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

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)7124-7137
Number of pages14
JournalNucleic acids research
Volume46
Issue number14
DOIs
Publication statusPublished - Jan 1 2018

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Nucleosomes
Yeasts
DNA
Digestion
Saccharomycetales
Mechanics
Histones
Transcriptional Activation

All Science Journal Classification (ASJC) codes

  • Genetics

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MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. / Luo, Di; Kato, Daiki; Nogami, Jumpei; Ohkawa, Yasuyuki; Kurumizaka, Hitoshi; Kono, Hidetoshi.

In: Nucleic acids research, Vol. 46, No. 14, 01.01.2018, p. 7124-7137.

Research output: Contribution to journalArticle

Luo, Di ; Kato, Daiki ; Nogami, Jumpei ; Ohkawa, Yasuyuki ; Kurumizaka, Hitoshi ; Kono, Hidetoshi. / MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. In: Nucleic acids research. 2018 ; Vol. 46, No. 14. pp. 7124-7137.
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