Differences in genome structure between humans and apes: test for hypothesis concerning recombination frequency

• Project/Area Number: 15H04427
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical anthropology
• Research Institution: Kyoto University
• Principal Investigator: Koga Akihiko 京都大学, 霊長類研究所, 教授 (80192574)
• Co-Investigator(Kenkyū-buntansha): 田辺 秀之 総合研究大学院大学, 先導科学研究科, 准教授 (50261178) ; 平井 啓久 京都大学, 霊長類研究所, 教授 (10128308)
• Project Period (FY): 2015-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥15,730,000 (Direct Cost: ¥12,100,000、Indirect Cost: ¥3,630,000); Fiscal Year 2018: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2017: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2016: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2015: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
• Keywords: 進化 / ヒト / 類人猿 / ゲノム / 染色体 / 反復配列 / 多様性 / 霊長類 / ヘテロクロマチン / 遺伝学 / 人類学 / 組換え

Outline of Final Research Achievements

Chimpanzees and gorillas carry at chromosome termini a specific structure consisting mainly of repetitive DNA, while humans do not. Its artificial removal from chimpanzee chromosomes resulted in an increase in the recombination frequency on chromosome arms. Another experiment to analyze the chimpanzee meiosis detected a phase suggesting the occurrence of recombination inside this structure and, in turn, suppression of recombination on chromosome arms. These results support our hypothesis that loss of this structure led to increased diversity in the chromosome organization of humans.

Academic Significance and Societal Importance of the Research Achievements

ゲノムプロジェクトの結果から、ヒトとチンパンジーの間の塩基配列の違いは数％程度と推定された。しかしこれは、塩基配列の対応がつく部分を選び出しての推定値である。対応がつかない領域は、比較の対象に含まれていない。そのような領域の大部を占める要素として、反復DNAを主成分とする染色体端部の特殊な構造物がある。本研究課題は、この構造物の消失がヒトの進化へ及ぼした影響を追求し、ゲノム構成の多様性につながったとの推測を支持する結果を得た。ヒトへの進化に関して、効果は大きいと考えられるものの見過ごされている一面である。

Research Products

• [Int'l Joint Research] University of Firenze(イタリア)
• [Int'l Joint Research] Kasetsart University(タイ)
• [Int'l Joint Research] フィレンツェ大学(イタリア)
• [Int'l Joint Research] Kasetsart University(タイ)
• [Int'l Joint Research] University of Florence(イタリア)
• [Int'l Joint Research] Kasetsart University(タイ)
• [Journal Article] Fusion of piggyBac-like transposons and herpesviruses occurs frequently in teleosts (2018)
  • Author(s): Inoue Y, Kumagai M, Zhang X, Saga T, Wang D, Koga A, *Takeda H
  • Journal Title: Zoological Letters Volume: 4 Issue: 1 Pages: 6-6
  • DOI: 10.1186/s40851-018-0089-8
  • Peer Reviewed / Open Access
• [Journal Article] Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle (2017)
  • Author(s): Nishihara Hidenori、Stanyon Roscoe、Kusumi Junko、Hirai Hirohisa、Koga Akihiko
  • Journal Title: Genome Biology and Evolution Volume: 10 Issue: 1 Pages: 157-165
  • DOI: 10.1093/gbe/evx281
  • NAID: 120006469173
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara’s OwlMonkey (2017)
  • Author(s): 1)Koga A, Tanabe H, Hirai Y, Imai H, Imamura M, Oishi T, Stanyon R, Hirai H
  • Journal Title: Genome Biology and Evolution Volume: 9 Issue: 7 Pages: 1963-1970
  • DOI: 10.1093/gbe/evx142
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] DNA-based transposable elements with nucleotide sequence similar to Tol2 from medaka fish are prevalent in cyprinid fishes (2017)
  • Author(s): Ishiyama S Yamazaki K, Kurihara F, Yamashita D, Sao K, Hattori A, *Koga A
  • Journal Title: Gene Repors Volume: 9 Pages: 37-45
  • DOI: 10.1016/j.genrep.2017.08.004
  • Peer Reviewed
• [Journal Article] Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish (2017)
  • Author(s): Inoue Yusuke、Saga Tomonori、Aikawa Takumi、Kumagai Masahiko、Shimada Atsuko、Kawaguchi Yasushi、Naruse Kiyoshi、Morishita Shinichi、Koga Akihiko、Takeda Hiroyuki
  • Journal Title: Nature Communications Volume: 8 Issue: 1 Pages: 551-551
  • DOI: 10.1038/s41467-017-00527-2
  • NAID: 120006822516
  • Peer Reviewed / Open Access
• [Journal Article] Night monkey hybrids exhibit de novo genomic and karyotypic alterations: the first such case in primates (2017)
  • Author(s): *Hirai H, Hirai Y, Morimoto M, Kaneko A, Kamanaka Y, Koga A
  • Journal Title: Genome Biology and Evolution Volume: 9 (4) Issue: 4 Pages: 945-955
  • DOI: 10.1093/gbe/evx058
  • NAID: 120006822503
  • Peer Reviewed / Open Access
• [Journal Article] Formation of functional CENP-B boxes at diverse locations in repeat units of centromeric DNA in New World monkeys. (2016)
  • Author(s): Kugou K, Hirai H, Masumoto H, Koga A.
  • Journal Title: Scientific Reports Volume: 6 Issue: 1 Pages: 27833-27833
  • DOI: 10.1038/srep27833
  • NAID: 120005818231
  • Peer Reviewed / Open Access
• [Journal Article] An LTR retrotransposon-derived gene displays lineage-specific structural and putative species-specific functional variations in eutherians (2016)
  • Author(s): Irie M, Koga A, Kaneko-Ishino T, *Ishino F
  • Journal Title: Frontiers in Chemistry Volume: 23 (4) Pages: 26-26
  • DOI: 10.3389/fchem.2016.00026
  • NAID: 120005838154
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] CENP-B box, a nucleotide motif involved in centromere formation, occurs in a New World monkey (2016)
  • Author(s): Suntronpong A, Kugou K, Masumoto H, Srikulnath K, Ohshima K, Hirai H, *Koga A
  • Journal Title: Biology Letters Volume: 12 Issue: 3 Pages: 20150817-20150817
  • DOI: 10.1098/rsbl.2015.0817
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Regulation of functional KCNQ1OT1 lncRNA by beta-catenin (2016)
  • Author(s): Sunamura, N. Ohira, T. Kataoka, M. Inaoka, D. Tanabe, H. Nakayama, Y. Oshimura, M. Kugoh, H.
  • Journal Title: Scientific reports Volume: 6 Issue: 1 Pages: 1-11
  • DOI: 10.1038/srep20690
  • Peer Reviewed / Open Access
• [Journal Article] Higher-order repeat structure in alpha satellite DNA occurs in New World monkeys and is not confined to hominoids (2015)
  • Author(s): Penporn Sujiwattanarat, Watcharaporn Thapana, Kornsorn Srikulnath, Yuriko Hirai, Hirohisa Hirai, Akihiko Koga
  • Journal Title: Scientific Reports Volume: 14 Issue: 1 Pages: 10315-10315
  • DOI: 10.1038/srep10315
  • NAID: 120005758209
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Adaptation of owl monkeys to nocturnal lifestyle driven by rapid expansion of simple repeat sequence to form megasatellite DNA (2018)
  • Author(s): Koga A, Nishihara H, Stanyon R, Hirai H
  • Organizer: Society for Molecular Biology and Evolution 2018
  • Int'l Joint Research
• [Presentation] 夜猿はサテライトDNAを巧みに利用し短期間で夜間視力を高めた (2018)
  • Author(s): 古賀章彦、田辺秀之、Roscoe Stanyon、西原秀典、平井啓久
  • Organizer: 日本遺伝学会第９０回大会
  • Invited
• [Presentation] Recruitment and co-option of megasatellite DNAs coordinately facilitated adaptation of owl monkeys to nocturnal lifestyle (2018)
  • Author(s): Koga A
  • Organizer: 第４１回日本分子生物学会年会
  • Invited
• [Presentation] Dynamic role changes among three megasatellite DNAs associated with adaptation of owl monkeys to nocturnal lifestyle (2018)
  • Author(s): Koga A
  • Organizer: 2018 International Joint Conference on Genetics and Medicine
  • Int'l Joint Research / Invited
• [Presentation] 反復 DNA の出現・移動・消失でもたらされるゲノムの大きな変化 (2017)
  • Author(s): 古賀章彦、平井啓久
  • Organizer: 第３３回日本霊長類学会大会
• [Presentation] 夜猿が昼行性から夜行性に戻ったことの分子レベルでの証拠 (2017)
  • Author(s): 古賀章彦
  • Organizer: 日本進化学会第１９回大会
  • Invited
• [Presentation] Tol2トランスポゾンの分布と構造から推測されるホスト間の移動 (2017)
  • Author(s): 石山涼太郎、山﨑健太朗、栗原史弥、山下大介、佐尾賢太郎、服部明正、古賀章彦
  • Organizer: 日本遺伝学会第８９回大会
• [Presentation] Amplification of tandem repeat DNA may be responsible for a rapid shift from diurnality to nocturnality in a primate taxon (2016)
  • Author(s): Koga A, Tanabe H, Hirai H
  • Organizer: 第３９回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜（横浜市）
  • Year and Date: 2016-11-30
  • Invited
• [Presentation] セントロメア反復配列の急速な入れ替わり：テナガザルとヨザルの例 (2016)
  • Author(s): 古賀章彦、平井啓久
  • Organizer: 日本遺伝学会第８８回大会
  • Place of Presentation: 日本大学国際関係学部（静岡県三島市）
  • Year and Date: 2016-09-07
• [Presentation] Rapid replacement of centromeres by a varianttype repetitive DNA in a primate taxon (2016)
  • Author(s): Koga A
  • Organizer: Society for Molecular Biology and Evolution Conference 2016
  • Place of Presentation: Gold Coast Convention and Exhibition Centre (Australia)
  • Year and Date: 2016-07-03
  • Int'l Joint Research
• [Presentation] ヘルペスウイルスと一体化した巨大DNAトランスポゾンAlbatross (2015)
  • Author(s): 井上雄介、佐賀友則、相川拓海、森下真一、成瀬清、島田敦子、古賀章彦、武田洋幸
  • Organizer: 第３８回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド（神戸市）
  • Year and Date: 2015-12-01
• [Presentation] CENP-B box is likely to confer a selective advantage on its host organism (2015)
  • Author(s): Suntrompong A,、久郷和人、舛本寛、平井啓久、古賀章彦
  • Organizer: 第８７回日本遺伝学会大会
  • Place of Presentation: 東北大学川内北キャンパス（仙台市）
  • Year and Date: 2015-09-24
• [Presentation] Transition from diurnal to nocturnal life in the owl monkey may be associated with rapid amplification of constitutive heterochromatin (2015)
  • Author(s): Koga A
  • Organizer: International Symposium "Non-coding DNA and Chromosomal Integrity"
  • Place of Presentation: 淡路夢舞台国際会議場（兵庫県淡路市）
  • Year and Date: 2015-08-07
  • Int'l Joint Research
• [Presentation] 夜行性への移行に関与したと考えられるヨザルの大規模反復配列 (2015)
  • Author(s): 古賀章彦、平井啓久
  • Organizer: 第３１ 回日本霊長類学会大会
  • Place of Presentation: 京都大学百周年時計台記念館（京都市）
  • Year and Date: 2015-07-18
• [Presentation] Higher-order repeat structure in centromere-region satellite DNA occurs in a wide range of primates (2015)
  • Author(s): Koga A, Hirai Y, Sujiwattanarat P, Thapana W, Baicharoen S, Srikulnath K, Hirai H
  • Organizer: The 5th Asian Chromosome Colloquium
  • Place of Presentation: Kasetsart University（タイ王国バンコク市）
  • Year and Date: 2015-04-29
  • Int'l Joint Research / Invited
• [Presentation] Role of spatial positioning of chromosome territories: Evolutionary views and characteristics (2015)
  • Author(s): Tanabe H
  • Organizer: The 5th Asian Chromosome Colloquium
  • Place of Presentation: Kasetsart University（タイ王国バンコク市）
  • Year and Date: 2015-04-29
  • Int'l Joint Research / Invited
• [Book] ヒトと類人猿に見られる非コードDNAの大きな違い（小林武彦編「ゲノムを司るインターメア：非コードDNAの新たな展開」の第１５章） (2015)
  • Author(s): 古賀章彦
  • Total Pages: 12
  • Publisher: 化学同人