1

The essential oil of ARTEMISIA VESTITA (Compositae) was investigated by GLC, NMR, and mass spectrometry. Main constituents are alpha-, beta-, gamma-himachalene, caryophyllene, germacrene D, himachalol, allohimachalol, alpha-, gamma-atlantone, 1,8-cineole, yomogi alcohol, artemisia, and santolina alcohol and their acetates, and the thujones and thujanols. The characteristic oder of the oil is determined by the freshly smelling, 1, 8-cineole and thujone, and by the woody and sweet note of himachalol and atlantone.

Volatile constituents of Plectranthus rugosus leaf oil

The essential oil of Plectranthus rugosus (Labiatae) was investigated by GLC, NMR and mass spectrometry. Main constituents are caryophyllene, germacrene D, alpha-phellandrene, alpha-pinene, caryophyllene oxide, alpha-cadinol, delta-cadinene, limonene, beta-phellandrene, myrcene, and p-cymene.