# Structural Biochemistry/Control of Gene Expression in Eukaryotes

The Control of Gene Expression in Eukaryotes
    Chromatin are a combination of eukaryotic DNA and histones. The eukaryotic DNA binds tightly to the histones, which are basic proteins. Changes in the structure of chromatin are largely responsible for the regulation of gene expression. Other regulators of gene expression include interactions between proteins and translation.
    In Eukaryotes, as compared to prokaryotes, gene regulation is a lot more complex. This is because the Eukaryotic genome is a lot larger and therefore encodes for a lot more proteins. There are also many different types of cells in eukaryotes, such as liver cells, pancreatic cells, and etc. The genes that are in these highly specialized cells have a huge difference in expression. Another reason for the complexity is that eukaryotic genes that encode proteisn are usually spread throughout the enormously large genome. The final reason is that eukaryotic transcription and translation are not coupled, and this negates some of the gene regulation mechanisms that prokarotes utilize.
Chromatin Structure
    Chromatin is composed of units that repeat. Each of these units are composed of 200 base pairs of DNA, and two copies each of the four histones H2A, H2B, H3, and H4. This unit is called the histone octomer, and the repeating units are referred to as nucleosomes. The five main histones present in chromatin are H2A, H2B, H3, H4, and H1, but H1 is not part of the histone octomer. Each histone also has a flexible amino tail that have various lysine and arginine residues and extends beyond the core. These tails are very important because covalent modifications of them alter the DNA affinity of the histones. When chromatin is digested, it yields only 145 base pairs of DNA binding to the histone octomer, and this smaller unit is called the nucleosome core particle. The DNA that connects these nucleosome core particles in undigested chromatin is referred to as linker DNA. This is where H1 binds.
    The three dimensional structure of the nucleosome is composed of eight histones arranged into a tetramer, and a pair of dimers. When the tetramer comes together with the dimers, they form a superhelical ramp that is left-handed, and DNA wraps around it forming a left-handed superhelix. The contact between the superhelical ramp and the DNA superhelix occurs primarily along the phosophodiester backbone and minor groove of the DNA. The winding of this DNA reduces its length by packing it together very tightly.
Chromatin Remodeling
    The DNA adjacent to actively transcribed genes in chromatin are more sensitive to being cleaved, indicating that those sites contain less compact DNA. Additionally, some other sites, usually within proximity to the start of an actively transcribed gene, are also more sensitive to cleavage by nucleases. These sites are referred to as hypersensitive sites, and they either have fewer nucleosomes, or nucleosomes that are in an altered conformation. These hypersensitive sites specific to different cell types and are developmentally regulated. This indicates that a prerequisite for gene expression lies within chromatin.
    Chromatin structure differs between active and inactive genes, and this indicates that some form of modification must be done to modify chromatin structure. Enhancers are DNA sequences that increase the activity of many promoters, even when they are thousands of base pairs away. Enhancers work by binding certain regulatory proteins, and they are only effective in the unspecific type of cell that express those regulatory proteins. These proteins may disrupt chromatin structure, exposing a gene and/or regulatory sites and thus influence transcription. This accounts for its ability to function at a distance from the gene being expressed.
DNA Modification
    Gene expression can be inhibited by modifying DNA. This conclusion was drawn by studying sequences in the mammalian genomes. Lots of sequences in mammalian genomes have cytosines that are methylated at the C5 carbon. These cytosines have differing distribution throughout the genome depending on cell type.
Transcriptional Activation and Repression
    Interactions between proteins mediate much transcriptional activation and repression. Eukaryotic transcription factors recruit proteins, which build large complexes that interact with and thus activate or repress transcription. This type of regulation is extremely advantageous because depending on the different proteins present in the cell, the regulation can have different effects. This is referred to as combinatorial control, and it is responsible for generating different types of cells.
    Hormone receptors on the nucleus recruit various proteins to the transcription complex. These proteins are generally coactivators and corepressors. Coactivators are proteins that contain three repeated sequences within a central region of 200 amino acids. The repeated sequence is Leu-X-X-Leu-Leu, where X can be any amino acid, and they form short alpha helices that bind to the hormone receptors on the nucleus, inducing a change in conformation that enables the receptors to recruit the entire coactivator. Corepressors repress transcription. Sometimes repression can be done without binding a ligand, such as the receptors for retinoic acid and thyroid hormone. When unbound, the receptors bind to corepressors. The site in which the corepressor binds overlaps with the binding site for the coactivator and thus serves to repress transcription.
So What?
    Tamoxifen and raloxifene are drugs used in the treatment of breast cancer. Tamoxifen inhibits the activation of gene expression by blocking coactivators from binding. This is important because cancer is such a prevalent disease in today's society, and by studying and understanding the mechanisms of gene activation and repression, new drugs can be produced to combat the disease by altering gene expression.
Source: Berg, Jeremy and Stryer, Lubert. Biochemistry: Fifth Edition. United States of America: W.H. Freeman and Company, 2002.