We have analyzed the set of genes expressed from the yeast genome, herein called the transcriptome, using serial analysis of gene expression. Analysis of 60,633 transcripts revealed 4,665 genes, with expression levels ranging from 0.3 to over 200 transcripts per cell. Of these genes, 1981 had known functions, while 2684 were previously uncharacterized. The integration of positional information with gene expression data allowed for the generation of chromosomal expression maps identifying physical regions of transcriptional activity and identified genes that had not been predicted by sequence information alone. These studies provide insight into global patterns of gene expression in yeast and demonstrate the feasibility of genome-wide expression studies in eukaryotes.

The murine gene CHD1 (MmCHD1) was previously isolated in a search for proteins that bound a DNA promoter element. The presence of chromo (chromatin organization modifier) domains and an SNF2-related helicase͞ ATPase domain led to speculation that this gene regulated chromatin structure or gene transcription. This study describes the cloning and characterization of three novel human genes related to MmCHD1. Examination of sequence databases produced several more related genes, most of which were not known to be similar to MmCHD1, yielding a total of 12 highly conserved CHD genes from organisms as diverse as yeast and mammals. The major region of sequence variation is in the C-terminal part of the protein, a region with DNA-binding activity in MmCHD1. Targeted deletion of ScCHD1, the sole Saccharomyces cerevesiae CHD gene, was performed with deletion strains being less sensitive than wild type to the cytotoxic effect of 6-azauracil. This finding suggested that enhanced transcriptional arrest at RNA polymerase II pause sites due to 6-azauracil-induced nucleotide pool depletion was reduced in the deletion strain and that ScCHD1 inhibited transcription. This observation, along with the known roles of other proteins with chromo or SNF2-related helicase͞ATPase domains, suggests that alteration of gene expression by CHD genes might occur by modifications of chromatin structure, with altered access of the transcriptional apparatus to its chromosomal DNA template.Attempting to clone Y, a DNA-binding nuclear protein with affinity for Ig promoters, Delmas et al.(1) identified a novel murine protein with chromo (chromatin organization modifier) domains, SNF2-related helicase͞ATPase domain and a DNA-binding domain (GenBank accession no. L10410). To denote the presence of these domains the protein was named CHD1. For clarity, it will be referred to as MmCHD1.Chromo domains are found in a variety of proteins including the Drosophila melanogaster proteins HP1, which binds to heterochromatin at chromocenters and telomeres, and Polycomb, an inhibitor of homeotic gene expression responsible for maintaining a repressive heterochromatic structure at loci on polytene chromosomes (2). Although the mechanism by which chromo domains interact with heterochromatin is unclear, synthetic chromo domain peptides self-associate, giving chromo domain-containing proteins the potential to bind to each other and form complexes with as yet undetermined components of heterochromatin (3).The SNF2-related family of proteins each contain a region of Ϸ400 amino acids with seven highly conserved helicase motifs (4). There are several subfamilies of SNF2-related genes, but none have chromo domains or DNA-binding domains similar to those found in MmCHD1. Some act either as activators (e.g., SNF2 and Brahma) or inhibitors (e.g., MOT1) of transcription whereas others are involved in DNA repair (e.g., RAD16 and ERCC6) or recombination (e.g., RAD54). Although none of the proteins coded for by these genes have been shown to possess helicase activity, sev...