Eukaryotic Nuclear Genomes Genomics Eukaryotic Nuclear Genomes

The haploid human genome contains approximately 3 billion base pairs of DNA packaged into 23 chromosomes. That makes a total of 6 billion base pairs of DNA per diploied cell. Because each base pair is around 0.34 nanometers long, each diploid cell therefore contains about 2 meters of DNA [(0.34 × 10-9) × (6 × 109)]. Moreover, it is estimated that the human body contains about 50 trillion cells—which works out to 100 trillion meters of DNA per human. Now, consider the fact that the Sun is 150 billion meters from Earth. This means that each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth's equator 2.5 million times! How is this possible?

Nuclear Genomes are Contained in Chromosomes The nuclear genome is split into a set of linear DNA molecules, each contained in a chromosome The only variability at this level of eukaryotic genome structure lies with chromosome number, which appears to be unrelated to the biological features of the organism.

Figure 7.1 Genomes 3 (© Garland Science 2007)

Figure 7.2a Genomes 3 (© Garland Science 2007)

Figure 7.2b Genomes 3 (© Garland Science 2007)

Figure 7.2c Genomes 3 (© Garland Science 2007)

The solenoid model (A) has been in favor for several years but recent experimental evidence supports the helical ribbon (B). Figure 7.3 Genomes 3 (© Garland Science 2007)

Chromosomes Are Most Compacted During Metaphase Figure 7.4 Genomes 3 (© Garland Science 2007)

Table 7.1 Genomes 3 (© Garland Science 2007)

Figure 7.5 part 1 of 3 Genomes 3 (© Garland Science 2007)

Figure 7.5 part 2 of 3 Genomes 3 (© Garland Science 2007)

Figure 7.5 part 3 of 3 Genomes 3 (© Garland Science 2007)

Minichromosomes Minichromosomes are relatively short in length but rich in genes The chicken genome is split into 39 chromosomes: six macrochromosomes containing 66% of the DNA but only 25% of the genes and 33 minichromosomes containing the remaining one-third of the genome and 75% of the genes. The gene density in the minichromosomes is therefore some six times greater than that in the macrochromosomes.

B chromosomes B chromosomes (also known as supernumerary or accessory chromosomes) are additional chromosomes possessed by some individuals in a population, but not all They are common in plants and also known in fungi, insects, and animals.

Holocentric chromosomes Holocentric chromosomes do not have a single centromere but instead have multiple structures spread along their length. The nematode worm Caenorhabditis elegans has holocentric chromosomes

DNA–protein interactions in centromeres and telomeres Arabidopsis centromeres span 0.9–1.2 Mb of DNA and each one is made up largely of 180 bp repeat sequences. In humans the centromeric DNA sequences are 171 bp in length and are called alphoid DNA, with 1500–30,000 copies per centromere

DNA–protein interactions in centromeres and telomeres Centromere of Saccharomyces cerevisiae is defined by a single sequence, approximately 125 bp in length. Figure 7.6 Genomes 3 (© Garland Science 2007)

Figure 7.7 Genomes 3 (© Garland Science 2007)

Figure 7.8 Genomes 3 (© Garland Science 2007)

Mammalian centromeres contain CENP-A- and H3-nucleosomes. One possibility is that the H3-nucleosomes are located mainly in the central core of the centromere, with the CENP-A versions forming an outer shell onto which the kinetochore is constructed. Figure 7.9 Genomes 3 (© Garland Science 2007)

Telomeric DNA is made up of hundreds of copies of a repeated motif, 5ʹ–TTAGGG–3ʹ in humans, with a short extension of the 3ʹ terminus of the double-stranded DNA molecule Two special proteins (TRF1, TRF2) bind to the repeat sequences in human telomeres.

Telomers This sequence of TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kbp at birth to less than four Kbp in old age, with average rate of decline being greater in men than in women.

Where are the genes in a nuclear genome? Gene density along the largest of the five Arabidopsis thaliana chromosomes. The density varies from 1 to 38 genes per 100kb Figure 7.11 Genomes 3 (© Garland Science 2007)

Figure 7.12 Genomes 3 (© Garland Science 2007)

Figure 7.13 Genomes 3 (© Garland Science 2007)

Figure 7.14 Genomes 3 (© Garland Science 2007)

Table 7.2 Genomes 3 (© Garland Science 2007)

C-value paradox Single-celled amoebae have some of the largest genomes, up to 100-fold larger than the human genome. C-value paradox is the complex puzzle surrounding the extensive variation in nuclear genome size among eukaryotic species.

Figure 7.15 Genomes 3 (© Garland Science 2007)

Table 7.3 Genomes 3 (© Garland Science 2007)

How many genes are there and what are their functions? Table 7.4 Genomes 3 (© Garland Science 2007)

The pie chart shows a categorization of the identified human protein-coding genes. Figure 7.16 Genomes 3 (© Garland Science 2007)

Genes are categorized according to their function, as deduced from the protein domains specified by each gene Figure 7.17 Genomes 3 (© Garland Science 2007)

Table 7.5 Genomes 3 (© Garland Science 2007)

Figure 7.18 Genomes 3 (© Garland Science 2007)

Families of genes every eukaryote that has been studied has multiple copies of the genes for the ribosomal RNAs. Figure 7.19 Genomes 3 (© Garland Science 2007)

Pseudogenes and other evolutionary relics conventional pseudogene processed pseudogene

Figure 7.20 Genomes 3 (© Garland Science 2007)

Figure 7.21 Genomes 3 (© Garland Science 2007)

Figure 7.22 Genomes 3 (© Garland Science 2007)

Figure 7.23 Genomes 3 (© Garland Science 2007)