MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast.
MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast.
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DOI：
10.1093/nar/gky502
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发表时间：
2018-08-21
影响因子：
14.9
通讯作者：
Kono H
中科院分区：
文献类型：
--
作者：
Luo D;Kato D;Nogami J;Ohkawa Y;Kurumizaka H;Kono H
转录起始位点下游的第一个核小体被称为+1核小体，预期其易于解包以用于DNA转录。为了研究+1核小体中的DNA可及性，用20个复溶的芽殖酵母的+1核小体进行MNase-seq实验。虽然MNase在DNA双链断裂中以其序列偏好性而闻名，但我们通过鉴定序列驱动和可接近性驱动的切割，证实了这种序列偏好性被DNA可接近性所压倒。具体而言，我们发现，MNase在末端区域（如TA二核苷酸）偏好的序列在消化的早期阶段被禁止在内部位点切割。然而，在末端区域不太受MNase青睐的序列如AA/TT二核苷酸在消化的早期阶段主要在内部位点被切割。由于AA/TT被认为是一个刚性的二核苷酸的步骤，耐DNA弯曲，这些内部裂解反映了局部网站的曝光诱导的DNA力学。由于酵母+1核小体的DNA进入位点富含AA/TT，该序列元件可能通过降低DNA转录方向沿着的DNA-组蛋白亲和力而在基因激活中发挥作用。
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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影响因子：
64.8
作者：
Brogaard, Kristin;Xi, Liqun;Wang, Ji-Ping;Widom, Jonathan
通讯作者：
Widom, Jonathan
影响因子：
5.6
作者：
Allan, James;Fraser, Ross M.;Owen-Hughes, Tom;Keszenman-Pereyra, David
通讯作者：
Keszenman-Pereyra, David
影响因子：
14.9
作者：
Jimeno-González S;Ceballos-Chávez M;Reyes JC
通讯作者：
Reyes JC
DOI：
10.1073/pnas.76.6.2551
发表时间：
1979-01-01
影响因子：
11.1
作者：
COTTON, FA;HAZEN, EE;LEGG, MJ
通讯作者：
LEGG, MJ
影响因子：
5.6
作者：
Gardiner, EJ;Hunter, CA;Willett, P
通讯作者：
Willett, P