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PMID: 17141428 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Repetitive sequence environment distinguishes housekeeping genes.

Gene ·Vol. 390 ·No. 1-2 ·2007-04-01 ·Pages 153-65

Eller CD, Regelson M, Merriman B, Nelson S, Horvath S, Marahrens Y

Abstract

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.

MeSH Terms
3' Flanking Region 5' Flanking Region Alu Elements Base Composition CpG Islands DNA/chemistry,genetics Genome, Human Humans Long Interspersed Nucleotide Elements Repetitive Sequences, Nucleic Acid Selection, Genetic Short Interspersed Nucleotide Elements Tissue Distribution
Chemicals
DNA
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Eller C Daniel
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
Merriman Barry
Nelson Stan
Horvath Steve
Marahrens York
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Article Info
Journal
Gene
Abbr.
Gene
ISSN
0378-1119
DOI
10.1016/j.gene.2006.09.018
Published
2007-04-01
Epub
2006-00-05
Pages
153-65
Language
English
Region
Netherlands
NLM ID
7706761
PMCID
PMC1857324
Subset
IM
Grants
NCI NIH HHS · T32 CA09056 · United States
NIGMS NIH HHS · R01 GM061007 · United States
NHGRI NIH HHS · T32 HG002536 · United States
NICHD NIH HHS · HD041451-02 · United States
NICHD NIH HHS · R01 HD041451 · United States
NCI NIH HHS · T32 CA009056 · United States
NIGMS NIH HHS · GM6100701 · United States
External Links
PubMed source DOI: 10.1016/j.gene.2006.09.018 PMC Full Text View journal details
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