Nucleosome Positioning and Its Role in Gene Regulation in Yeast

Abstract

Nucleosome, composed of a 147-bp segment of DNA helix wrapped around a histone protein octamer, serves as the basic unit of chromatin. Nucleosome positioning refers to the relative position of DNA double helix with respect to the histone octamer. The positioning has an important role in transcription, DNA replication and other DNA transactions since packing DNA into nucleosomes occludes the binding site of proteins. Moreover, the nucleosomes bear histone modiications thus having a profound efect in regulation. Nucleosome positioning and its roles are extensively studied in model organism yeast. In this chapter, nucleosome organization and its roles in gene regulation are reviewed. Typically, nucleosomes are depleted around transcription start sites (TSSs), resulting in a nucleosome-free region (NFR) that is lanked by two well-positioned H2A.Z-containing nucleosomes. The nucleosomes downstream of the TSS are equally spaced in a nucleosome array. DNA sequences, especially 10-11 bp periodicities of some speciic dinucleotides, partly determine the nucleosome positioning. Nucleosome occupancy can be determined with high throughput sequencing techniques. Importantly, nucleosome positions are dynamic in diferent cell types and diferent environments.Histones depletions, histones mutations, heat shock and changes in carbon source will profoundly change nucleosome organization. In the yeast cells, upon mutating the histones, the nucleosomes change drastically at promoters and the highly expressed genes, such as ribosome genes, undergo more change. The changes of nucleosomes tightly associate the transcription initiation, elongation and termination. H2A.Z is contained in the +1 and −1 nucleosomes and thus in transcription. Chaperon Chz1 and elongation factor Spt16 function in H2A.Z deposition on chromatin. The chapter covers the basic concept of nucleosomes, nucleosome determinant, the techniques of mapping nucleosomes, nucleosome alteration upon stress and mutation, and Hz1 dynamics on chromatin.Keywords: nucleosome, 10-11 bp periodicities, nucleosome-free region, MNase-sequencing, histone mutation, H2A.Z © 2018 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Basic conceptions about chromatin and nucleosome1.1. Chromatin of eukaryotic DNA, nucleosome, nucleosome compositions, and histone ChromatinEukaryotic DNA exists as chromatin structure, which is composed of DNA and proteins in the nucleus (Figure 1). The proteins can divide into histone proteins (H1/H5, H2A, H2B, H3, and H4) and non-histone ones. The former acts as core which DNA winds. The histone winding with DNA acts as a ball that forms the basic structure. Non-histone proteins have three main functions: (1) enzyme used in diferent DNA activities, for example, DNA reparation, duplication, and translation, such as DNA ...

Journal of Plant Protection Research

“…Hence, nucleosome positioning participates in gene regulation since the DNA packing on the surface of the histone octamer can occlude the binding sites of transcription factors (TFs) on genomic DNA. Thus, the nucleosome positioning at promoters negatively regulates gene transcription events (Liu et al 2018). The nucleosome positioning controls both the nucleosome packaging in discrete chromatin regions and the accessibility of transcription factor binding sites (TFBS) (Kiyama and Trifonov 2002).…”