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The local state of chromatin compaction at transcription start sites controls transcription levels

View ORCID ProfileSatoru Ishihara, Yohei Sasagawa, Takeru Kameda, Mana Umeda, Hayato Yamashita, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido
doi: https://doi.org/10.1101/782060
Satoru Ishihara
Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
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  • ORCID record for Satoru Ishihara
  • For correspondence: satorui@fujita-hu.ac.jp itoshi.nikaido@riken.jp
Yohei Sasagawa
Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
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Takeru Kameda
Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, JapanGraduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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Mana Umeda
Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
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Hayato Yamashita
Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Naoe Kotomura
Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
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Masayuki Abe
Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Yohei Shimono
Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
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Itoshi Nikaido
Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
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  • For correspondence: satorui@fujita-hu.ac.jp itoshi.nikaido@riken.jp
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SUMMARY

A defined amount of transcript is produced from the transcription start site (TSS) of each gene, suggesting that the binding frequency of RNA polymerase varies among genes. However, what structural feature of the genome controls this frequency remains elusive. We established a method to fractionate chromatin according to its degree of compaction. Histone H3 was evenly detected in open and compact chromatin, but histone H1 was enriched in compact chromatin. Similarly, HP1α and MBD2b were more abundant in compact chromatin, but the levels of tri-methylated H3 (lysine 9) and 5-methyl cytosine subtly increased. Via a genome-wide analysis, nearly the entire genome was found to exist in compact chromatin with no variations between repeat and non-repeat sequences; however, active TSSs were rarely found in compact chromatin. Based on a correlation between weak compaction and RNA polymerase binding at TSSs, it appears that the local state of chromatin compaction establishes transcription levels.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 25, 2019.
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The local state of chromatin compaction at transcription start sites controls transcription levels
Satoru Ishihara, Yohei Sasagawa, Takeru Kameda, Mana Umeda, Hayato Yamashita, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido
bioRxiv 782060; doi: https://doi.org/10.1101/782060
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The local state of chromatin compaction at transcription start sites controls transcription levels
Satoru Ishihara, Yohei Sasagawa, Takeru Kameda, Mana Umeda, Hayato Yamashita, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido
bioRxiv 782060; doi: https://doi.org/10.1101/782060

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