Repetitive sequence environment distinguishes housekeeping genes

C. Daniel Eller, Moira Regelson, Barry Merriman, Stan Nelson, Steve Horvath, York Marahrens

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)153-165
Number of pages13
Issue number1-2
StatePublished - Apr 1 2007

Bibliographical note

Funding Information:
C.D.E. was supported by a UCLA-IGERT bioinformatics traineeship (NSF DGE-9987641). M.R. was supported by a Tumor Cell Biology Fellowship (USHHS Institutional National Research Service Award #T32 CA09056). Y.M. was supported in part by National Institutes of Health Grants GM6100701 and HD041451-02.


  • Alu
  • Isochores
  • LINE
  • Random forest
  • Repeat
  • SINE
  • Tissue-specific genes


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