Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes
- Environmental Genomics Group, Laboratory of Computational Biology and Risk Analysis, National Institute of Environmental Health Sciences, Mail Drop C3-03, PO Box 12233, Research Triangle Park, NC 27709 (United States)
Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes.
- OSTI ID:
- 20721893
- Journal Information:
- Toxicology and Applied Pharmacology, Vol. 207, Issue 2,suppl.1; Conference: ICT X 2004: 10. international congress of toxicology: Living in a safe chemical world, Tampere (Finland), 11-15 Jul 2004; Other Information: DOI: 10.1016/j.taap.2004.09.024; PII: S0041-008X(05)00351-0; Copyright (c) 2005 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA); ISSN 0041-008X
- Country of Publication:
- United States
- Language:
- English
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