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 language | English |
|---|---|
| Pages (from-to) | 7124-7137 |
| Number of pages | 14 |
| Journal | Nucleic acids research |
| Volume | 46 |
| Issue number | 14 |
| DOIs | |
| Publication status | Published - Jan 1 2018 |
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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 journal › Article
}
TY - JOUR
T1 - MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast
AU - Luo, Di
AU - Kato, Daiki
AU - Nogami, Jumpei
AU - Ohkawa, Yasuyuki
AU - Kurumizaka, Hitoshi
AU - Kono, Hidetoshi
PY - 2018/1/1
Y1 - 2018/1/1
N2 - 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.
AB - 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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U2 - 10.1093/nar/gky502
DO - 10.1093/nar/gky502
M3 - Article
C2 - 29893974
AN - SCOPUS:85055042541
VL - 46
SP - 7124
EP - 7137
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 14
ER -