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Chapter 7

Genome Organization
and Expression

7.1 Genes and chromosomes
7.2 Nuclear genome organization
7.3 Transposable elements
7.4 Gene expression
7.5 Role of chromatin in chromosome organization and gene expression
7.6 Epigenetic mechanisms of gene regulation

Robert Ferl
Anna-Lisa Paul




The essence of every characteristic of a species, from morphology to timing of senescence, resides in information stored in the species’ DNA: its genome. All of that information, encoded in thousands of genes in even simple organisms, requires some sort of organization. In eukaryotes, the first level of organization is the chromosome (Fig. 7.1). With so many genes and so few chromosomes (five, for example, in Arabidopsis), a vast array of genes must reside on any one chromosome. How all of these genes are organized is an important question of molecular genetic research. This chapter will focus on the informational organization of the genes within chromosomes. Our current understanding of genome organization and expression reflects the capabilities and limitations of widely varied current technologies. Merging the data from these technologies into a complete picture of genome structure is a major research goal. Most of an organism’s genes reside on nuclear DNA. However, plastids and mitochondria also contain DNA that encodes some of the gene products required for organelle function and reproduction. Several traits encoded by organelle genes are in commercial use in plant crops, such as cytoplasmic male sterility in sorghum and maize. Traits arising from organelle genes can be clearly recognized by their uniparental inheritance patterns, because in many species mitochondria and chloroplasts are inherited only through the maternal contribution to the seed. In the 1950s, plant geneticists found evidence that pieces of genetic material could move from place to place in the DNA. These mobile genetic elements were subsequently found to be ubiquitous components of genomes, providing the possibility for genomic changes on a larger scale than the accumulation of single-point mutations and thereby speeding evolutionary change. Our examination of genome organization and genetic regulation begins with a historical perspective and proceeds to a state-of-the-art view of the function of single genes (Fig. 7.2). The historical perspective conveys the development of genetic theory and illustrates the continued value of “classic” approaches. However, our ability to characterize the chromosome and the genes contained therein with increasingly finer resolution has developed tremendously since the time of Mendel. Elucidating the workings of genetics has been, and continues to be, one of the most fruitful of biological disciplines, changing the way we view our world and think about ourselves as biological organisms. In 1958 George Beadle, Joshua Lederberg, and Edward Tatum were awarded the Nobel Prize for their work in gene regulation. Since then, almost half of all the Nobel Prizes awarded for Chemistry and Medicine or Physiology have been for innovations in our understanding of genetics and gene regulation.

Figure 7.1
Electron micrograph of a metaphase chromosome, showing the structure of a chromosome in its most compact state. C, centromere.

Figure 7.2
Levels of genetic and molecular organization: Chromosomes (especially those in metaphase) can be characterized by structural features, such as the position of the centromere, and by banding patterns seen in the presence of certain cytological dyes. A genetic map can be created for a chromosome by assigning genes to their relative positions on that chromosome. Smaller sections of the genome can be precisely ordered into a physical map by using molecular tools such as restriction fragment length polymorphism (RFLP) analyses (see Fig. 7.18). Individual genes within the physical map can be analyzed as to their specific sequence of nucleotides by using DNA sequencing (not shown). Functional analyses evaluate the importance of certain sequence features to the transcriptional regulation of that gene (see Box 7.5).

© Copyright American Society of Plant Biologists 2013 (All Rights Reserved)