Histone Research Paper

1. To make a fundamental advance in the computational modeling of nucleosome stability. Understanding the base-pair sequence dependence of the propensities for nucleosome formation has been a long-sought goal in cell biology as nucleosome stability is thought to be an important component of transcriptional regulation. In particular DNA methylation and histone acetylation, which play key roles in

DNA is long polymer made up of subunits called nucleotides. Nucleotides are basic building blocks of DNA. Each nucleotide consist of a nitrogenous base, a 5’carbon, deoxyribose sugar and a phosphate group. In a DNA molecule there are four nitrogenous bases: cytosine, Thymine, Adenine and Guanine. Adenine pairs with Thymine and Cytosine pairs with Guanine. When these four nucleotides are bonded to each other they interact in a specific according to their chemical structure. Anything that an organism has to do or make is specified in the macromolecule called DNA.

Histone deacetylases (HDACs), a family of enzymes deacetylating lysines on core histones and other cellular proteins, play an key role in epigenetic regulation of gene transcription and control other cellular functions including cell death, proliferation, and motility.

As cells differentiate into specialized cell types they undergo re-organization and many structural changes which affects gene expression patterns and cell functions. Chromatin interactions have important roles in gene regulation.

The nucleus contains chromatin and often one or more small spherical structures, each called the nucleolus. Chromatin is made from proteins and DNA which comprises the chromosomes. The chromosomes direct protein synthesis because they are the site of transcription. The DNA also provides a template for DNA replication and controls the cells activities. The nucleolus are the sites of formation of rRNA, a constituent of ribosomes.

Chromosomes are composed of chromatin (DNA and protein complex). The DNA is wrapped around histones to form a nucleosome.

The DNA is organized in linear chromosomes in which a long strand of DNA is tightly coiled and packaged around special proteins known as histones.

Using total internal reflection fluorescence (TIRF)-coupled photobleaching-assisted copy-number counting of single nucleosomes obtained from cultured cells, Padeganeh et. al. found that the majority of CENP-A nucleosomes contain CENP-A dimers[37, 42]. More recently, through the use of novel sequencing techniques, it was found that the CENP-A nucleosome protects a 133 bp genomic region consistent with octameric nucleosomes with DNA unwrapping at entry and exit[43]. While the existence of hemisomes (one molecule of each of CENP-A, H4, H2A and H2B forms nucleosomes) at specific cell cycle phases in flies, humans and yeast were proposed[44-47], predominant model of the CENP-A nucleosome is octameric structure. Such nucleosomes contain two molecules each of CENP-A, H4, H2A and H2B interspersed with canonical octameric H3 nucleosomes (Figure 1).

1 G banding techniques enhances the basic structures of chromosomes. The chromosomes consists of 8 histones proteins molecules , each of which is wrapped around by DNA of 146bp long to form a repeating units called nucleosomes, then successive nucleosomes are arranged to form a structure similar to that of beads of a string which again coil themselves to form chromatin fiber. Chromosome package is form when chromatin fiber are further loop and coiled.

Histone chaperones facilitate incorporation of histones on DNA by neutralizing their positive charges, and thus play key roles in regulating nucleosome assembly (Philpott, Krude, & Laskey, 2000). Nucleosomes are assembled via a stepwise process. First, the H3–H4 tetramer is deposited on DNA, followed by the addition of two H2A–H2B dimers (S. Smith & Stillman, 1991). This process is reversible to allow disassembly of nucleosomes (Figure 6B). Each of the canonical histones is encoded by multiple genes and most of these genes are organized into clusters throughout the genome to ensure that the expression of canonical histones during S-phase generates large and equal amounts of all four nucleosome core histone proteins (Albig, Kioschis, Poustka, Meergans, & Doenecke, 1997).

Also, a recent study of an H2A.Z/H2A nucleosome structure shows that the H2A.Z L1 loop domain was drastically altered without any structural changes of the H2A L1 loop, thus avoiding steric clash. So, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z nucleosome (H2A.Z/H2A.Z) (Horikoshi, Arimura et al. 2016). Consequently, the presence of H2A versus H2A.Z in the histone octamer affects the stability of the nucleosome (Coleman-Derr & Zilberman, 2012b; Jin & Felsenfeld, 2007; Jin et al., 2009; Kumar & Wigge, 2010).

It is fascinating to know that two meters of human DNA are packed inside ∼1000 µm3 nucleus. How this amazing packing occurs in nature was a great mystery until the discovery of nucleosome and its structural organizations. Nucleosome is a basic unit of chromatin that consists of 146 bp fragment of DNA wrapped around a protein octamer known as histone. One nucleosome contains two molecules of each Histone 2A, Histone 2B, Histone 3 and Histone 4. Besides that, Histone 1 is linked with DNA that connects various histones in the nucleosome (Kamakaka and Biggins, 2005). All these histone proteins belong to different gene families but this review will focus on histone 3 gene family in Arabidopsis thaliana.

DNA (deoxyribonucleic acid) is a self-replicating nucleic acid that carries the genetic information in cells in a double helix structure. The 2 stranded helix is composed of 4 nucleotides, Adenine (A), Thymine (T), Guanine (G), and Cytosine (C). The base pairs only form between A and T connected by 2 Hydrogen bonds and G and C connected by 3 hydrogen bonds. Foremost DNA wrapping comes about as DNA wraps around protein called histones. These combined loops of DNA and protein are called nucleosomes and the nucleosomes are packaged into a thread called chromatin. Chromosomes are made up of packaged chromatin and can be seen in the nucleus of dividing cells and form around DNA replication. Furthermore, DNA replication begins with 2 DNA strands being separated by the helicase enzyme. Single stranded DNA binding proteins attach to these strands to keep them from re-connecting. 1 DNA strand begins to encode called the leading strand, which Forms from 5’ to 3’ end using DNA polymerase 3 the primary polymerase. The other strand is referred to as the lagging strand, which presents problems because it has to form from the 5’ to 3’end as well. As continuous replication of the leading strand continues the lagging strand forms in pieces called Okazaki fragments. RNA primase forms as RNA primer and polymerase III lay down new DNA. This process repeats again and again. DNA polymerase I replaces RNA primers with DNA and DNA ligase links the Okazaki fragments. Along with the process of DNA

‘Epigenetics,’ derived from the Greek root ‘epi ' meaning on top of, is the study of dynamic regulation of gene expression due to factors that act on chromatin structure, nuclear architecture and other molecular events that do not change the DNA sequence (Stilling et al., 2014). In addition, epigenetics has sometimes been defined as sequence- independent heritable changes in gene expression (Holliday, 1987). Epigenetic processes include post-translational histone modification, as well as cytosine methylation and interactions of non-coding RNAs (Jaenisch & Bird, 2003; Landry et al., 2013). Post-translational histone acetylation results in a decreased

Hence, although H3K9me2/3 methylation mark may be required, nucleation could occur from the inherent demixing ability of HP1a.