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Chapter 7

Genome Organization
and Expression

 
The characteristics of an organism are encoded in its DNA. In the eukaryotic nucleus, most of this information resides within thousands of genes and is organized into linear chromosomes. A few genes are also encoded by DNA found in plant mitochondria and plastids. The entirety of this genetic material is referred to as an organism’s genome. The study of the organization and regulation of the nuclear genome is the fundamental basis for genetic and molecular genetic research. In the 1850s Gregor Mendel developed the science of genetics by proposing that particular factors (now called genes) gave rise to specific traits. Mendel’s pea experiments were the first to correlate physical traits (phenotype) with heritable components (genotype). About 50 years after Mendel’s work, genes were postulated to reside on chromosomes in the nucleus; it took another 50 years for scientists to identify the molecule responsible for transmitting genetic information, deoxyribonucleic acid (DNA). During the century after Mendel, elucidation of the organization of the nuclear genome included the discovery that genes are aligned on chromosomes and can be inherited in linkage groups and, moreover, that genetic recombination within a linkage group plays a role in the generation of new phenotype combinations. The analysis of genetic recombination also gave rise to the ability to map genes to their relative positions in a chromosome. The role of a gene is to encode a product that contributes to the phenotype of that organism; often, however, only a small percentage of an organism’s genome actually encodes gene products. The intervening and flanking noncoding sequences are integral parts of a typical gene and contribute to some of the diversity in genome size observed among similar organisms. The intervening sections of noncoding DNA are called introns, and the sections of coding sequence are referred to as exons. In addition, repetitive noncoding DNA sequences contribute to the character and function of specialized structures in chromosomes such as the centromere and telomere. Another specialized class of DNA sequence that can make up a significant portion of the genome is the transposable elements. Transposable elements of sections of DNA move, or transpose, from one site in the genome to another, carrying genetic information with them as they transpose. Not all genes of a nuclear genome are expressed all the time. Selective expression gives rise to cellular differentiation during development and enables cells to respond to environmental signals accordingly. Genes are divided into two fundamental regions. The coding region is transcribed into the gene product, and the regulatory region contains a variety of sequence elements that function in the recruitment of protein transcription factors, which facilitate transcription. Another feature of the genome that plays a role in the selective expression and regulation of genes is the chromatin structure associated with a given gene. Chromatin refers to the complex of DNA and protein that makes up the chromosome and organizes the genome within the nucleus. In addition to these large-scale roles, the fine-scale features of chromatin influence gene regulation by manipulating the accessibility of a gene promoter to the factors required for initiating transcription.

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