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Medaka pp 39-47 | Cite as

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

  • Shin Sasaki
  • Cecilia C. Mello
  • Atsuko Shimada
  • Yoichiro Nakatani
  • Shin-ichi Hashimoto
  • Masako Ogawa
  • Kouji Matsushima
  • Sam Guoping Gu
  • Masahiro Kasahara
  • Budrul Ahsan
  • Atsushi Sasaki
  • Taro Saito
  • Yutaka Suzuki
  • Sumio Sugano
  • Yuji Kohara
  • Hiroyuki Takeda
  • Andrew Fire
  • Shinichi Morishita

Abstract

Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? We investigated this question using the medaka (Japanese killifish, Oryzias latipes) by comparing the genomic sequences of two strains (Hd-rR and HNI) and by mapping approximately 37.3 million nucleosome cores from Hd-rR blastulae and 11,654 representative transcription start sites from six embryonic stages. We observed a distinctive ∼200-base pair (bp) ­periodic ­pattern of genetic variation downstream of transcription start sites; the rate of insertions and deletions longer than 1 bp peaked at positions of approximately +200, +400, and +600 bp, whereas the point mutation rate showed corresponding valleys. This ∼200-bp periodicity was correlated with the chromatin structure, with nucleosome occupancy minimized at positions 0, +200, +400, and +600 bp. These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale.

Keywords

Single Nucleotide Polymorphism Nucleosome Position Nucleosome Occupancy Nucleosome Core Indel Mutation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer 2011

Authors and Affiliations

  • Shin Sasaki
    • 1
  • Cecilia C. Mello
    • 7
  • Atsuko Shimada
    • 10
  • Yoichiro Nakatani
    • 2
  • Shin-ichi Hashimoto
    • 12
  • Masako Ogawa
    • 13
  • Kouji Matsushima
    • 14
  • Sam Guoping Gu
    • 8
  • Masahiro Kasahara
    • 3
  • Budrul Ahsan
    • 4
  • Atsushi Sasaki
    • 5
  • Taro Saito
    • 6
  • Yutaka Suzuki
    • 15
  • Sumio Sugano
    • 16
  • Yuji Kohara
    • 17
  • Hiroyuki Takeda
    • 11
  • Andrew Fire
    • 9
  • Shinichi Morishita
    • 18
  1. 1.Department of Computational Biology, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  2. 2.Department of Computational Biology, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  3. 3.Department of Computational Biology, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  4. 4.Department of Computational Biology, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  5. 5.Department of Computational Biology, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  6. 6.Department of Computational Biology, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  7. 7.Departments of Pathology and Genetics, School of MedicineStanford UniversityStanfordUSA
  8. 8.Departments of Pathology and Genetics, School of MedicineStanford UniversityStanfordUSA
  9. 9.Departments of Pathology and Genetics, School of MedicineStanford UniversityStanfordUSA
  10. 10.Department of Biological Sciences, Graduate School of ScienceThe University of TokyoBunkyo-kuJapan
  11. 11.Department of Biological Sciences, Graduate School of ScienceThe University of TokyoBunkyo-kuJapan
  12. 12.Department of Molecular Preventive Medicine, School of MedicineThe University of TokyoBunkyo-kuJapan
  13. 13.Department of Molecular Preventive Medicine, School of MedicineThe University of TokyoBunkyo-kuJapan
  14. 14.Department of Molecular Preventive Medicine, School of MedicineThe University of TokyoBunkyo-kuJapan
  15. 15.Department of Medical Genome Sciences, Graduate School of Frontier SciencesThe University of TokyoMinato-kuJapan
  16. 16.Department of Medical Genome Sciences, Graduate School of Frontier SciencesThe University of TokyoMinato-kuJapan
  17. 17.Center for Genetic Resource Information, National Institute of GeneticsMishima, ShizuokaJapan
  18. 18.Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan andBioinformatics Research and Development (BIRD)Japan Science and Technology Agency (JST)Chiyoda-ku, TokyoJapan

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