Repetitive sequence environment distinguishes housekeeping genes.
Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes by their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element-1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, was used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.
Eller
C Daniel
CD
UCLA Department of Human Genetics, David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA.
Regelson
Moira
M
Merriman
Barry
B
Nelson
Stan
S
Horvath
Steve
S
Marahrens
York
Y
D024509:3' Flanking Region; D024506:5' Flanking Region; D020087:Alu Elements; D001482:Base Composition; D018899:CpG Islands; D004247:DNA / Q000737:chemistry / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D012091:Repetitive Sequences, Nucleic Acid; D012641:Selection, Genetic; D020086:Short Interspersed Nucleotide Elements; D014018:Tissue Distribution
D004247:DNA