ABSTRACT
In an effort to identify sets of yeast genes that are coregulated across various cellular transitions, gene expression data sets derived from yeast cells progressing through the cell cycle, sporulation, and diauxic shift were analyzed. A partitioning algorithm was used to divide each data set into 24 clusters of similar expression profiles, and the membership of the clusters was compared across the three experiments. A single cluster of 189 genes from the cell cycle experiment was found to share 65 genes with a cluster of 159 genes from the sporulation data set. Many of these genes were found to be clustered in the diauxic-shift experiment as well. The overlapping set was enriched for genes required for rRNA biosynthesis and included genes encoding RNA helicases, subunits of RNA polymerases I and III, and rRNA processing factors. A subset of the 65 genes was tested for expression by a quantitative-relative reverse transcriptase PCR technique, and they were found to be coregulated after release from alpha factor arrest, heat shock, and tunicamycin treatment. Promoter scanning analysis revealed that the 65 genes within this ribosome and rRNA biosynthesis (RRB) regulon were enriched for two motifs: the 13-base GCGATGAGATGAG and the 11-base TGAAAAATTTT consensus sequences. Both motifs were found to be important for promoting gene expression after release from alpha factor arrest in a test rRNA processing gene (EBP2), which suggests that these consensus sequences may function broadly in the regulation of a set of genes required for ribosome and rRNA biosynthesis.
Subject(s)
Carrier Proteins/metabolism , Carrier Proteins/physiology , Nuclear Proteins/metabolism , Nuclear Proteins/physiology , RNA, Ribosomal/metabolism , Ribosomes/metabolism , Transcription, Genetic , Algorithms , Amino Acid Motifs , Base Sequence , Cell Cycle , Fungal Proteins/metabolism , Gene Expression Regulation , Hot Temperature , Models, Genetic , Models, Theoretical , Molecular Sequence Data , Multigene Family , Oligonucleotide Array Sequence Analysis , Plasmids/metabolism , Polymerase Chain Reaction , Promoter Regions, Genetic , Reverse Transcriptase Polymerase Chain Reaction , Saccharomyces cerevisiae Proteins , Time Factors , Tunicamycin/pharmacologyABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC), the primary form of liver carcinoma, is increasing in incidence worldwide. The increasing numbers of Hispanic immigrants in Florida suggest that the rate of HCC in the Hispanic population should be of special concern. This study describes racial and ethnic distribution and trends of incident HCC in Florida from 1985 to 1995. METHODS: A total of 2837 cases of incident HCC from 1985 to 1995 were examined from Florida's incident cancer registry, the Florida Cancer Data System. Age standardized and age specific average annual incidence rates were calculated for the state of Florida by gender and by racial and ethnic group. RESULTS: Over the study period, the average annual incidence HCC rates in Florida among male and female Hispanics and blacks were consistently and significantly twice the rate of white males and females as standardized rate ratios. Males were at least twice as likely to have HCC compared with females in all three racial and ethnic subpopulations. CONCLUSIONS: The incidence of HCC in Florida was comparable to the overall U.S. incidence with respect to average annual incidence and gender distribution. Florida blacks and Hispanics are at significantly increased risk for HCC incidence compared with Florida whites. These results have implications for preventive HCC recommendations in growing racial and ethnic subpopulations in the United States.
