5-methyl-cytosines at CpG sites frequently mutate into thymines, accounting for a large proportion of spontaneous point mutations. The repair system would leave substantial numbers of errors in neighboring regions if the synthesis of erased gaps around deaminated 5-methyl-cytosines is error-prone. Indeed, we identified an unexpected genome-wide role of the CpG methylation state as a major determinant of proximal natural genetic variation. Specifically, 507 Mbp (∼18%) of the human genome was within 10 bp of a CpG site; in these regions, the single nucleotide polymorphism (SNP) rate significantly increased by ∼50% ( P < 10 −566 by a two-proportion z -test) if the neighboring CpG sites are methylated. To reconfirm this finding in another vertebrate, we compared six single-base resolution methylomes in two inbred medaka ( Oryzias latipes ) strains with sufficient genetic divergence (3.4%). We found that the SNP rate also increased by ∼50% ( P < 10 −2170 ), and the substitution rates in all dinucleotides increased simultaneously ( P < 10 −441 ) around methylated CpG sites. In the hypomethylated regions, the “CGCG” motif was significantly enriched ( P < 10 −680 ) and evolutionarily conserved ( P = ∼ 0.203%), and slow CpG deamination rather than fast CpG gain was seen, indicating a possible role of CGCG as a candidate cis -element for the hypomethylation state. In regions that were hypermethylated in germline-like tissues but were hypomethylated in somatic liver cells, the SNP rate was significantly smaller than that in hypomethylated regions in both tissues, suggesting a positive selective pressure during DNA methylation reprogramming. This is the first report of findings showing that the CpG methylation state is significantly correlated with the characteristics of evolutionary change in neighboring DNA.

10.1101/gr.140236.112

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Citations (50)

Visualization of Actin Cytoskeleton in Cellular Protrusions in Medaka Embryos

BIO-PROTOCOL (2023)

Toru Kawanishi Ann Kathrin Heilig Atsuko Shimada Hiroyuki Takeda

Cellular protrusions are fundamental structures for a wide variety of cellular behaviors, such as cell migration, cell-cell interaction, and signal reception. Visualization of cellular protrusions in living cells can be achieved by labeling of cytoskeletal actin with genetically encoded fluorescent probes. Here, we describe a detailed experimental procedure to visualize cellular protrusions in medaka embryos, which consists of the following steps: preparation of Actin-Chromobody-GFP and α-bungarotoxin mRNAs for actin labeling and immobilization of the embryo, respectively; microinjection of the mRNAs into embryos in a mosaic fashion to sparsely label individual cells; removal of the hard chorion, which hampers observation; and visualization of cellular protrusions in the embryo with a confocal microscope. Overall, our protocol provides a simple method to reveal cellular protrusions in vivo by confocal microscopy.

Live cell imaging

10.21769/bioprotoc.4710

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Citations (0)

The medaka midblastula transition as revealed by the expression of the paternal genome

Gene Expression Patterns (2003)

Kouichi Aizawa Atsuko Shimada Kiyoshi Naruse Hiroshi Mitani Akihiro Shima

Oryzias

Blastula

Transcription

10.1016/s1567-133x(02)00075-3

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Citations (49)

Degree of Grittiness Perceived as Mouth Feeling

Journal of home economics (1995)

Etsuko Imai Keiko Hatae Atsuko Shimada

Degree (music)

10.11428/jhej1987.46.1151

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Citations (1)

THE PRESERVATION AND UTILIZATION OF WILD POPULATIONS OF THE MEDAKA ORYZIAS LATIPES

Akihiro Shima Atsuko Shimada J. Komura Khalid Isa Kiyoshi Naruse

Oryzias

10.18999/meda.3.1

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Citations (9)

Universal Dependencies 2.1

Joakim Nivre Željko Agić Lars Ahrenberg Lene Antonsen María Jesús Aranzabe

Source

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Citations (12)

Objective Scoring Method for Grilled Fish Quality.

Nippon Shokuhin Kagaku Kogaku Kaishi (1996)

Keiko Hatae Rieko Yoshimura Atsuko Shimada Satomi Sugiyama

加熱機器や調理条件の検討に有用な,アジ焼き魚の評価シートの作成を試みた.日本料理専門調理人および調理学研究室員を試験室パネルとして,アジ焼き魚の好ましさを評価する言葉を調査したところ,約50語が収集された.なかでも,外観とテクスチャーに関する言葉が多かった.これを整理して14項目とした.これら14項目を説明用語になおして,それらの重要度を調査した.その結果に基づいて項目を7に絞った.数値配分法で7項目の重み付けを行った後,試験室パネルによる官能検査の結果に重回帰分析を応用し,配点を修正した.最終的に選ばれた評価項目と配点は,姿,形の良さ(10点),表面の状態(8点),焼きムラ(6点),全体的な焦げ色(20点),身のほぐれ具合(6点),汁け(25点),アジのうまみ(25点)となった。得られた評価シートを用いて市場パネルによる官能検査を行い,その妥当性を確認した.

10.3136/nskkk.43.1314

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Citations (1)

Dominant lethal mutations induced by MMS and mitomycin C in the fish Oryzias latipes

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis (1984)

Atsuko Shimada Nobuo Egami

Oryzias

Mitomycin C

Ethyl methanesulfonate

Spermatocyte

10.1016/0027-5107(84)90072-1

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Citations (9)