title: Comparative Analysis of Genome and Epigenome in Closely Related Medaka Species Identifies Conserved Sequence Preferences for DNA Hypomethylated Domains.
abstract: The genomes of vertebrates are globally methylated, but a small portion of genomic regions are known to be hypomethylated. Although hypomethylated domains (HMDs) have been implicated in transcriptional regulation in various ways, how a HMD is determined in a particular genomic region remains elusive. To search for DNA motifs essential for the formation of HMDs, we performed the genome-wide comparative analysis of genome and DNA methylation patterns of the two medaka inbred lines, Hd-rRII1 and HNI-II, which are derived from northern and southern subpopulations of Japan and exhibit high levels of genetic variations (SNP, ∼ 3%). We successfully mapped > 70% of HMDs in both genomes and found that the majority of those mapped HMDs are conserved between the two lines (common HMDs). Unexpectedly, the average genetic variations are similar in the common HMD and other genome regions. However, we identified short well-conserved motifs that are specifically enriched in HMDs, suggesting that they may play roles in the establishment of HMDs in the medaka genome.
authors: 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan.
authors: Ayako
authors: A
authors: Uno
authors: 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan.
authors: Ryohei
authors: R
authors: Nakamura
authors: 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan.|2 Department of Neurobiology, Harvard Medical School, 220 Longwood Ave,Boston, Massachusetts 02115, USA.
authors: Tatsuya
authors: T
authors: Tsukahara
authors: 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan.
authors: Wei
authors: W
authors: Qu
authors: 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan.
authors: Sumio
authors: S
authors: Sugano
authors: 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan.
authors: Yutaka
authors: Y
authors: Suzuki
authors: 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan.
authors: Shinichi
authors: S
authors: Morishita
authors: 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan.|4 CREST, Japan Science and Technology Agency.
authors: Hiroyuki
authors: H
authors: Takeda
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics*; D019175:DNA Methylation; D049810:Genetic Speciation; D014644:Genetic Variation; D016678:Genome; D009990:Oryzias / Q000145:classification / Q000235:genetics*
chemical_list: D004247:DNA
keywords: DNA methylation; SNP; methylome; pluripotent cell; speciation; transcriptome