MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast

Di Luo, Daiki Kato, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka, Hidetoshi Kono

研究成果: ジャーナルへの寄稿記事

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The first nucleosomes in the downstream of transcription starting sites are called +1 nucleosomes, which are expected to be readily unwrapped for DNA transcription. To investigate DNA accessibility in +1 nucleosomes, MNase-seq experiments were carried out with 20 reconstituted +1 nucleosomes of budding yeast. Although MNase has been known for its sequence preference in DNA digestions, we confirmed that this sequence preference is overwhelmed by DNA accessibility by identifying the sequence-driven and accessibility-driven cleavages. Specifically, we find that sequences favoured by MNase at the end regions such as TA dinucleotide are prohibited from cleavage at the internal sites in the early stage of digestion. Nevertheless, sequences less favoured by MNase at the end regions such as AA/TT dinucleotide are predominantly cleaved at the internal sites in the early stage of digestion. Since AA/TT is known as a rigid dinucleotide step resistant to DNA bending, these internal cleavages reflect the local site exposures induced by DNA mechanics. As the DNA entry site of +1 nucleosomes in yeast is found AA/TT-rich, this sequence element may play a role in gene activation by reducing DNA-histone affinities along the direction of DNA transcription.

元の言語英語
ページ(範囲)7124-7137
ページ数14
ジャーナルNucleic acids research
46
発行部数14
DOI
出版物ステータス出版済み - 1 1 2018

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All Science Journal Classification (ASJC) codes

  • Genetics

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