International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

C16. Fluctuation and Identification of Housekeeping Genes on Large-Scale RIKEN Mouse cDNA Microarray

Koji Kadota1,2, Yasushi Okazaki1, Hidemasa Bono1, Rika Miki1, Kentaro Shimizu2, Yoshihide Hayashizaki1
1Genome Science Lab., Genomic Sciences Center, RIKEN, 3-1-1 Koyadai, Tsukuba-city, Ibaraki 305-0074, Japan.
2Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku 113-8657, Tokyo, Japan.

Detecting housekeeping gene is very important to understand the maintenance of cell cycle, metabolism and so on. However, few housekeeping genes, which are expressed in every tissue and at anytime, have been found. Recently, 535 housekeeping genes have been identified using Affimetrix-type DNA chip technology (about 7,000 full-length genes in 11 different human adult and fetal tissues), which can simultaneously monitor the expression level of massive genes using single-dye system.

We have established massive expression profile of cDNA microarray using mouse full-length 19K set in 49 different stages of the embryo and adult tissues. Since cDNA microarray uses dual-dye system, we used 17.5-day embryos (whole body) as reference and the ratio of each tissue was measured. We have tried to identify housekeeping genes from the cDNA microarray data by taking the log-transformed ratio and the signal intensity into account.

As a result, we identified hundreds of genes that were expressed with minimal fluctuation in 49 tissues, suggesting that those genes may have a useful internal control as so-called "housekeeping genes". We also found that most of genes showed large fluctuation of expression ratio. For example, actin related genes which are frequently used as controls in standard expression analysis were found to vary in expression level by 4- to 29-folds, and the result was similar to those previously reported.

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