Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue 14, Pages 7124-7137Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky502
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Funding
- Ministry of Education, Culture, Sports, Science and Technology (MEXT) Strategic Programs for Innovative Research, Computational Life Science and Application in Drug Discovery and Medical Development [hp160223, hp170255, hp18019]
- Japan Society for the Promotion of Science KAKENHI [JP25116002, JP17H01408, JP25116003, JP251160010]
- Platform Project for Supporting in Drug Discovery and Life Science Research from the Japan Agency for Medical Research and Development (AMED) [JP18am0101076, JP18am0101106]
- Japan Science and Technology Agency CREST [JPMJCR16G1]
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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.
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