New elements of glucocorticoid-receptor binding sites of hormone-regulated genes

Identification of promoter regions and regulatory sites

Promoter sequences are the main regulatory elements of gene expression. Their recognition by computer algorithms is fundamental for understanding gene expression patterns, cell specificity and development. This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences.

Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells

Composite elements are regulatory modules of promoters or enhancers that consist of binding sites of two different but synergizing transcription factors. A well-studied example is nuclear factors of activated T-cell (NFAT) sites which are composite elements of a NFATp/c and an activating protein 1 (AP-1) binding site. We have developed a computational approach to identify potential NFAT target genes which (a) comprises an improved method to scan for individual NFAT composite elements; (b) considers positional effects relative to transcription start sites; and (c) involves cluster analysis of potential NFAT composite elements. All three steps progressively helpX?ed to discriminate T-cell-specific promoter sequences against other functional regions (coding and intronic sequences) of the same genes, against promoters of muscle-specific genes or against random sequences. Using this approach, we identified potential NFAT composite elements in promoters of cytokine genes and their receptors as well as in promoters of genes for AP-1 family members, Ca2+-binding proteins and some other components of the regulatory network operating in activated T-cells and other immune cells. The method developed can be adapted to characterize and identify other composite elements as well. The program for recognition NFAT composite elements is available through the World Wide Web (http://compel.bionet.nsc.ru/FunSite/CompelScan. html and http://transfac.gbf.de/dbsearch/funsitep/s _comp.html).

Prediction of function in DNA sequence analysis

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

The immediate vicinity of mouse metallothionein-I gene contains two sites conferring glucocorticoid inducibility to the heterologous promoter

Glucocorticoid responsive elements (GREs) located -252 to -209 by upstream and +1011 to +1054 bp downstream of the transcription initiation site of the mouse metallothionein-I (mMT-I) gene were identified in transient experiments. However, the promoter region of the mMT-I gene (-330 to +70 bp) was found to provide low, if any, glucocorticoid induction of the linked CAT gene, while showing strong cadmium regulation, comparable with the in vivo level.

Glucocorticoid-receptor binding sites at the 5' flanking region of a rat cytochrome CYP2B2 gene predicted with a novel computer method

Using an original computer method to search for potential DNA binding sites for glucocorticoid-receptor complexes (GRC) (Seledtsov, I.A., Solovjev, V.V. and Merkulova, T.I. (1991) Biochim. Biophys. Acta 1089, 367-376), the presence of two such sites in the 5' flanking region of a rat cytochrome CYP2B2 gene has been predicted. This prediction has been confirmed by gel retardation experiments.