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Lecture No.2: Chromatin structure and function I

Hence this course is mainly focusing on gene regulation,
on both levels (transcriptional and post transcriptional, we have first to be familiar with the structure and the packaging of the DNA. As structure of the DNA was previously taught early in your undergraduate stage, this lecture will focus on DNA packaging which is mainly achieved by what so called Chromatin.

Chromatin:

DNA is packaged into a small volume to fit in the cell and to strengthen DNA to protect it from damage. The main proteins which do this job are called histones. The combination between DNA and histones is known as chromatin. The primary functions of the chromatin is packaging of DNA to allow mitosis and meiosis and to control gene expression and DNA replication. Chromatin is only found in euokaryotic cells, while prokaryotic cells have a very different organization of their DNA which is referred to as a genophore (a chromosome
without chromatin).

The structure of chromatin depends on several factors. The overall structure depends on the stage of the cell cycle: during interphase the chromatin is structurally loose to allow access to RNA and DNA polymerases that transcribe and replicate the DNA. The local structure of chromatin during interphase depends on the genes present on the DNA: DNA coding genes that are actively transcribed ("turned on") are more loosely packaged and are found associated with RNA polymerases (referred to as euchromatin) while DNA coding inactive genes ("turned off") are found associated with structural proteins and are more tightly packaged (heterochromatin). Epigenetic chemical modifications of the structural proteins in chromatin are responsible for the tightness of the DNA packaging and therefore they control gene expression. These modifications include primarily methylation and acetylation of histone proteins. As the cell prepares to divide, i.e. enters mitosis or meiosis, the epigenetic modifications of the chromatin make DNA packaging tighter to facilitate segregation of the chromosomes during anaphase. During this stage of the cell cycle this makes the individual chromosomes in many cells visible by optical microscope. [1]

There are three levels of chromatin organization; Euchromatin, Heterochromatin and higher level DNA packaging. When DNA wraps around histone proteins forming a structure known as nucleosome it is called euchromatin.
However, when multiple histones wrap into a fibre consisting of nucleosome arrays in their most compact form it is known as heterochromatin. The Higher-level DNA packaging represents the most compact form of DNA packaging and it occurs mainly during the metaphase of cell division to form chromosomes (metaphase chromosome). Heterochromatin is highly condensed, gene-poor, and transcriptionally silent, whereas euchromatin is less condensed, gene-rich, and more easily transcribed. Nucleosome modifications distinguish heterochromatin from euchromatin. Euchromatin is typically enriched in acetylated histones H3 and H4 and H3K4 methylation (H3K4me) (which all are transcription activators),
whereas heterochromatin is characterized by hypoacetylation of histones, H3K9me, association of heterochromatin protein-1 (HP1), and DNA cytosine methylation (5mC) (which are transcriptional repressors). It is usually stated that heterochromatin structure is more compact than euchromatin making the interaction of regulatory factors with their DNA targets difficult. However, very recently an interaction of general transcription factors with heterochromatin was shown (Morales, etal., 2001).

It appears that the three levels of chromatin organizations are based mainly on the formation of nucleosomes. Thus we will talk a bit more about the nucleosomes.

Nucleosomes

The nucleosome is the basic unit of an eukaryotic
chromosome, consisting of 146 base pairs (bp) of DNA coiled around a core consisting of a histone octamer, H2A, H2B, H3, and H4. Histones H3 and H4 form a dimer, two H3-H4 dimers associate into a (H3-H4)2 tetramer. DNA wraps around this tetramer, forming a tetrameric particle. Histones H2A and H2B heterodimerize and heterodimers associate on each side of the tetrameric particle to form a nucleosome (Fig 3). In addition to the core histones, there is the linker histone, H1, which contacts the exit/entry of the DNA strand on the nucleosome. Nucleosomes are interconnected by sections of linker DNA, a far shorter arrangement than pure DNA in solution. Nucleosomes are organized forming a simple helix or solenoid with 6 nucleosomes per turn (Fig. 1), in which the linker DNA is folded between consecutive nucleosomes
(Daban, etal., 2011). The nucleosomes bind DNA non-specifically, as required by their function in general
DNA packaging. There are, however, large DNA sequence preferences that govern nucleosome positioning. Nucleosomes can be positioned on the DNA either precisely or randomly (Fig 4). Nucleosome positioning on the DNA has direct consequences on the accessibility of DNA regulatory sequences to cognate regulators ((Morales, et al., 2001; Daban, et al., 2011).

Nucleosome modulation

The nucleosome structure can be modulated by the substitution of one of the histones for a variant counterpart. The most studied are the centromeric histone H3-variant CENP-A , histone H2A.Z found in the active chromatin and histone H2AX that is phosphorylated in response to DNA
double strand breaks




















Fig1. (Daban, etal., 2011).



Fig2 : Selenoid shape






Fig3 (Morales, etal., 2001)


Fig 4: nucleosome positioning (((Morales, etal., 2001).