In silico genetics: identification of a functional element regulating H2-Ealpha gene expression.

TitleIn silico genetics: identification of a functional element regulating H2-Ealpha gene expression.
Publication TypeJournal Article
Year of Publication2004
AuthorsLiao, G, Wang, J, Guo, J, Allard, J, Cheng, J, Ng, A, Shafer, S, Puech, A, McPherson, JD, Foernzler, D, Peltz, G, Usuka, J
Date Published2004 Oct 22
KeywordsAlleles, Animals, Binding Sites, Computational Biology, Electrophoretic Mobility Shift Assay, Gene Expression Profiling, Gene Expression Regulation, Genes, MHC Class II, Genetic Variation, H-2 Antigens, Haplotypes, Hydrocarbons, Aromatic, Introns, Liver, Lung, Major Histocompatibility Complex, Mice, Mice, Inbred Strains, Oligodeoxyribonucleotides, Oligonucleotide Array Sequence Analysis, Phenotype, Polymorphism, Single Nucleotide, Receptors, Aryl Hydrocarbon, Regulatory Sequences, Nucleic Acid, Serum Response Factor, Transcription Factors

Computational tools can markedly accelerate the rate at which murine genetic models can be analyzed. We developed a computational method for mapping phenotypic traits that vary among inbred strains onto haplotypic blocks. This method correctly predicted the genetic basis for strain-specific differences in several biologically important traits. It was also used to identify an allele-specific functional genomic element regulating H2-Ealpha gene expression. This functional element, which contained the binding sites for YY1 and a second transcription factor that is probably serum response factor, is located within the first intron of the H2-Ealpha gene. This computational method will greatly improve our ability to identify the genetic basis for a variety of phenotypic traits, ranging from qualitative trait information to quantitative gene expression data, which vary among inbred mouse strains.

Alternate JournalScience
PubMed ID15499019
Grant List1 R01 HG02322-01 / HG / NHGRI NIH HHS / United States

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