title: Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: ADP-ribosylation in Oncology Project, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan. hogino@gan2.res.ncc.go.jp <hogino@gan2.res.ncc.go.jp>
authors.forename: Hideki
authors.initials: H
authors.lastname: Ogino
authors.forename: Tadashige
authors.initials: T
authors.lastname: Nozaki
authors.forename: Akemi
authors.initials: A
authors.lastname: Gunji
authors.forename: Miho
authors.initials: M
authors.lastname: Maeda
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Suzuki
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Ohta
authors.forename: Yasufumi
authors.initials: Y
authors.lastname: Murakami
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Nakagama
authors.forename: Takashi
authors.initials: T
authors.lastname: Sugimura
authors.forename: Mitsuko
authors.initials: M
authors.lastname: Masutani
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D015536:Down-Regulation; D053595:Embryonic Stem Cells / Q000378:metabolism*; D020869:Gene Expression Profiling; D008099:Liver / Q000166:cytology / Q000378:metabolism*; D051379:Mice; D018345:Mice, Knockout; D020411:Oligonucleotide Array Sequence Analysis; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
chemical_list: C499321:Parp1 protein, mouse; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases