ORIGINAL CONTRIBUTIONS An epigenetic aberration increased in intergenic regions of cloned mice Hiromi Nishida Æ Shinji Kondo Æ Takahiro Suzuki Æ Yuki Tsujimura Æ Shunsuke Komatsu Æ Teruhiko Wakayama Æ Yoshihide Hayashizaki Received: 20 August 2008 / Accepted: 25 September 2008 / Published online: 29 October 2008 Ó Springer Science+Business Media, LLC 2008 Abstract The causes of frequent abnormal phenotypes and low success rate in mammalian cloning are poorly understood. Although epigenetic aberration is suspected to be a cause, its connection to the phenotypes has yet to be investigated. To measure the level of reprogramming of an epigenetic mark, acetylation at lysine 9 of histone H3 (H3K9Ac), in cloned mice, we examined its conservation between two cloned mice derived from distinct cell nuclei and their natural donors by utilizing whole-genome tiling arrays and quantitative PCR. Pairwise comparison of the H3K9Ac enrichment profile between the four mice revealed that H3K9Ac is less conserved in intergenic regions than in promoter regions of protein-coding genes. Intriguingly, the variation of H3K9Ac enrichment in intergenic regions is the most prominent in comparison of the two clones, possibly reflecting an additive effect of aberrant reprogramming of this epigenetic information occurring specifically in each of the two clones. Introduction Cloning of various mammalian organisms has been achieved by somatic cell nuclear transfer (Wilmut et al. 2002). However, the production rate of cloned animals is quite low (e.g., 1–2% in mouse; Wakayama 2004). In addition, cloned animals frequently show abnormal phe- notypes (Cibelli et al. 2002). A possible cause of the low success rate of cloning and the abnormal symptoms in the cloned animals is incomplete reestablishment of epigenetic information after the nuclear transfer. Abnormal gene expressions reported in cloned mice (Humpherys et al. 2002; Kohda et al. 2005) may have been caused by aber- rant methylation of genomic DNA often found in them (Chung et al. 2003; Dean et al. 2001; Humpherys et al. 2001; Mann et al. 2003; Ohgane et al. 2001; Xue et al. 2002). In this study we focused on other epigenetic informa- tion, i.e., acetylation of histone H3 at lysine 9 (H3K9Ac). H3K9Ac is an important histone modification implicated in transcriptional activation possibly inducing nucleosome depletion in the vicinity of transcription start sites in human cells (Nishida et al. 2006). Although H3K9Ac enrichment H. Nishida, S. Kondo, and T. Suzuki contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s00335-008-9146-5) contains supplementary material, which is available to authorized users. H. Nishida Á S. Kondo Á T. Suzuki Á Y. Tsujimura Á S. Komatsu Á Y. Hayashizaki Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama, Japan H. Nishida (&) Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan e-mail: hnishida@iu.a.u-tokyo.ac.jp T. Suzuki Á Y. Hayashizaki Division of Genomic Information Resources, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, Yokohama, Japan T. Wakayama Laboratory for Genome Reprogramming, RIKEN Center for Developmental Biology (CDB), Kobe, Japan Y. Hayashizaki Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, Wako, Japan 123 Mamm Genome (2008) 19:667–674 DOI 10.1007/s00335-008-9146-5