Identification and functional analysis of human transcriptional promoters.

Genomic and full-length cDNA sequences provide opportunities for understanding human gene structure and transcriptional regulatory elements. The simplest regulatory elements to identify are promoters, as their positions are dictated by the location of transcription start sites. We aligned full-length cDNA clones from the Mammalian Gene Collection to the human genome rough draft sequence to estimate the start sites of more than 10,000 human transcripts. We selected genomic sequence just upstream from the 5' end of these cDNA sequences and designated these as putative promoters. We assayed the functions of 152 of these DNA fragments, chosen at random from the entire set, in a luciferase-based transfection assay in four human cultured cell types. Ninety-one percent of these DNA fragments showed significant transcriptional activity in at least one of the cell lines, whereas 89% showed activity in at least two of the lines. We analyzed the distributions of strengths of these promoter fragments in the different cell types and identified likely alternative promoters in a large fraction of the genes. These data indicate that this approach is an effective method for predicting human promoters and provide the first set of functional data collected in parallel for a large set of human promoters.

Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic variation during the cell cycle. Hierarchical clustering of the expression patterns revealed coexpressed groups of previously well-characterized genes involved in essential cell cycle processes such as DNA replication, chromosome segregation, and cell adhesion along with genes of uncharacterized function. Most of the genes whose expression had previously been reported to correlate with the proliferative state of tumors were found herein also to be periodically expressed during the HeLa cell cycle. However, some of the genes periodically expressed in the HeLa cell cycle do not have a consistent correlation with tumor proliferation. Cell cycle-regulated transcripts of genes involved in fundamental processes such as DNA replication and chromosome segregation seem to be more highly expressed in proliferative tumors simply because they contain more cycling cells. The data in this report provide a comprehensive catalog of cell cycle regulated genes that can serve as a starting point for functional discovery. The full dataset is available at http://genome-www.stanford.edu/Human-CellCycle/HeLa/.