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1998 Fiscal Year Final Research Report Summary

Molecular mechanism of the diversification of genome by retroposons

Research Project

Project/Area Number 08408030
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Molecular biology
Research InstitutionTOKYO INSTITUTE OF TECHNOLOGY

Principal Investigator

OKADA Norihiro  Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Professor, 生命理工学部, 教授 (60132982)

Co-Investigator(Kenkyū-buntansha) OHSIMA Kazuhiko  Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Lecturer, 生命理工学部, 講師 (60282852)
Project Period (FY) 1996 – 1998
KeywordsSINE / LINE / CR1 / reverse transcriptase / Ebox / zine finger motif
Research Abstract

CR1 elements are a family of retroposons. They are classified as long interspersed elements (LINEs) or non-long terminal repeat (non-LTR) retrotransposons, and they have been found in the genomes of many vertebrates. However, they have been only partially characterized and only a 2-kbp region of the 3' end of chicken CR1 has been sequenced. In the present study, we determined the entire consensus sequence of CR1 elements in the turtle genome, designated PsCR1.
The first open reading frame (ORF1) of PsCR1 has two unusual arrangements of Cys residues. One of them includes a zinc finger motif, CX_2CX_<14>CX_2C.The putative zinc finger has cysteine residues with identical spacing and a similar amino acid composition to those found in the species-specific transcription initiation factors, SL1 and TIF-IB.
The 5'-untranslated region (5' UTR) of PsCR1 contains a sequence similar to part of the human L1 promoter, L1 site A, and several cis elements of the type found in eukaryotic genes. Within a region of about 500 bp, there are nine "E boxes", cis elements that are recognized by the basic helix-loop-helix (bHLH) family of proteins. This observation raises the possibility that cellular transcription factors that bind to these sequences might act in concert to regulate the expression of PsCR1.
The extent of the sequence divergence of the 3' UTR of CR1-between species was found to be lower than the rate of nonsynonymous substitutions per site in ORF2, suggesting that a strict functional constraint must exist for this region. This result strongly suggests that the conserved 3'-end sequence of CR1 is the recognition site for the reverse transcriptase of CR1. A discussion is presented of a possible mechanism for the integration of CR1 elements and, also, of the intriguing possible recruitment of the reverse transcriptase for the retroposition of SINEs.

  • Research Products

    (20 results)

All Other

All Publications (20 results)

  • [Publications] Terai, Y., Takahashi, K.& Okada, N.: "SINE cousins : The3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3'ends of LINEs with the same genealogical origin." Mol.Biol.Evol.15. 1460-1471 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Hamada, M., Takasaki, N., Reist, J.D., DeCicco, A.L., Goto, A.and Okada, N.: "Detection of the on-going sorting of ancestrally polymorphic SINEs towards fixation or loss in populations of two species of charr during speciation." Genetics. 150. 301-311 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Shimamura, M., Nikaido, M., Ohshima, K.and Okada, N.: "A SINE that acquired a role in signal transduction during evolution." Mol.Biol.Evol.15. 923-925 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Takahashi, K., Terai, Y.and Okada, N.: "A novel family of short interspersed repetitive elements (SINEs) from cichlids : the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika." Mol.Biol.Evol.15. 391-407 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kajikawa, M., Ohshima, K.and Okada, N.: "Determination of the entire sequence of turtle CR1 : the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif." Mol.Biol.Evol.14. 1206-1217 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Simimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I.and Okada, N.: "Molecular evidence that whales form a clade within even-toed ungulates." Nature. 388. 666-670 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ohshima, K., Hamada, M., Terai, Y.& Okada, N.: "The 3'ends of tRNA-deriverd short interspersed repetitive elements are deriverd from the 3'ends of long interspersed repetitive elements." Mol.Cell.Biol.16. 3756-3764 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Terai, Y., Takahashi, K.& Okada, N.: "SINE cousins : The3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin" Mol.Biol.Evol.15. 1460-1471 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Hamada, M., Takasaki, N., Reist, J.D., DeCicco, A.L., Goto, A.and Okada, N.: "Detection of the on-going sorting of ancestrally polymorphic SINEs towards fixation or loss in populations of two species of charr during speciation" Genetics. 150. 301-311 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Shimamura, M., Nikaido, M., Ohsima, K.and Okada, N.: "A SINE that acquired a role in signal transduction during evolution." Mol.Biol.Evol.15. 923-925 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Murata, S., Takasaki, N., Okazaki, T., Kobayashi, T., Numachi, K., Chang, K.and Okada, N.: "Molecular evidence from short interspersed elements (SINEs) that Oncorhynchus masou (cherry salmon) is monophyletic" Can.J.Fish.Aquat.Sci.55. 1-7 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takahashi, K., Terai, Y., Nishida, M.and Okada, N.: "Anovel family of short interspersed repetitive elements (SINEs) from cichlids : the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika." Mol.Biol.Evol.15. 391-407 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Okada, N., Hamada, M., Ogiwara, I.and Ohshima, K.: "SINEs and LINEs share common 3' sequences : a review." Gene. 205. 229-243 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kajikawa, M., Ohshima, K.and Okada, N.: "Determination of the entire sequence of turtle CR1 : the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif." Mol.Biol.Evol.14. 1206-1217 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Simimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I.and Okada, N.: "Molecular evidence that whales form a clade within even-toed ungulates." Nature. 388. 666-670 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Hamada, M., Kido, Y., Himberg, M., Hasegawa, M.and Okada, N.: "A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefishes) with sequences that are almost identical to those of the Sma I family of repeats : possible evidence for the horizontal transfer of SINEs." Genetics. 146. 355-367 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takasaki, N., Yamaki, T., Hamada, M., Park, L.and Okada, N.: "The salmon Sma I family of SINEs : interspecific and intraspecific polymorphism of the insertion of SINEs in the genomes of chum and pink salmon." Genetics. 146. 369-380 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ohshima, K., Hamada, M., Terai, Y.& Okada, N.: "The 3' ends of tRNA-deriverd short interspersed repetitive elements are deriverd from the 3' ends of long interspersed repetitive elements." Mol.Cell.Biol.16. 3756-3764 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Murata, S., Takasaki, N., Saitoh, M., Tachida, H.and Okada, N.: "Details of retropositional genome dynamics that provide a rational for a generic division : The distinct branching of all the Pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout(Salmo)." Genetics. 142. 915-926 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takasaki, N., Park, L., Kaeriyama, M., Gharrett, A.J.and Okada, N.: "Characterization of species-specifically amplified SINEs in three salmonid species, chum salmon, pink salmon and kokanee : the local environment of the genome might be important for the generation of a dominant source gene at a newly retroposed locus." J.Mol.Evol.42. 103-116 (1996)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 1999-12-08  

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