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Open Access Research article

Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells

Hideki Ogino12, Tadashige Nozaki2, Akemi Gunji2, Miho Maeda3, Hiroshi Suzuki4, Tsutomu Ohta5, Yasufumi Murakami3, Hitoshi Nakagama2, Takashi Sugimura2 and Mitsuko Masutani12*

Author Affiliations

1 ADP-ribosylation in Oncology Project, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan

2 Biochemistry Division, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan

3 Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba 278-8510, Japan

4 Chugai Pharmaceutical Co Ltd., 1-135, Komakado, Gotemba, Shizuoka, 412-0038, Japan

5 Center for Medical Genomics, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan

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BMC Genomics 2007, 8:41  doi:10.1186/1471-2164-8-41

Published: 7 February 2007

Abstract

Background

Many lines of evidence suggest that poly(ADP-ribose) polymerase-1 (Parp-1) is involved in transcriptional regulation of various genes as a coactivator or a corepressor by modulating chromatin structure. However, the impact of Parp-1-deficiency on the regulation of genome-wide gene expression has not been fully studied yet.

Results

We employed a microarray analysis covering 12,488 genes and ESTs using mouse Parp-1-deficient (Parp-1-/-) embryonic stem (ES) cell lines and the livers of Parp-1-/- mice and their wild-type (Parp-1+/+) counterparts. Here, we demonstrate that of the 9,907 genes analyzed, in Parp-1-/- ES cells, 9.6% showed altered gene expression. Of these, 6.3% and 3.3% of the genes were down- or up-regulated by 2-fold or greater, respectively, compared with Parp-1+/+ ES cells (p < 0.05). In the livers of Parp-1-/- mice, of the 12,353 genes that were analyzed, 2.0% or 1.3% were down- and up-regulated, respectively (p < 0.05). Notably, the number of down-regulated genes was higher in both ES cells and livers, than that of the up-regulated genes. The genes that showed altered expression in ES cells or in the livers are ascribed to various cellular processes, including metabolism, signal transduction, cell cycle control and transcription. We also observed expression of the genes involved in the pathway of extraembryonic tissue development is augmented in Parp-1-/- ES cells, including H19. After withdrawal of leukemia inhibitory factor, expression of H19 as well as other trophoblast marker genes were further up-regulated in Parp-1-/- ES cells compared to Parp-1+/+ ES cells.

Conclusion

These results suggest that Parp-1 is required to maintain transcriptional regulation of a wide variety of genes on a genome-wide scale. The gene expression profiles in Parp-1-deficient cells may be useful to delineate the functional role of Parp-1 in epigenetic regulation of the genomes involved in various biological phenomena.