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The Construction of A sequence-ready Map of Human Chromosome 2l and Gene Hunting Involved in Down Syndrome

Research Project

Project/Area Number 07558295
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section展開研究
Research Field Biomedical engineering/Biological material science
Research InstitutionThe Institute of Physical and Chemical Research (RIKEN) (1996-1997)
Okayama University (1995)

Principal Investigator

SOEDA Eiichi (1996-1997)  RIKEN,Gene Bank, Senior Researcher, ジーンバンク室, 副主任研究員 (00039330)

片山 泰人 (1995)  岡山大学, 医学部, 講師 (40033352)

Co-Investigator(Kenkyū-buntansha) HOSOKAWA Keiichi  Kawasaki Medical School, Professor, 医学部, 教授 (00104787)
KATAYAMA Yasuhito  Medical School of Okayama, Lecturer, 医学部, 講師 (40033352)
添田 栄一  理化学研究所, ジーンバンク室, 副主任研究員 (00039330)
Project Period (FY) 1995 – 1997
Project Status Completed (Fiscal Year 1997)
Budget Amount *help
¥5,500,000 (Direct Cost: ¥5,500,000)
Fiscal Year 1997: ¥2,600,000 (Direct Cost: ¥2,600,000)
Fiscal Year 1996: ¥2,900,000 (Direct Cost: ¥2,900,000)
Keywordssequence-ready map / CpG-islands / chromosome walking / CpG-tagged sequence / PAC contigs / 筋萎縮側鎖硬化症 / PAC / ダウン症 / PCRスクリーニング / 大腸菌人工染色体 / ショットガンシークエンス / 染色体21番疾病関連遺伝子 / ゲノム物理地図 / コスミド整列化 / CpGアイランド / PAC末端シークエンス / ヒト21番染色体 / 遺伝子物理地図 / 遺伝子発現地図 / ヒトゲノム解析計画 / ALS
Research Abstract

A sequence-ready map or the human genome will be generated from PAC contigs because they have provided unique materials for high resolution map and sequencing. We have developed rapid screening and chromosome walking with which almost all gaps were able to be sealed with use of a half million PAC clones, representing approx. 20-fold equivalents of the total genome.
We extracted 1440 DNAs from 384-well plates which have been arrayd with PAC clones, and prepared "PCR screening kits" for the plate selection. For the isolation of clone from the plate, we devised "ditch plates" for mixing bacteria for PCR with which enabled us to isolate any PAC with STS or PCR-primers within a couple of days. For chromosome walking, we applied direct sequencing from the ends of PAC inserts and read consistently more than 500 bases from which we designed PCR-primers for the confirmation of the existing contigs and screening of next PACs. With this system, we have completed a 7-Mb high resolution map from SOD … More l to ETS2. The full integrity of PAC and high dense cosmid overlap map shows the fidelity in cloning with the bacterial system.
Approximately 60 % of the expressed genes of the human genome is known to be associated with CpG islands, most of which are able to be detected with BssHII, EagI and SacII.To help isolate and identify genes, we have sought CpG-islands in the cosmid/PAC contigs with these diagnostic enzymes, assuming close clustering (within l kb) of two or more cutting sites as potential CpG islands. The sequences around the sites have revealed known and unknown genes in this region. Of those, the sequences in PAC 25P16 clone identified.CBR and its analogue, respectively. To verify this approach, we completed the sequence of this clone in shotgun strategies and defined seven CpG islands with which three known and three unknown genes were associated. This approach, designated as CpG-tagged sequence, is rapid and convenient for searching genes and will provide a scaffold for the construction of a transcription map. Less

Report

(4 results)
  • 1997 Annual Research Report   Final Research Report Summary
  • 1996 Annual Research Report
  • 1995 Annual Research Report
  • Research Products

    (37 results)

All Other

All Publications (37 results)

  • [Publications] Soeda, E.: "Cosmid Assembly and Anchoring to Human Chromosome21" Genomics. 25. 73-84 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Miyoshi, H.: "Alternative Splicing and Genomic Structure of the AML1 Gene Involved Acute Myeloid Leukemia" Nucl.Acids Res.23. 2762-2769 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Osoegawa, K.: "An Integrated Map with Cosmid/PAC Contigs of 4-Mb Down Syndrome Critical Region" Genomics. 32. 375-387 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Osoegawa, K.: "Potential CpG-rich islands clustering around single-minded gene in Down syndrome critical region" Mammalian Genome. 7. 461-463 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Ohta, T.: "Isolation of a cosmid clone corresponding to an inv(21)breakpoint of a patient with transient abnormal myelopoiesis" Am.J.Hum.Genet,. 58. 544-550 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Osoegawa, K.: "A 19-kb CpG island associated with single-minded gene in Down syndrome chromosomal region." DNA research. 3. 1-5 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 添田 栄一: "パルスフィールドゲル電気泳動法14「新遺伝子工学ハンドブック」" 羊土社, 106-110 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 添田 栄一: "ヒトゲノム解析計画の成果と展望-ダウン症の病理解明- 「Misc.Publ.Natl.Inst.Seric.Entomol.Sci.」" 蚕糸昆虫研, 13-22 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Osoegawa, K., Susukida, R., Okano, S., Kudoh, J., Minoshima, S., Shimizu, N., de Jong, P., Groet, J., Ives, J., Lehrach, H., Nizetic, D.and Soeda ; E.: "An integrated map with cosmid/PAC contigs of 4-Mb Down syndrome critical region." Genomics. 32. 375-387 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 0soegawa, K., Susukida, R., 0kano, S,Kato, Y., Lehrach, H., Nizetic, D.and Soeda, E.: "Potential CpG-rich islands clustering around single-minded gene in Down syndrome critical region." Mammalian Genome. 7. 46l-463 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 0hta, T., Nakano, M., Tsujita, T., Abe, K., 0soegawa, K., Yamagata, T., Yoshira, K., Jinno, Y., Soeda, E., Nakamura, Y.and Nikawa, N.: "Isolation of a cosmid clone corresponding to an inv (21) breakpoint of a patient with transient abnormal myelopoiesis." Am.J.Hum.Genet. 58. 544-550 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Osoegawa, K., Okano, S., Kato, Y., Nishimura, Y.and Soeda, E.: "A 19-kb CpG island associated with single-minded gene in Down syndrome chromosomal region." DNA Research. 3. l-5 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Matsumoto, N., Soeda, E., Ohashi, H., Fujimoto, M., Kato, R., Tsujita T., Tomita, H., Kondo, S., Fukushima Y.and Niikawa N.: "A l.2-Megabase BAC/PAC contig spanning the 14ql3 breakpoint of t (2 ; 14) in a mirror-image polydactyly patient" Genomics. 45. 11-16 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Matsumoto, N., 0hashi, H., Tsukahara, M., Chang Kim, K., Soeda, E.and Niikawa, N.: "Possible narrowed assignment of the loci of monosomy 21-associated microcephaly and intrauterine growth retardation to a 1.2-Mb segment at 21q22.2" Am.J.Hum.Genet. 60. 1997-999 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Kitamura, E., Hosoda, F., Fukushima, M., Asakawa, S., Shimizu, N., Imai, T., Soeda, E.and 0hki, M.: "A 3-Mb sequence-ready contig map encompassing the multiple disease gene cluster on chromosome 11ql3.1-ql3.3" DNA Reserch. 4. 281-289 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Soeda,E.: "Cosmid Assembly and Anchoring to Human Chromosome 21" Genomics. 25. 73-84 (1995)

    • Related Report
      1997 Annual Research Report
  • [Publications] Miyoshi,H.: "Alternative Splicing and Genomic Structure of the AML1 Gene Involved Acute Myeloid Leukemia" Nucl.Acids Res.23. 2762-2769 (1995)

    • Related Report
      1997 Annual Research Report
  • [Publications] Osoegawa,K.: "An Integrated Map with Cosmid/PAC Contigs of 4-Mb Down Syndrome Critical Region" Genomics. 32. 375-387 (1996)

    • Related Report
      1997 Annual Research Report
  • [Publications] Osoegawa,K.: "Potential CpG-rich islands clustering around single-minded gene in Down syndrome critical region" Mammalian Genome. 7. 461-463 (1996)

    • Related Report
      1997 Annual Research Report
  • [Publications] Ohta,T.: "Isolation of a cosmid clone corresponding to an inv(21) breakpoint of a patient with transient abnormal myelopoiesis" Am.J.Hum.Genet.58. 544-550 (1996)

    • Related Report
      1997 Annual Research Report
  • [Publications] Osoegawa,K.: "A 19-kb CpG island associated with single-minded gene in Down syndrome chromosomal region." DNA research. 3. 1-5 (1996)

    • Related Report
      1997 Annual Research Report
  • [Publications] 添田栄一: "パルスフィールドゲル電気泳動法14「新遺伝子工学ハンドブック」" 羊土社, 106-110 (1996)

    • Related Report
      1997 Annual Research Report
  • [Publications] 添田栄一: "ヒトゲノム解析計画の成果と展望-ダウン症の病理解明-「Misc.Publ.Natl.Inst.Seric.Entomol.Sci.」" 蚕糸昆虫研, 13-22 (1996)

    • Related Report
      1997 Annual Research Report
  • [Publications] Soeda,E.: "Cosmid Assembly and Anchoring to Human Chromosome 21" Genomics. 25. 73-84 (1995)

    • Related Report
      1996 Annual Research Report
  • [Publications] Miyoshi,H.: "Alternative Splicing and Genomic Structure of the AML1 Gene Involved Acute Myeloid Leukemia" Nucl.Acids Res.23. 2762-2769 (1995)

    • Related Report
      1996 Annual Research Report
  • [Publications] Osoegawa,K.: "An Integrated Map with Cosmid/PAC Contigs of 4-Mb Down Syndrome Critical Region" Genomics. 32. 375-387 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Osoegawa,K.: "Potential CpG-rich islands clustering around single-minded gene in Down syndrome critical region" Mammalian Genome. 7. 461-463 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Ohta,T.: "Isolation of a cosmid clone corresponding to an inv (21) breakpoint of a patient with transient abnormal myelopoiesis" Am.J.Hum.Genet.58. 544-550 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Osoegawa,K.: "A 19-kb CpG island associated with single-minded gene in Down syndrome chromosomal region." DNA research. 3. 1-5 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] 添 田 栄 一: "パルスフィールドゲル電気泳動法14 「新遺伝子工学ハンドブック」" 羊土社, 106-110 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] 添 田 栄 一: "ヒトゲノム解析計画の成果と展望 -ダウン症の病理解明- 「Misc.Publ.Natl.Inst.Seric.Entomol.Sci」" 蚕糸昆虫研, 13-22 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Soeda, E., Hou, D. -X., Osoegawa, K., Atsuchi, Y., Yamagata, T., Shimokawa, T., Kishida, H., Soeda, E., Okano, S., Chumakov, I., Cohen, D., Raff, M., Gardiner, K., Graw, S. L., Patterson, D., de Jong, P., Ashworth, L. K., Slezak, T., and Carrano, A. V.: "Cosmid Assembly and Anchoring to Human Chromosome 21" Genomics. 25. 73-84 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Murakami, Y., Naitou, M., Hagiwara, H., Shibata, T., Ozawa, M., Sasanuma, S. -I., Sasanuma, M., Tsuchiya, Y., Soeda, E., Yokoyama, K., Yamazaki, M., Tashiro, H., and Eki, T.: "Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae" Nature (genetics). 10. 261-268 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Miyoshi, H., Ohira, M., Shimizu, K., Mitani, K., Hirai, H., Imai, T., Yokoyama, K., Soeda, E., and Ohki, M.: "Alternative splicing and genomic structure of the AML1 gene involved acute myeloid leukemia" Nucleic Acids Res.23. 2762-2769 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Ohta, T., Nakano, M., Tsujita, T., Abe, K., Osoegawa, K., Yamagata, T., Yoshiura, K., Jinno, Y., Soeda, E., Nakamura, Y. and Nikawa, N.: "Isolation of a cosmid clone corresponding to an inv (21) breakpoint of a patient with transient abnormal myelopoiesis" Am. Soc. Hum. Genet.(in press). (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Osoegawa, K., Susukida, R., Okano, S., Kudoh, J., Minoshima, S., Shimizu, N., de Jong, P., Groet, J., Ives, J., Lehrach, H., Nizetic, D., and Soeda, E.: "An integrated map with cosmid/PAC contings of a 4-Mb Down syndrome critical region" Genomics. 32(in press). (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] 添田栄一、牟田滋: "新遺伝子工学ハンドブック" パルスフィールドゲル電気泳動法, 1996 (14(印刷中))

    • Related Report
      1995 Annual Research Report

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Published: 1996-04-01   Modified: 2016-04-21  

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