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.
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.
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
T. Suzuki Á Y. Hayashizaki
Division of Genomic Information Resources, Science of
Biological Supramolecular Systems, Graduate School of
Integrated Science, Yokohama City University, Yokohama,
Laboratory for Genome Reprogramming, RIKEN Center for
Developmental Biology (CDB), Kobe, Japan
Genome Science Laboratory, Discovery and Research Institute,
RIKEN Wako Main Campus, Wako, Japan
Mamm Genome (2008) 19:667–674