1. Chapter 2 Genome Organization and Evolution Dr Achraf El Allali

2. Genes ● A gene is the basic physical and functional unit of heredity. ● Genes, which are made up of DNA, act as instructions to make proteins – DNA which codes for functional RNA? – Control regions?

3. Gene organization ● A gene may occur on either strand of DNA ● Genes are continuous stretches (almost always) in prokaryotes ● Genes are (often) discontinuous stretches (exons) in eukaryotes. The intervening regions are called introns ● Upstream is a binding site ● Location of regulatory region is less predictable

4. The Central Dogma ● One gene, one protein ● Like most dogmas, not entirely true ● Alternative splicing permits the manufacture of many products from a single gene ● The protein products are sometimes called the proteome ● With current technology, more gene information is available than protein information

5. Transmission of information ● How hereditary information is stored, passed on, and implemented is considered a fundamental problem is biology. ● Three types of maps are essential: – Linkage maps of genes – Banding patterns of chromosomes – DNA sequences

6. Gene maps ● Gene maps help describe the spatial arrangement of genes on a chromosome. ● Genes are designated to a specific location on a chromosome known as the locus and can be used as molecular markers to find the distance between other genes on a chromosome. ● Maps provide researchers with the opportunity to predict the inheritance patterns of specific traits

7. Chromosome banding pattern maps ● Chromosomes are identified by the banding patterns revealed by different staining techniques.

8. DNA sequence ● Physically a sequence of nucleotides in the molecule, ● Computationally a string of characters: A, T, G, and C ● Genes are regions of the sequence, in many cases interrupted by noncoding regions

9. High-resolution maps ● Variable number tandem repeats (VNTRs – minisatellites), 10-100 bp, are a sort of genetic fingerprint ● Short tandem repeat polymorphisms (STRPs – microsatellites), 2-5 bp, are another kind of marker ● A contig is a series of overlapping DNA clones of known order along a chromosome from an organism ● A sequence tagged site (STS), 200-600 bp, is a known unique location in the genome

10. Identifying genes ● Open Reading Frames (ORF) is a region of DNA that begins with an initiation codon and ends with a stop codon. ● An ORF is a potential gene ● Gene finding techniques are based on one or a combination of the following: – Similarity to known genes – Properties of the DNA sequence itself (ab-initio approaches)

11. Prokaryote genomes ● Genetic material of the cell takes the form of a large single circular piece of double stranded DNA. Example: E. coli 4,639,211 pb ● 89% coding ● 4,285 genes ● 122 structural RNA genes ● Prophage remmants ● Insertion sequence elements ● Horizontal transfers

12. Metagenome ● Genetic information of an entire environmental sample ● DNA is extracted directly from the environment using Next Generation Sequencing ● Determine the sequences directly from a sample without culturing individual strains ● Provide information about species that cannot be cloned in the traditional way

13. Eukaryotic genome ● The full genetic information in a eukaryotic cell ● Example: C. elegans ● 10 chromosomes ● 19,099 genes ● Coding region – 27% ● Average of 5 introns/gene ● Both long and short duplications

14. Human Genome Project ● At the height of the Human Genome Project, sequencing factories were generating DNA sequences at a rate of 1000 nucleotides per second 24/7. ● Technical breakthroughs that allowed the Human Genome Project to be completed have had an enormous impact on all of biology….. Molecular Biology Of The Cell. Alberts et al. 491-495

15. Human Genome Project Goals: ■ identify all the approximate 30,000 genes in human DNA, ■ determine the sequences of the 3 billion chemical base pairs that make up human DNA, ■ store this information in databases, ■ improve tools for data analysis, ■ transfer related technologies to the private sector, and ■ address the ethical, legal, and social issues (ELSI) that may arise from the project. Milestones: ■ 1990: Project initiated as joint effort of U.S. Department of Energy and the National Institutes of Health ■ June 2000: Completion of a working draft of the entire human genome (covers >90% of the genome to a depth of 3-4x redundant sequence) ■ February 2001: Analyses of the working draft are published ■ April 2003: HGP sequencing is completed and Project is declared finished two years ahead of schedule U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org http://www.sanger.ac.uk/HGP/overview.shtml

16. What does the draft human genome sequence tell us? By the Numbers The human genome contains 3 billion chemical nucleotide bases (A, C, T, and G). The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases. The total number of genes is estimated at around 30,000--much lower than previous estimates of 80,000 to 140,000. Almost all (99.9%) nucleotide bases are exactly the same in all people. The functions are unknown for over 50% of discovered genes. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

17. What does the draft human genome sequence tell us? How It's Arranged The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C. In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes. Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between. Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the "junk DNA." These CpG islands are believed to help regulate gene activity. Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231). U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

18. What does the draft human genome sequence tell us? The Wheat from the Chaff Less than 2% of the genome codes for proteins. Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome. Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, creating entirely new genes, and modifying and reshuffling existing genes. The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%). U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

19. What does the draft human genome sequence tell us? How the Human Compares with Other Organisms Unlike the human's seemingly random distribution of gene-rich areas, many other organisms' genomes are more uniform, with genes evenly spaced throughout. Humans have on average three times as many kinds of proteins as the fly or worm because of mRNA transcript "alternative splicing" and chemical modifications to the proteins. This process can yield different protein products from the same gene. Humans share most of the same protein families with worms, flies, and plants; but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity. Although humans appear to have stopped accumulating repeated DNA over 50 million years ago, there seems to be no such decline in rodents. This may account for some of the fundamental differences between hominids and rodents, although gene estimates are similar in these species. Scientists have proposed many theories to explain evolutionary contrasts between humans and other organisms, including those of life span, litter sizes, inbreeding, and genetic drift. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

20. What does the draft human genome sequence tell us? Variations and Mutations Scientists have identified about 3 million locations where single-base DNA differences (SNPs) occur in humans. This information promises to revolutionize the processes of finding chromosomal locations for disease-associated sequences and tracing human history. The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. Researchers point to several reasons for the higher mutation rate in the male germline, including the greater number of cell divisions required for sperm formation than for eggs. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

21. What does the draft human genome sequence tell us? ● Led to the discovery of whole new classes of proteins and genes, while revealing that many proteins have been much more highly conserved in evolution than had been suspected. ● Provided new tools for determining the functions of proteins and of individual domains within proteins, revealing a host of unexpected relationships between them. Molecular Biology Of The Cell. Alberts et al. 491-495

22. What does the draft human genome sequence tell us? ● By making large amounts of protein available, it has yielded an efficient way to mass produce protein hormones and vaccines ● Dissection of regulatory genes has provided an important tool for unraveling the complex regulatory networks by which eukaryotic gene expression is controlled. Molecular Biology Of The Cell. Alberts et al. 491-495

23. How does the human genome stack up? OrganismGenome Size (Bases)Estimated Genes Human (Homo sapiens)3 billion30,000 Laboratory mouse (M. musculus)2.6 billion30,000 Mustard weed (A. thaliana)100 million25,000 Roundworm (C. elegans)97 million19,000 Fruit fly (D. melanogaster)137 million13,000 Yeast (S. cerevisiae)12.1 million6,000 Bacterium (E. coli) 4.6 million3,200 Human immunodeficiency virus (HIV) 97009 http://doegenomes.org

24. Gene number, exact locations, and functions Gene regulation DNA sequence organization Chromosomal structure and organization Noncoding DNA types, amount, distribution, information content, and functions Coordination of gene expression, protein synthesis, and post-translational events Interaction of proteins in complex molecular machines Predicted vs experimentally determined gene function Evolutionary conservation among organisms Protein conservation (structure and function) Proteomes (total protein content and function) in organisms Correlation of SNPs (single-base DNA variations among individuals) with health and disease Disease-susceptibility prediction based on gene sequence variation Genes involved in complex traits and multigene diseases Complex systems biology including microbial consortia useful for environmental restoration Developmental genetics, genomics Future Challenges: What We Still Don’t Know U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

25. Evolution of genomes ● Adaptation of species is coterminous with adaptation of genomes ● Where do genes come from? (Answer: from other genes) ● Homologs and paralogs ● Lateral transfer ● Molecular species each have their own family tree ● Genes are widely shared

26. Close relatives ● Yeast, fly, worm and human share at least 1308 groups of proteins ● Unique to vertebrates: immune proteins (for example) ● Unique molecules are adapted from ancient molecules of different purpose but similar design ● Most new proteins come from domain rearrangement ● Most new species come from control region variation