Adaptive evolution through digital changes in the epigenome

• Project/Area Number: 25291080
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Evolutionary biology
• Research Institution: The University of Tokyo
• Principal Investigator: KOBAYASHI Ichizo 東京大学, 新領域創成科学研究科, 教授 (30126057)
• Co-Investigator(Renkei-kenkyūsha): FURUTA Yoshikazu 東京大学, 新領域創成科学研究科, 特任助教 (40613667) ; YANO Hirokazu 東京大学, 新領域創成科学研究科, 特任助教 (20646773) ; HASEBE Mitsuyasu 基礎生物学研究所, 生物進化研究部門, 教授 (40237996) ; OHTSUKI Hisashi 総合研究大学院大学, 先導科学研究科, 助教 (50517802)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000); Fiscal Year 2015: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2014: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2013: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
• Keywords: 適応進化 / エピジェネティクス / メチローム / トランスクリプトーム / 集団構造 / ピロリ菌 / 制限修飾系 / DNAメチル化 / 進化 / ゲノム / 細菌 / バイオテクノロジー / 遺伝学

Outline of Final Research Achievements

We examined the possibility that diverse epigenomes as opposed to diverse genomes might serve as units of adaptive evolution. We used Helicobacter pylori. We knocked out several genes determining sequence specificity of DNA methylation and analyzed their effects on transcriptome. Based on these, we examined adaptation-related phenotype sets and found unique effects. From 30 H. pylori genome comparison, we revealed high diversity in the restriction-modification systems. It did not closely match the population structure based on genome sequences. We looked for codons with diversifying selection, and found some in the specificity subunits of the restriction-modification systems.

Research Products

• [Int'l Joint Research] マウントサイナイ医科大学(米国)
• [Int'l Joint Research] CNRS(フランス)
• [Int'l Joint Research] グダンスク大学(ポーランド)
• [Int'l Joint Research] Chinese CDC(中国)
• [Int'l Joint Research] Indian Institute of Science/National Center of Basic Sciences/NICED(インド)
• [Journal Article] Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. (2016)
  • Author(s): ・Koji Yahara, Yoshikazu Furuta, Shinpei Morimoto, Chie Kikutake, Sho Komukai, Dorota Matelska, Stanisław Dunin-Horkawicz, Janusz M. Bujnicki, Ikuo Uchiyama, Ichizo Kobayashi
  • Journal Title: DNA Research Volume: - Issue: 2 Pages: 135-43
  • DOI: 10.1093/dnares/dsw003
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] 進化の単位としてのエピゲノム： 配列特異性を変える細菌のDNAメチル化系からの仮説． (2016)
  • Author(s): 小林一三
  • Journal Title: 「種生物学研究」第39号「エコロジカル・エピジェネティクス－生物の柔軟性の分子生態学－」 Volume: -
• [Journal Article] ゲノム 育種からエピゲノム育種へ． (2016)
  • Author(s): 小林一三
  • Journal Title: 「化学と生物」日本農芸化学会 Volume: -
  • NAID: 130006772570
• [Journal Article] Microevolution of virulence-related genes in Helicobacter pylori familial infection. (2015)
  • Author(s): Furuta Y, Konno M, Osaki T, Yonezawa H, Ishige T, Imai Mi, Shiwa Y, Shibata-Hatta M, Kanesaki Y, Yoshikawa H, Kamiya S, Kobayashi I
  • Journal Title: PLoS ONE Volume: 10 Issue: 5 Pages: e0127197-e0127197
  • DOI: 10.1371/journal.pone.0127197
  • Peer Reviewed / Open Access
• [Journal Article] Transmission of the PabI family of restriction DNA glycosylase genes: mobility and long-term inheritance. (2015)
  • Author(s): Kenji K. Kojima, Ichizo Kobayashi
  • Journal Title: BMC Genomics Volume: 16 Issue: 1 Pages: 817-817
  • DOI: 10.1186/s12864-015-2021-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The Landscape of Realized Homologous Recombination in Pathogenic Bacteria. (2015)
  • Author(s): Koji Yahara, Xavier Didelot, Keith A. Jolley, Ichizo Kobayashi, Martin C.J. Maiden, Samuel K. Sheppard and Daniel Falush
  • Journal Title: Molecular Biology and Evolution Volume: 33 Issue: 2 Pages: 456-471
  • DOI: 10.1093/molbev/msv237
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Microevolution of virulence-related genes in Helicobacter pylori familial infection. (2015)
  • Author(s): Yoshikazu Furuta, Mutsuko Konno, Takako Osaki, Hideo Yonezawa, Taichiro Ishige, Misaki Imai, Yuh Shiwa, Mari Shibata-Hatta, Yu Kanesaki, Hirofumi Yoshikawa, Shigeru Kamiya, Ichizo Kobayashi
  • Journal Title: Plos One Volume: 印刷中
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities (2015)
  • Author(s): Masaki Fukuyo, Toshiaki Nakano, Yingbiao Zhang, Yoshikazu Furuta, Ken Ishikawa, Miki Watanabe-Matsui, Hirokazu Yano, Takeshi Hamakawa, Hiroshi Ide, Ichizo Kobayashi
  • Journal Title: Nucleic Acids Research Volume: Vol. 43, No. 5 Issue: 5 Pages: 2841-2852
  • DOI: 10.1093/nar/gkv116
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] To be or not to be: regulation in restriction-modification systems and other toxin-antitoxin systems (2014)
  • Author(s): Iwona Mruk, Ichizo Kobayashi
  • Journal Title: Nucleic Acids Res. Volume: 42 (1) Issue: 1 Pages: 70-86
  • DOI: 10.1093/nar/gkt711
  • Peer Reviewed / Open Access
• [Journal Article] A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi. (2014)
  • Author(s): Ken-ichi Miyazono, Yoshikazu Furuta, Miki Watanabe-Matsui, Takuya Miyakawa, Tomoko Ito, Ichizo Kobayashi, Masaru Tanokura
  • Journal Title: Nat. Commun. Volume: 5 Issue: 1 Pages: 3178-3178
  • DOI: 10.1038/ncomms4178
  • Peer Reviewed / Open Access
• [Journal Article] Methylome diversification through changes in DNA methyltransferase sequence specificity. (2014)
  • Author(s): Yoshikazu Furuta, Hiroe Namba-Fukuyo, Tomoko F. Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Ichizo Kobayashi
  • Journal Title: PLoS Genetics Volume: 10
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] DNA Double‐strand Breaks and Their Consequences in Bacteria and Their Genomes. (2014)
  • Author(s): Ichizo Kobayashi, Naofumi Handa, Kohji Kusano
  • Journal Title: Encyclopedia of Life Sciences (eLS) Volume: -
  • Acknowledgement Compliant
• [Journal Article] Alterations in rRNA-mRNA interaction during plastid evolution. (2014)
  • Author(s): Kyungtaek Lim, Ichizo Kobayashi, and Kenta Nakai
  • Journal Title: Molecular Biology and Evolution Volume: 31 Issue: 7 Pages: 1728-1740
  • DOI: 10.1093/molbev/msu120
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Methylome diversification through changes in DNA methyltransferase sequence specificity. (2014)
  • Author(s): Yoshikazu Furuta, Hiroe Namba-Fukuyo, Tomoko F. Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Ichizo Kobayashi
  • Journal Title: PLoS Genetics Volume: 10(4) Issue: 4 Pages: e1004272-e1004272
  • DOI: 10.1371/journal.pgen.1004272
  • Peer Reviewed / Open Access
• [Journal Article] ゲノムからみるピロリ菌 (2013)
  • Author(s): 小林一三
  • Journal Title: 日本臨牀 Volume: 第71巻・第8号 Pages: 1352-1367
• [Journal Article] Chromosome painting in silico in a bacterial species reveals fine population structure (2013)
  • Author(s): Koji Yahara, Ynshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
  • Journal Title: Molecular Biology and Evolution Volume: 30(6) Issue: 6 Pages: 1454-64
  • DOI: 10.1093/molbev/mst055
  • Peer Reviewed / Open Access
• [Presentation] ピロリ菌の適応形質を支配するDNAメチル化系ネットワークの発見 (2016)
  • Author(s): 矢野大和、Zobaidul Alam、林原絵美子、古田芳一、鈴木穣、菅野純夫、柴山恵吾、小林一三
  • Organizer: 日本農芸化学会2016年度大会
  • Place of Presentation: 札幌コンベンションセンター（北海道札幌市）
  • Year and Date: 2016-03-27
• [Presentation] 「一分子リアルタイムシーケンサー」によるメチローム解読 (2016)
  • Author(s): 小林一三
  • Organizer: 第89回日本細菌学会総会
  • Place of Presentation: 大阪国際交流センター（大阪府大阪市）
  • Year and Date: 2016-03-23
• [Presentation] Elucidation of recombination hot regions and population structure in bacteria. (2016)
  • Author(s): Koji Yahara
  • Organizer: International Symposium on Genome Microbiology
  • Place of Presentation: 東京工業大学（東京都目黒区）
  • Year and Date: 2016-03-06
  • Int'l Joint Research
• [Presentation] Epigenetic network of gene expression involving DNA methyltransferases (2016)
  • Author(s): 矢野大和、Zobaidul Alam、林原絵美子、古田芳一、鈴木穣、菅野純夫、柴山恵吾、小林一三
  • Organizer: 第10回ゲノム微生物学会
  • Place of Presentation: 東京工業大学（東京都目黒区）
  • Year and Date: 2016-03-04
• [Presentation] Methods for studying recombination hot regions and population structure in bacteria. (2016)
  • Author(s): Koji Yahara
  • Organizer: Satellite meeting of Society of Molecular Biology and Evolution
  • Place of Presentation: 志賀レークホテル（長野県下高井郡）
  • Year and Date: 2016-02-23
  • Int'l Joint Research / Invited
• [Presentation] Genome/Epigenome Dynamics in Bacterial Evolution (2015)
  • Author(s): Ichizo Kobayashi
  • Organizer: MCB75: from Molecules to Organisms
  • Place of Presentation: バンガロール（インド）
  • Year and Date: 2015-12-11
  • Int'l Joint Research / Invited
• [Presentation] エピジェネティックス駆動進化：細菌でのOMICSによる検証 (2015)
  • Author(s): 小林一三
  • Organizer: BMB2015
  • Place of Presentation: 神戸ポートアイランド（兵庫県神戸市）
  • Year and Date: 2015-12-01
• [Presentation] Network of DNA methyltransferases behind the adaptive phenotype in Helicobacter pylori, 3P0588 (2015)
  • Author(s): Hirokazu Yano, Zobaidul Alam, Emiko Rimbara, Yoshikazu Furuta, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: BMB2015
  • Place of Presentation: 神戸ポートアイランド（兵庫県神戸市）
  • Year and Date: 2015-12-01
• [Presentation] Genome/epigenome evolution of H. pylori (2015)
  • Author(s): Ichizo Kobayashi
  • Organizer: Campylobacter, Helicobacter & Related Organisms (CHRO) 2015
  • Place of Presentation: ロトルア（ニュージーランド）
  • Year and Date: 2015-11-01
  • Int'l Joint Research / Invited
• [Presentation] A novel method for efficient inference of recombination hot regions in bacterial genomes and its application to 200 C. jejuni genomes (2015)
  • Author(s): Koji Yahara, Xavier Didelot, M. Azim Ansari, Samuel K. Sheppard and Daniel Falush
  • Organizer: The 18th International workshop on Campylobacter, Helicobacter & Related Organisms (CHRO) 2015
  • Place of Presentation: ロトルア（ニュージーランド）
  • Year and Date: 2015-11-01
  • Int'l Joint Research
• [Presentation] Efficient inference of recombination hot regions in bacterial genomes. (2015)
  • Author(s): Koji Yahara, Xavier Didelot, M. Azim Ansari, Samuel K. Sheppard and Daniel Falush
  • Organizer: Conference to celebrate the opening of our new MRC CLIMB centre “What can we learn from hundreds of bacterial genomes?”
  • Place of Presentation: スウォンジー（英国）
  • Year and Date: 2015-10-22
  • Int'l Joint Research
• [Presentation] メチローム変換に基づく進化 (2015)
  • Author(s): 矢野大和、古田芳一、Zobaidul Alam、林原絵美子、柴田朋子、鈴木穣、菅野純夫、重信秀治、長谷部光泰、小林一三
  • Organizer: 日本遺伝学会第87回大会
  • Place of Presentation: 東北大学（宮城県仙台市）
  • Year and Date: 2015-09-24
• [Presentation] Adaptive evolution and ever metamorphosing DNA methylation systems (2015)
  • Author(s): Hirokazu Yano, Yoshikazu Furuta, Zobaidul M. Alam, Emiko Rimbara, Hiroe Namba-Fukuyo, Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: 7th NEB Meeting on DNA Restriction and Modification
  • Place of Presentation: グダンスク（ポーランド）
  • Year and Date: 2015-08-24
  • Int'l Joint Research
• [Presentation] 「エピジェネティックスに基づく進化」の細菌での検証 (2015)
  • Author(s): 小林一三
  • Organizer: 日本進化学会第17回大会
  • Place of Presentation: 中央大学後楽園キャンパス（東京都文京区）
  • Year and Date: 2015-08-20
• [Presentation] ピロリ菌の適応形質を支配するDNAメチル化系ネットワークの発見 (2015)
  • Author(s): 矢野大和、Zobaidul M. Alam、林原絵美子、古田芳一、鈴木穣、菅野純夫、柴山恵吾、小林一三
  • Organizer: 日本進化学会第17回大会
  • Place of Presentation: 中央大学後楽園キャンパス（東京都文京区）
  • Year and Date: 2015-08-20
• [Presentation] Network of DNA methyltransferase behind the adaptive phenotype in Helicobacteri pylori. (2015)
  • Author(s): Hirokazu Yano, Zobaidul M. Alam, Emiko Rimbara, Yoshikazu Furuta, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: Gordon Research Conference, Microbial Population Biology
  • Place of Presentation: アンドーバー（米国）
  • Year and Date: 2015-07-19
• [Presentation] ピロリ菌の病原因子はなぜあるのか？ 小児を含む家族間感染株の全ゲノム配列比較から (2015)
  • Author(s): 古田芳一、今野武津子、大崎敬子、米澤英雄、神谷茂、小林一三
  • Organizer: 第21回日本ヘリコバクター学会学術集会
  • Place of Presentation: 神戸ポートピアホテル（兵庫県神戸市）
  • Year and Date: 2015-06-26
• [Presentation] 特定のエピゲノム状態がピロリ菌ストレス耐性を支配する (2015)
  • Author(s): 矢野大和
  • Organizer: 第21回日本ヘリコバクター学会学術集会
  • Place of Presentation: 神戸ポートピアホテル（兵庫県神戸市）
  • Year and Date: 2015-06-26
• [Presentation] Methylome Diversification in Human Gastric Pathogen Helicobacter pylori (2015)
  • Author(s): Hirokazu Yano, Zobaidul M. Alam, Yoshikazu Furuta, Emiko Rimbara, Hiroe Namba-Fukuyo, Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: 42nd IMSUT Founding Commemorative Symposium (医科研創立記念シンポジウム)
  • Place of Presentation: 東京大学医科学研究所（東京都港区）
  • Year and Date: 2015-06-01
• [Presentation] Repbase: A Comprehensive database of eukaryotic repeat sequences (2015)
  • Author(s): Kenji K. Kojima, Weidong Bao, Jerzy Jurka
  • Organizer: 42nd IMSUT Founding Commemorative Symposium (医科研創立記念シンポジウム)
  • Place of Presentation: 東京大学医科学研究所（東京都港区）
  • Year and Date: 2015-06-01
• [Presentation] Methylome Diversification in Human Gastric Pathogen Helicobacter pylori (2015)
  • Author(s): Yoshikazu Furuta, Hirokazu Yano, Zobaidul M. Alam, Emiko Rimbara, Hiroe Namba-Fukuyo, Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: International Symposium of Corrective Gene System “Establishing Next-Generation Genetics”
  • Place of Presentation: 奈良春日野国際フォーラム 甍～I・RA・KA～（奈良県奈良市）
  • Year and Date: 2015-05-28
  • Int'l Joint Research
• [Presentation] エピジェネティクス駆動進化：細菌種内複数系列でのOMICS比較による実証 (2015)
  • Author(s): 小林一三
  • Organizer: インシリコメガバンク研究会セミナー
  • Place of Presentation: 東北大学メディカル・メガバンク棟 （宮城県仙台市）
  • Year and Date: 2015-04-16
  • Invited
• [Presentation] ピロリ菌の家族内感染におけるゲノム進化 (2015)
  • Author(s): 古田芳一、大崎敬子、米澤英雄、神谷茂、小林一三
  • Organizer: 第88回日本細菌学会
  • Place of Presentation: 長良川国際会議場（岐阜県岐阜市）
  • Year and Date: 2015-03-26 – 2015-03-28
• [Presentation] ゲノムのミクロ進化：ピロリ菌家族内感染の場合 (2015)
  • Author(s): 古田芳一、今野武津子、大崎敬子、米澤英雄、石毛太一郎、今井美咲、志波優、柴田（八田）真理、兼崎友、吉川博文、神谷茂、小林一三
  • Organizer: 第9回日本ゲノム微生物学会
  • Place of Presentation: 神戸大学（兵庫県神戸市）
  • Year and Date: 2015-03-06 – 2015-03-08
• [Presentation] 特定のエピゲノム状態がピロリ菌ストレス耐性を支配する (2015)
  • Author(s): 矢野大和、Md.Zobaidul Alam, 林原絵美子、古田芳一、鈴木穣、菅野純夫、柴山恵吾、小林一三
  • Organizer: 第9回日本ゲノム微生物学会
  • Place of Presentation: 神戸大学（兵庫県神戸市）
  • Year and Date: 2015-03-06 – 2015-03-08
• [Presentation] Methylome Diversification in Human Gastric Pathogen Helicobacter pylori (2015)
  • Author(s): Yoshikazu Furuta, Hirokazu Yano, Zobaidul M. Alam, Emiko Rimbara, Hiroe Namba-Fukuyo,Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Yutaka Suzuki,Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: International Symposium on Genome Science 2015
  • Place of Presentation: 一橋ホール（東京都千代田区）
  • Year and Date: 2015-01-20 – 2015-01-21
• [Presentation] Epigenetics Driven Evolution (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: Baylor College での講演
  • Place of Presentation: ヒューストン（米国）
  • Year and Date: 2014-12-08
  • Invited
• [Presentation] H. pylori evolution (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: VI International Symposium of Helicobacter pylori: natural history and implications for human health
  • Place of Presentation: サンホセ（米国）
  • Year and Date: 2014-12-03
  • Invited
• [Presentation] Epigenetics Driven Evolution (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: Emory Universityにおける講演
  • Place of Presentation: アトランタ（米国）
  • Year and Date: 2014-11-17
  • Invited
• [Presentation] 細菌エピゲノムの進化：PacBioマ シンによるピロリ菌メチローム解読から (2014)
  • Author(s): 小林一三
  • Organizer: 第97回日本細菌学会関東支部総会
  • Place of Presentation: 東京ドームホテル（東京都文京区）
  • Year and Date: 2014-10-30 – 2014-10-31
• [Presentation] Genome/methylome evolution in H. pylori: oncogenic bacteria (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: Center for Disease Control of China における講演
  • Place of Presentation: 北京（中国）
  • Year and Date: 2014-10-10
  • Invited
• [Presentation] Methylome dynamics in H. pylori (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: XXVIIth International Workshop on Helicobacter and Microbiota in Chronic Digestive Inflammation and Gastric Cancer.
  • Place of Presentation: ローマ（イタリア）
  • Year and Date: 2014-09-11 – 2014-09-13
• [Presentation] Epigenetics-driven evolution? (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: 16th Annual Meeting of the Society of Evolutionary Studies
  • Place of Presentation: 高槻現代劇場（大阪府高槻市）
  • Year and Date: 2014-08-22
• [Presentation] 配列特異的ＤＮＡメチル化酵素によるエピゲノム工学：合成生物学・ゲノム工学の拡張へ (2014)
  • Author(s): 小林一三
  • Organizer: ゲノム支援拡大班会議
  • Place of Presentation: 神戸国際会議場(兵庫県神戸市）
  • Year and Date: 2014-08-20 – 2014-08-21
• [Presentation] 比較ゲノミクス・メチロミクス・トランスクリプトミクスでのエピゲノム駆動進化の実証 (2014)
  • Author(s): 矢野大和、小林一三、福世真樹
  • Organizer: ゲノム支援拡大班会議
  • Place of Presentation: 神戸国際会議場(兵庫県神戸市）
  • Year and Date: 2014-08-20 – 2014-08-21
• [Presentation] Evolution of H. pylori (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: 11th International Workshop on Pathogenesis and Host Response in Helicobacter Infections
  • Place of Presentation: ヘルシンゴー（デンマーク）
  • Year and Date: 2014-07-02
  • Invited
• [Presentation] Evolution of H. pylori (2014)
  • Author(s): Ichizo Kobayashi
  • Organizer: University of Gdansk での講演
  • Place of Presentation: グダンスク（ポーランド）
  • Year and Date: 2014-07-01
  • Invited
• [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure (2014)
  • Author(s): Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, and Ichizo Kobayashi
  • Organizer: 第8回日本ゲノム微生物学会年会
  • Place of Presentation: 東京農業大学世田谷キャンパス、東京都
• [Presentation] PacBio RSを用いたピロリ菌メチロームの種内比較解析 (2014)
  • Author(s): 古田芳一, 南波宏枝, 柴田朋子, 西山智明, 重信秀治, 鈴木穣, 菅野純夫, 長谷部光泰, 小林一三
  • Organizer: 第8回日本ゲノム微生物学会年会
  • Place of Presentation: 東京農業大学世田谷キャンパス、東京都
• [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure (2014)
  • Author(s): Koji Yahara, Yoshikazu Furuta, Masahira Hattori, and Ichizo Kobayashi
  • Organizer: 第87回日本細菌学会総会
  • Place of Presentation: タワーホール船堀、東京都
• [Presentation] Methylome diversification through changes in the sequence specificity of DNA methyltransferases (2014)
  • Author(s): Yoshikazu Furuta, Ichizo Kobayashi
  • Organizer: 第87回日本細菌学会総会
  • Place of Presentation: タワーホール船堀、東京都
• [Presentation] DNAメチル化系の認識配列変換によるエピゲノム多様化：PacBioマシンによる全メチローム解読からの証拠 (2014)
  • Author(s): 古田 芳一, 南波 宏枝, 柴田 朋子, 西山 智明, 重信 秀治, 鈴木 穣, 菅野 純夫, 長谷部 光泰, 小林 一三
  • Organizer: 日本農芸化学会2014年度大会
  • Place of Presentation: 明治大学生田キャンパス、神奈川県
• [Presentation] Chromosome painting in silico reveals fine population structure in Helicobacter pylori (2013)
  • Author(s): 小林一三
  • Organizer: 40th IMSUT Founding Commemorative Symposium (医科研創立記念シンポジウム)
  • Place of Presentation: 東京大学医科学研究所、東京都
• [Presentation] Mobility of restriction-modification systems and their domains (2013)
  • Author(s): Ichizo Kobayashi
  • Organizer: International Conference on Nucleic Acid Enzymes and Enzymes in Human Diseases (NAEEHD)
  • Place of Presentation: The Chinese University, Hong Kong
  • Invited
• [Presentation] DNAメチル化酵素のドメイン移動によるピロリ菌のエピゲノム多様化 (2013)
  • Author(s): 古田芳一、小林一三
  • Organizer: 第19回日本ヘリコバクター学会学術集会
  • Place of Presentation: 長崎大学、長崎県
  • Invited
• [Presentation] インシリコ染色体ペインティングでわかるピロリ菌の詳細な集団構造 (2013)
  • Author(s): 矢原耕史、古田芳一、 吉田優、東健、小林一三
  • Organizer: 第19回日本ヘリコバクター学会学術集会
  • Place of Presentation: 長崎大学、長崎県
• [Presentation] 種内集団構造のインシリコ染色体ペインティングによる解明 (2013)
  • Author(s): 矢原耕史、古田芳一、大島健志朗、吉田優、東健、服部正平、内山郁夫、小林一三
  • Organizer: 日本進化学会第15回つくば大会
  • Place of Presentation: 筑波大学、茨城県
• [Presentation] 第三世代シーケンサー（PacBio社）１分子リアルタイム（SMRT）シーケンシングでのメチローム解読による制限修飾系の認識配列の決定 (2013)
  • Author(s): 南波宏枝、古田芳一、柴田朋子、西山智明、重信秀治、Desirazu N. Rao、長谷部光泰、小林一三
  • Organizer: 日本進化学会第15回つくば大会
  • Place of Presentation: 筑波大学、茨城県
• [Presentation] DNAメチル化系の認識配列変換によるメチローム多様化：種内複数株でのメチローム解読からの証拠 (2013)
  • Author(s): 古田芳一、南波宏枝、柴田朋子、西山智明、重信秀治、鈴木 穣、菅野純夫、長谷部光泰、小林一三
  • Organizer: 日本進化学会第15回つくば大会
  • Place of Presentation: 筑波大学、茨城県
• [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure (2013)
  • Author(s): K. Yahara, Y. Furuta, K. Oshima, M. Yoshida, T. Azuma, M. Hattori, I. Uchiyama, I. Kobayashi
  • Organizer: EHSG XXVth International Workshop on Helicobacter and related bacteria in chronic digestive inflammation and gastric cancer
  • Place of Presentation: Madrid, Spain
  • Invited
• [Presentation] Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution (2013)
  • Author(s): Yoshikazu Furuta and Ichizo Kobayashi
  • Organizer: Helicobacter and Related Organisms (CHRO) 2013
  • Place of Presentation: Aberdeen Exhibition and Conference Centre, UK
• [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure (2013)
  • Author(s): Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, and Ichizo Kobayashi
  • Organizer: Campylobacter, Helicobacter and Related Organisms (CHRO) 2013
  • Place of Presentation: Aberdeen Exhibition and Conference Centre, UK
• [Presentation] 種内集団構造のインシリコ染色体ペインティングによる解明 (2013)
  • Author(s): 矢原耕史、古田芳一、大島健志朗、吉田優、東健、服部正平、内山郁夫、小林一三
  • Organizer: 日本遺伝学会第85回大会
  • Place of Presentation: 慶應大学、神奈川県
• [Presentation] 分子リアルタイム(SMRT)シークエンシングによるメチローム解読と「エピジェネティクス駆動進化」仮説 (2013)
  • Author(s): 古田芳一、南波宏枝、柴田朋子、西山智明、重信秀治、鈴木 穣、菅野純夫、長谷部光泰、小林一三
  • Organizer: 日本遺伝学会第85回大会
  • Place of Presentation: 慶應大学、神奈川県
• [Presentation] Methylome diversification through changes in the sequence specificity of DNA methyltransferases (2013)
  • Author(s): Ichizo Kobayashi, Hiroe Namba, Tomoko F. Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Yoshikazu Furuta
  • Organizer: Infectious Disease Genomics & Global Health Conference
  • Place of Presentation: Wellcome Trust Conference Centre, Cambridge, UK
• [Presentation] Why restriction enzymes? RM, epigenetic powers driving evolution (2013)
  • Author(s): Ichizo Kobayashi
  • Organizer: The History of Restriction Enzymes
  • Place of Presentation: The History of Restriction Enzymes
• [Presentation] 進化する能力を細胞に持たせるには、どうすればいいだろうか？ (2013)
  • Author(s): 小林一三
  • Organizer: 「細胞を創る」研究会6.0
  • Place of Presentation: 鶴岡メタボロームキャンパスレクチャーホール、山形県
• [Presentation] Epigenetics in evolution (2013)
  • Author(s): Ichizo Kobayashi
  • Organizer: Commemorative Symposium for the 29th International Prize for Biology（第29回 国際生物学賞記念シンポジウム）
  • Place of Presentation: 九州大学、福岡県
  • Invited
• [Presentation] DNA メチル化系の認識配列変換によるメチローム多様化：種内複数株でのメチローム解読からの証拠 (2013)
  • Author(s): 古田 芳一，南波 宏枝，柴田 朋子，西山 智明，重信 秀治，鈴木 穣，菅野 純夫，長谷部 光泰，小林 一三
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸国際会議場、兵庫県
• [Book] Helicobacter pylori Research: From Bench to Bedside. (2016)
  • Author(s): Ichizo Kobayashi, Steffen Backert, Yoshio Yamaoka (editors)
  • Total Pages: 613
  • Publisher: Springer Japan
• [Book] Epigenetics mediated by restriction-modification systems. (2016)
  • Author(s): Iwona Mruk and Ichizo Kobayashi, Frans J. de Bruijn (editor)
  • Publisher: Wiley-Blackwell Publishers
• [Book] Stress and Environmental Control of Gene Expression in Bacteria (2016)
  • Author(s): Iwona Mruk and Ichizo Kobayashi, Frans J. de Bruijn, Editor
  • Publisher: Wiley-Blackwell Publishers
• [Book] Helicobacter pylori Research: From Bench to Bedside (2015)
  • Author(s): Ichizo Kobayashi, Steffen Backert, Yoshio Yamaoka (editors)
  • Publisher: Springer Japan
• [Book] 「種生物学研究」第39号「エコロジカル・エピジェネティクス－生物の柔軟性の分子生態学－」 (2015)
  • Author(s): 小林一三 (責任編集者：荒木希和子・土畑重人）
  • Publisher: 文一総合出版
• [Book] Encyclopedia of Life Sciences (eLS) (2014)
  • Author(s): Ichizo Kobayashi, Naofumi Handa, Kohji Kusano.
  • Publisher: Wiley
• [Remarks] 小林研究室ホームページ
  • URL: http://www.ims.u-tokyo.ac.jp/ikobaya/index.html
• [Remarks] 小林研究室ホームページ
  • URL: http://www.ims.u-tokyo.ac.jp/ikobaya/index.html
• [Remarks] 日経バイオテクオンラインに掲載された本研究に関する記事
  • URL: https://bio.nikkeibp.co.jp/article/news/20140325/174958/