Establishment and diagnostic application of epigenome sequencing methods for imprinted differentially methylated regions

• Project/Area Number: 17K08689
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Human genetics
• Research Institution: National Center for Child Health and Development
• Principal Investigator: Nakabayashi Kazuhiko 国立研究開発法人国立成育医療研究センター, 周産期病態研究部, 室長 (10415557)
• Project Period (FY): 2017-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2019: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2017: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
• Keywords: DNAメチル化 / ゲノムインプリンティング / 遺伝学的検査 / インプリンティング / エピゲノム診断 / アレル別エピゲノム解析 / クロマチン高次構造 / シーケンス / エピゲノム

Outline of Final Research Achievements

We established a catalog of 789 probes corresponding to 50 known imprinted differentially methylated regions (DMRs) on the Infinium HumanMethylationEPIC BeadChip and also identified two novel maternally methylated regions associated with PTCHD3 and JAKMIP1. We also established experimental and bioinformatic protocols to conduct amplicon bisulfite sequencing using a bench-top NGS system. These outcomes enable researchers and clinicians to more easily and rapidly conduct genome-wide DNA methylation analyses to diagnose imprinting disorder patients. We also conducted ATAC sequencing on F1 hybrid mouse 9.5dpc embryos from the reciprocal crosses of C57B6 and JF1 strains, and obtained genome-wide allele-specific open chromatin information. This dataset will help us to further elucidate regulatory mechanisms of imprinted gene expression.

Academic Significance and Societal Importance of the Research Achievements

国内外のインプリンティング疾患研究者が、本研究成果の既知インプリンティング制御領域位置情報を参照し、アンプリコンバイサルファイトシーケンス法を用いることで、インプリンティング疾患症例の網羅的DNAメチル化解析をより簡便かつ迅速に実施できること、延いては当該疾患群の遺伝学的検査の網羅性向上・精度向上をもたらすと予想されること、に本研究の社会的意義がある。疾患研究における複数の応用例に留まらず、霊長類からげっ歯類までを対象としたエピゲノム制御進化研究においても本研究の成果がその推進基盤となったことは、本研究成果の学術的意義が広範分野に及ぶことを示している。

Research Products

• [Int'l Joint Research] University of British Columbia(カナダ)
• [Int'l Joint Research] PEBC IDIBELL(スペイン)
• [Int'l Joint Research] IDIBELL(スペイン)
• [Int'l Joint Research] IDIBELL (Barcelona)(Spain)
• [Journal Article] Identification of epigenetic memory candidates associated with gestational age at birth through analysis of methylome and transcriptional data (2021)
  • Author(s): Kashima Kohei, Kawai Tomoko, 共同筆頭著者、他22名
  • Journal Title: Scientific Reports Volume: 11 Issue: 1 Pages: 3381-3381
  • DOI: 10.1038/s41598-021-83016-3
  • Peer Reviewed / Open Access
• [Journal Article] Rare variant of the epigenetic regulator SMCHD1 in a patient with pituitary hormone deficiency. (2020)
  • Author(s): Kinjo K, Nagasaki K, Muroya K, Suzuki E, Ishiwata K, Nakabayashi K, Hattori A, Nagao K, Nozawa R-S, Obuse C, Miyado K, Ogata T, Fukami M and Miyado M.
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 10985-10985
  • DOI: 10.1038/s41598-020-67715-x
  • Peer Reviewed / Open Access
• [Journal Article] Contribution of gene mutations to Silver-Russell syndrome phenotype: multigene sequencing analysis in 92 etiology-unknown patients (2020)
  • Author(s): Inoue Takanobu、et al
  • Journal Title: Clinical Epigenetics Volume: 12 Issue: 1 Pages: 86-86
  • DOI: 10.1186/s13148-020-00865-x
  • Peer Reviewed / Open Access
• [Journal Article] Loss of imprinting of the human-specific imprinted gene ZNF597 causes prenatal growth retardation and dysmorphic features: implications for phenotypic overlap with Silver-Russell syndrome (2020)
  • Author(s): Yamazawa K, Inoue T, Sakemi Y, Nakashima T, Yamashita H, Khono K, Fujita H, Enomoto K, Nakabayashi K, Hata K, Nakashima M, Matsunaga T, Nakamura A, Matsubara K, Ogata T, Kagami M.
  • Journal Title: Journal of Medical Genetics Volume: - Issue: 6 Pages: 107019-107019
  • DOI: 10.1136/jmedgenet-2020-107019
  • Peer Reviewed / Open Access
• [Journal Article] Identification of distinct loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development (2020)
  • Author(s): Yagi Masaki、Kabata Mio、Tanaka Akito、Ukai Tomoyo、Ohta Sho、Nakabayashi Kazuhiko、Shimizu Masahito、Hata Kenichiro、Meissner Alexander、Yamamoto Takuya、Yamada Yasuhiro
  • Journal Title: Nature Communications Volume: 11 Issue: 1 Pages: 3199-3199
  • DOI: 10.1038/s41467-020-16989-w
  • NAID: 120006865709
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis (2020)
  • Author(s): Shuhei Ishikura, Kazuhiko Nakabayashi, Masayoshi Nagai, Toshiyuki Tsunoda, Senji Shirasawa
  • Journal Title: Nucleic Acids Research Volume: 48(19) Issue: 19 Pages: 10848-10866
  • DOI: 10.1093/nar/gkaa815
  • Peer Reviewed / Open Access
• [Journal Article] Gestational arsenic exposure induces site-specific DNA hypomethylation in active retrotransposon subfamilies in offspring sperm in mice (2020)
  • Author(s): Nohara Keiko、Nakabayashi Kazuhiko、Okamura Kazuyuki、Suzuki Takehiro、Suzuki Shigekatsu、Hata Kenichiro
  • Journal Title: Epigenetics & Chromatin Volume: 13 Issue: 1 Pages: 53-53
  • DOI: 10.1186/s13072-020-00375-3
  • Peer Reviewed / Open Access
• [Journal Article] Evolution of imprinting via lineage-specific insertion of retroviral promoters (2019)
  • Author(s): Bogutz Aaron B.、Brind’Amour Julie、Kobayashi Hisato、Jensen Kristoffer N.、Nakabayashi Kazuhiko、Imai Hiroo、Lorincz Matthew C.、Lefebvre Louis
  • Journal Title: Nature Communications Volume: 10 Issue: 1 Pages: 5674-5674
  • DOI: 10.1038/s41467-019-13662-9
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Exploring trophoblast-specific Tead4 enhancers through chromatin conformation capture assays followed by functional screening (2019)
  • Author(s): Tomikawa Junko、Takada Shuji、Okamura Kohji、Terao Miho、Ogata-Kawata Hiroko、Akutsu Hidenori、Tanaka Satoshi、Hata Kenichiro、Nakabayashi Kazuhiko
  • Journal Title: Nucleic Acids Research Volume: 48 Issue: 1 Pages: 278-289
  • DOI: 10.1093/nar/gkz1034
  • Peer Reviewed / Open Access
• [Journal Article] Placenta-specific epimutation at H19-DMR among common pregnancy complications: its frequency and effect on the expression patterns of H19 and IGF2 (2019)
  • Author(s): Yamaguchi Yuko、Tayama Chiharu、Tomikawa Junko、Akaishi Rina、Kamura Hiromi、Matsuoka Kentaro、Wake Norio、Minakami Hisanori、Kato Kiyoko、Yamada Takahiro、Nakabayashi Kazuhiko、Hata Kenichiro
  • Journal Title: Clinical Epigenetics Volume: 11 Issue: 1 Pages: 113-113
  • DOI: 10.1186/s13148-019-0712-3
  • Peer Reviewed / Open Access
• [Journal Article] DNA methylation changes involved in the tumor increase in F2 males born to gestationally arsenite‐exposed F1 male mice (2019)
  • Author(s): Okamura Kazuyuki、Nakabayashi Kazuhiko、Kawai Tomoko、Suzuki Takehiro、Sano Tomoharu、Hata Kenichiro、Nohara Keiko
  • Journal Title: Cancer Science Volume: 110 Issue: 8 Pages: 2629-2642
  • DOI: 10.1111/cas.14104
  • Peer Reviewed / Open Access
• [Journal Article] Characterization of parent-of-origin methylation using the Illumina Infinium MethylationEPIC array platform (2018)
  • Author(s): Hernandez Mora Jose R、Tayama Chiharu、S?nchez-Delgado Marta、Monteagudo-S?nchez Ana、Hata Kenichiro、Ogata Tsutomu、Medrano Jose、Poo-Llanillo Maria E、Sim?n Carlos、Moran Sebastian、Esteller Manel、Tenorio Jair、Lapunzina Pablo、Kagami Masayo、Monk David、Nakabayashi Kazuhiko
  • Journal Title: Epigenomics Volume: 10 Issue: 7 Pages: 941-954
  • DOI: 10.2217/epi-2017-0172
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Reciprocal changes of H3K27ac and H3K27me3 at the promoter regions of the critical genes for endometrial decidualization (2018)
  • Author(s): Katoh Noriko、Kuroda Keiji、Tomikawa Junko、Ogata-Kawata Hiroko、Ozaki Rie、Ochiai Asako、Kitade Mari、Takeda Satoru、Nakabayashi Kazuhiko、Hata Kenichiro
  • Journal Title: Epigenomics Volume: 10 Issue: 9 Pages: 1243-1257
  • DOI: 10.2217/epi-2018-0006
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Molecular and clinical analyses of two patients with UPD(16)mat detected by screening 94 patients with Silver-Russell syndrome phenotype of unknown aetiology (2018)
  • Author(s): Inoue Takanobu、Yagasaki Hideaki、Nishioka Junko、Nakamura Akie、Matsubara Keiko、Narumi Satoshi、Nakabayashi Kazuhiko、Yamazawa Kazuki、Fuke Tomoko、Oka Akira、Ogata Tsutomu、Fukami Maki、Kagami Masayo
  • Journal Title: Journal of Medical Genetics Volume: 印刷中 Issue: 6 Pages: 413-418
  • DOI: 10.1136/jmedgenet-2018-105463
  • Peer Reviewed
• [Journal Article] Elucidation of the developmental mechanism of ovarian mature cystic teratomas using B allele-frequency plots of single nucleotide polymorphism array data (2018)
  • Author(s): Usui Hirokazu、Nakabayashi Kazuhiko、Kaku Hiroshi、Maehara Kayoko、Hata Kenichiro、Shozu Makio
  • Journal Title: Genes, Chromosomes and Cancer Volume: 57 Issue: 8 Pages: 409-419
  • DOI: 10.1002/gcc.1
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A case of paternal uniparental isodisomy for chromosome 7 associated with overgrowth (2018)
  • Author(s): Nakamura Akie、Muroya Koji、Ogata-Kawata Hiroko、Nakabayashi Kazuhiko、Matsubara Keiko、Ogata Tsutomu、Kurosawa Kenji、Fukami Maki、Kagami Masayo
  • Journal Title: J Med Genet Volume: 55 Issue: 8 Pages: 2017-104986
  • DOI: 10.1136/jmedgenet-2017-104986
  • Peer Reviewed
• [Journal Article] Characterization of parent-of-origin methylation using the Illumina Infinium MethylationEPIC array platform (2018)
  • Author(s): Jose Ramon Hernandez Mora, Chiharu Tayama, Marta Sanchez-Delgado, Ana Monteagudo-Sanchez, Kenichiro Hata, Tsutomu Ogata, Jose Medrano, Maria Eugenia Poo-Llanillo, Carlos Simon, Sebastian Moran, Manel Esteller, Jair Tenorio, Pablo Lapunzina, Masayo Kagami, David Monk, Kazuhiko Nakabayashi
  • Journal Title: Epigenomics Volume: 印刷中
  • Peer Reviewed / Int'l Joint Research
• [Presentation] 先天性疾患ゲノム診断率向上のためのエピゲノムアプローチ (2020)
  • Author(s): 中林一彦
  • Organizer: 日本人類遺伝学会
  • Invited
• [Presentation] ヒトインプリンティング制御領域の網羅的同定と疾患エピ変異診断プラットフォームへの応用 (2019)
  • Author(s): 田山 千春、鏡 雅代、副島 英伸、緒方 勤、秦 健一郎、David Monk、中林 一彦
  • Organizer: エピジェネティックス研究会
• [Presentation] KLF14欠損マウスにおける腹部脂肪分布・脂質代謝の変化 (2019)
  • Author(s): 田山 千春、高梨 理絵子、齋藤 公亮、冨川 順子、進導 美幸、大喜多 肇、津村 秀樹、高田 修治、松本 健治、秦 健一郎、岡村 匡史、中林 一彦
  • Organizer: 日本分子生物学会
• [Presentation] 表現型可塑性におけるエピゲノムの役割 (2018)
  • Author(s): 中林一彦
  • Organizer: 第20回大会日本進化学会
  • Invited
• [Presentation] pigenomics for child health and development: genomic imprinting and beyond (2018)
  • Author(s): 中林一彦
  • Organizer: 30th Anniversary of Andrew Sass-Kortsak Award Symposium
  • Invited
• [Presentation] 発生段階特異的な機能的ゲノム高次構造の探索 (2018)
  • Author(s): 冨川順子，西園啓文，秦健一郎，中林一彦
  • Organizer: 第12回日本エピジェネティクス研究会年会
• [Presentation] 全エクソーム解析キット(SureSelect, TruSeq Exome)のパフォーマンス比較 (2018)
  • Author(s): 緒方（川田）広子，渡邊豊，長井陽子，秦健一郎，中林一彦
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] 霊長類エピゲノム多様性と進化（インプ リンティング制御領域を中心に） (2017)
  • Author(s): 中林一彦
  • Organizer: 日本進化学会
  • Invited
• [Presentation] エピゲノム研究： 最近の進歩と人類進化・多様性研究への応用 (2017)
  • Author(s): 中林一彦
  • Organizer: 日本人類学会
  • Invited
• [Book] 遺伝子医学MOOK36号 エピゲノムで新たな解明が進む「先天性疾患」 (2021)
  • Author(s): 中林一彦
  • Total Pages: 8
  • Publisher: メディカルドゥー社
• [Book] Epigenetics Methods (Volume 18 in Translational Epigenetics), 2020, Pages 117-140 (Chapter 7: The Illumina Infinium Methylation Assay for Genome-wide Methylation Analyses) (2020)
  • Author(s): Kazuhiko Nakabayashi
  • Total Pages: 24
  • Publisher: Springer
• [Book] Epigenetics Methods (2020)
  • Author(s): Kazuhiko Nakabayashi
  • Total Pages: 24
  • Publisher: Elsevier
• [Remarks]
  • URL: https://www.ncchd.go.jp/hospital/about/doctor/ntec/n02.html
• [Remarks]
  • URL: https://www.researchgate.net/profile/Kazuhiko_Nakabayashi