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Zhao H, Zhang F, Guo M, Xing Y, Liu G, Zhao X, Cai L. The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro. J Biomol Struct Dyn 2018; 37:1935-1943. [PMID: 30044196 DOI: 10.1080/07391102.2018.1477621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nucleosome positioning along the genome is partially determined by the intrinsic DNA sequence preferences on histone. RRRRRYYYYY (R5Y5, R = Purine and Y = Pyrimidine) motif in nucleosome DNA, which was presented based on several theoretical models by Trifonov et al., might be a facilitating sequence pattern for nucleosome assembly. However, there is not a high conformity experimental evidence to support the concept that R5Y5 motif is a key element for the determination of nucleosome positioning. In this work, the ability of the canonical, H2A.Z- and H3.3-containing octamers to assemble nucleosome on DNA templates containing R5Y5 motif and TA repeats within 10.5-bp periodicity was investigated by using salt-dialysis method in vitro. The results showed that the10.5-bp periodical distributions of both R5Y5 motif and TA repeats along DNA templates can significantly promote canonical nucleosome assembly and may be key sequence factors for canonical nucleosome assembly. Compared with TA repeats within 10.5-bp periodicity, R5Y5 motif in DNA templates did not elevate H2A.Z- and H3.3-containing nucleosome formation efficiency in vitro. This result indicates that R5Y5 motif probably isn't a pivotal factor to regulate nucleosome assembly on histone variants. It is speculated that the regulatory mechanism of nucleosome assembly is different between canonical and variant histone. These conclusions can provide a deeper insight on the mechanism of nucleosome positioning. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hongyu Zhao
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Fenghui Zhang
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China
| | - Mingxin Guo
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China
| | - Yongqiang Xing
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Guoqing Liu
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Xiujuan Zhao
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Lu Cai
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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