1. BCM302 Food Biotechnology
Topic 9: Genomics and Beyond

2. Learning objectives
After studying this chapter in the text, the student should be able to:
1. List and define the goals of genomics.
2. Be able to compare genetic linkage maps, cytological maps, and physical maps in terms of their resolution and how they are constructed.
3. List and define the types of physical maps.
4. Know the findings obtained from the Human Genome Project.
5. Be familiar with how the Human Genome Project has impacted the compiling of genomic information from other organisms, as well as the potential applications of this new information.
7. Know how the Human Genome Project has spawned functional genomics and proteomics, and studies of other “-omes.”
8. List and define bioinformatics, the tools of bioinformatics, and be familiar with various applications of bioinformatics.

3. Introduction to Genomics
Genomics is a scientific field involving the determination of the content, organization, and evolution of the genomes of different organisms.
Genomics is closely related to bioinformatics, which uses computers, computational tools, and databases to organize and analyze DNA and protein information.

4. Goals of genomics
1. The assembly of physical and genetic maps of the genomes of different organisms.
2. The compilation and organization of both expressed gene sequences and other non-expressed regions.
3. The generation of gene expression (that is, transcription, or the production of transcripts) profiles under different conditions.
4. Finding the location of all genes in a genome and annotating each gene.
5. The determination of gene function and regulation (functional genomics).

5. Goals of genomics (cont.)
6. The identification of all proteins in a genome and their functions, including the detection of protein–protein interactions (called “proteomics”).
7. The characterization of DNA polymorphisms within the genomes of a species.
8. The comparison of genes and proteins in the genome of one species with genomes of other species (called “comparative genomics”).
9. The implementation and management of databases and genome-based research tools accessed through the Internet.

6. Maps
Genetic linkage maps: determine the relative arrangement and approximate distances between markers on the chromosomes.
Physical maps determine the physical location on the chromosomes in base pairs, and the distance between genes or DNA fragments with unknown functions.

7. Genetic Linkage Maps
Show the order and distance between pairs of linked genes, located on the same chromosome.
Determine the arrangement of genes or markers with unknown functions on a chromosome based on how often two genes on the same chromosome are to be involved in crossing over,
Crossing over: exchange of genetic information between pairs of chromosomes during prophase I of meiosis
Two genes are measured and given distances in centimorgans (cM).
eg, if two genes were involved in crossing over 1% of the time, then the distance between the two genes would be one cM. One cM is about one million base pairs (one megabase)

8. Cytological maps
Helps to align the genetic linkage map with the more specific physical map.
Involves the banding pattern of a chromosome through karyotyping, which is the staining of chromosomes and viewing them with a microscope
Used to diagnose human genetic diseases caused by chromosomal abnormalities such as Down syndrome.

9. Fluorescence in situ hybridisation (FISH)
Metaphase chromosomes spread on a microscope slide.
Fluorescent-tagged DNA probe is added
Probe attaches to the chromosome and viewed with a fluorescence microscope
Sometimes used to locate genetic markers associated with observable traits.

10. Physical maps
Involve the assembly of contiguous stretches of DNA (“contigs”) where distances between landmark DNA sequences are shown in kilobases
Provide information about the physical organization of the piece of DNA (eg restriction enzyme sites)
Ultimate physical map is the complete DNA sequence of the genome, (about 3 billion bp in length in humans).

11. Genome fragments
Because many genomes are large, the DNA has to be cut into fragments and cloned:
Yeast artificial chromosomes (YACs): pieces of between 300,000 and 400,000 bp long.
Bacterial artificial chromosomes (BACs): pieces of DNA of up to 200,000 bp in length.

12. cDNA maps cDNA maps can also be generated:
Localizes coding regions to specific chromosome regions or bands.
Identifies the chromosomal location of specific genes

13. “Shotgun” mapping
Genome is cut into small, overlapping fragments with a restriction enzyme, and each piece is cloned, forming a DNA library.
Computers assemble the fragments into contigs by determining which DNA pieces have bands that are common.
Unique regions of DNA can also be used to identify contigs, called “sequence-tagged sites” (STSs), which are used as probes.

14. Map Resolution Genetic linkage map. Restriction map YAC clones
Contig. maps.
DNA sequence.
Lowest Res.
Highest Res.

15. Human Genome Project
1994—first high-resolution physical map for the human genome was published.
2001—the public human genome sequence draft was published.
2003—close to 99.9% of the gene-containing portion of the human genome was sequenced to 99.9% accuracy.

16. Potential uses for Genome Info.
Provide the location and identification of all the genes and other components of the human genome.
Increase understanding of human evolution, variation, gene regulation, development, and human disease.
Lead to new treatments and diagnostic methods.
Increased emphasis on fields such as genetic counseling.
Development of new technologies to analyze genome-related information.

17. Clone-by-clone approach
A public group, National Center for Human Genome Research, used a clone-by-clone sequencing approach.

18. “Shotgun” seq. approach
A private group, Celera Corporation, used a “shotgun” sequencing approach.

19. HGP findings
The human genome contains a little more than three billion base pairs ( million nucleotides).
The number of genes found was close to 1/3 of the expected number of genes in the genome (30,000–40,000 protein-encoding genes rather than the predicted 80,000–100,000).
Only approximately 1.5% of the human genome encodes for the production of proteins.
Repeated sequences that do not encode proteins make up at least 50% of the genome—they are thought to affect chromosome structure and dynamics.
The average length of a gene is 3000 nucleotides, although sizes vary greatly.

20. HGP findings (cont.)
Genes are not evenly distributed across a chromosome;
Gene-dense areas are composed primarily of G- and C- containing nucleotides.
Gene-poor regions have more A- and T- containing nucleotides.
The Y chromosome has the fewest genes (231),
Chromosome 1 has the most genes of all the chromosomes (2968).
Approximately 200 genes originated directly from bacteria.
Human proteins are more complex than proteins with similar functions in lower organisms.
The germline mutation rate in males is two times higher than in females.
The nucleotide sequence in all humans is 99.9% identical.
More than 50% of newly discovered genes have unknown functions.

21. Comparative genomics
Nonhuman genomes provide information about gene organization, function, and evolution.
Many organisms retain similar DNA sequences throughout evolution, and humans share many genes with other organisms

22. Other Genomes
Genes spaced more evenly throughout the genome than in humans.
Humans have, on average, three times as many kinds of proteins as the fruit fly or nematode worm because of alternative splicing of pre-mRNA.
Humans share most of the same protein families with worms, flies, and plants, but the number of members (individual genes) within gene families has increased in humans, especially for those proteins involved in development and immunity.
The human genome has a much greater proportion of repeat sequences—50%—than the plant Arabidopsis (11%), nematode worm Caenorhabditis (7%), and fruitfly Drosophila (3%).
Although humans appear to have stopped accumulating repeated DNA, there does not seem to be a decrease in accumulation in mice.

23. Mouse and other animals
Mice are used as human disease models, and mice have many features and genes in common with humans.
Researchers focus on identifying regions of conservation (similarities) between mouse and human genomes.
Genomes from other animals such as pigs and cows are now being studied for animal breeding, disease prevention, and evolution modeling.
Much of the genome information will be in the form of high-resolution genetic maps, ESTs, and polymorphic DNA data such as SNPs.
There are DNA databases for other organisms, such as the ArkDB, National Animal Genome Research (NAGRP), PigBase, and the Fred Hutchinson Cancer Research Center Dog Genome Project.

24. Invertebrates
The first two organisms to be sequenced were the fruit fly Drosophila melanogaster and the nematode worm Caenorhabditis elegans.
Because the genes in the organisms can be readily mutated, the functions of the genes can be identified
Nematode genomes are also be important in agriculture because the worms are involved in crop damage.

25. Plants
The first plant genome to be sequenced was Arabidopsis thaliana in 2000.
Rice, wheat, soybean, and corn are other plants that provide valuable information for crop-breeding plants.
Genes may code for enzymes for unique metabolic pathways that may have biotechnological applications, such as:
The production of secondary metabolites.
Plant cell wall synthesis.
Photosynthesis.
Pathogen resistance.

26. Microorganisms
Have evolved many different metabolic pathways to adapt to different places.
Three of the first bacterial genomes to be sequenced were Mycoplasma genitalium, Haemophilu influenzae, and Methanococcus janschii.

27. Yeast
A better understanding of the genomes of important parasite vectors
The accumulation of polymorphism data to gain insight into the genome diversity of specific parasites.
The identification of species-specific genes that may lead to new vaccines.
A better understanding of parasite life cycles and points in the cycle that may be effective targets for drugs.

28. Other genome sizes

29. Genome sequencing organisations
TIGR: The institute for Genome Research

30. Functional genomics
Once a DNA sequence is determined, the function must also be determined.
Molecular biology, genetics, biochemistry, recombinant DNA technology, and computational biology are used to fully characterize the biochemical, metabolic activity, cell and physiological function of genes.

31. Functional Genomics

32. Unknown functions
Exact locations and functions of all the genes in the genome.
How genes are regulated.
How chromosomes are organized.
The roles of DNA that doesn’t code for proteins.
How proteins interact with each other.

33. Proteome and Proteomics
After identifying the genes in the genome, the next step is to determine the protein complement of the genome, which is called the “proteome.”
Proteomics involve the following aspects:
The expression and identification of proteins in a given cell.
The structure of proteins (for example, tertiary folding).
How proteins interact with each other in the cell.
Listing proteins in computer databases.

34. Proteome and Proteomics
Proteomics better provides the tools to understand complex protein pathways and interpretations of metabolic responses to mutations.
Proteomics is difficult because each cell type has the same DNA complement, but a different proteome.
The proteome can change depending on the physiological state of the cell or the organism.

35. Other “-omes”
Transcriptome—full complement of genes called “transcripts” that are made in a specific cell type under a specific set of conditions, revealing changes in transcription for every gene in the genome.
Metabolome—entire metabolic state of a cell, including the array of substrates, metabolites, and other small molecules that are made in different cells and tissues.

36. Bioinformatics
Incorporates biology, computer science, and information technology.
Computational biology is a field within bioinformatics that involves the process of analyzing and interpreting collected data.

37. Bioinformatics
Tools that allow the efficient access and management of databases.
Analysis of the large amount of DNA and protein sequences being generated.
Molecular biology and computer science tools are used for gene identification, to help predict protein structure and function, to identify functional domains of proteins, and to conduct evolutionary analysis of genes and proteins.

38. Databases
Computerized body of data that allows someone to retrieve specific pieces of information.
They can be on the Internet, searchable, and updated daily.
An example of a DNA database is GenBank,
hosted at the National Center for Biotechnology Information (NCBI),
a searchable database located on the Internet at

39. Databases (cont.)
Researchers can obtain information about sequences and the species that the sequences were obtained from.
Other databases include the European Molecular Biology Laboratory (EMBL) and the DNA DataBank of Japan (DDBJ).

40. Examples of Bioinformatics tools
Retrieval of DNA and protein sequences from databases.
Database searches for similar DNA and protein sequences.
Sequence alignment for comparison—both global and local regions (two or more sequences).
Prediction of RNA secondary structure

41. Examples of Bioinformatics tools
Protein classification (amino acid patterns, motifs, functional domains, structural features, prediction of function) and prediction of protein secondary structure
Evolutionary relationships using DNA and protein sequences (phylogenetic prediction or production of phylogenetic trees).
Gene prediction using DNA sequences—finding open reading frames (ORFs), promoters, searching for special sequence motifs.
Genome analysis tools such as genome and sequence databases.

42. ANGIS Australian National Genomic Information service
Collection of DNA/Protein databases and software for analysis

43. Additional resources www.ncbi.nlm.nih.gov/BLAST
The Blast search at the National Center for Biotechnology Information—a searchable database of DNA sequences, protein sequences, and genomes, along with many other bioinformatics tools.
The Human Genome Organization—an international organization of scientists involved in the Human Genome Project.
Human Genome Project Information—hosted by Oak Ridge National Laboratory, this Web site provides information about the Human Genome Project, current genome research, and information about ethical, legal, and social issues regarding the Human Genome Project.
DOEGenomes.org—descriptions of the genome programs that are sponsored by the United States Department of Energy. The Web site contains many resources for educators and students who wish to learn more about the Human Genome Project and obtain educational materials related to the Human Genome Project.
DOE Genomes to Life—hosted by the United States Department of Energy, this Web site provides information regarding the DOE’s projects related to the Human Genome Project, along with the possible applications of information obtained through the Human Genome Project.
The National Human Genome Research Institute (NHRGI)—led the Human Genome Project for the National Institutes of Health; and they now lead research projects dealing with the information obtained from the Human Genome Project.
us.expasy.org
The ExPASy Molecular Biology Server—originally created by the Swiss Institute of Bioinformatics, this is a Web site devoted to the analysis of protein structures, protein sequences, and 2-D electrophoresis.

44. Additional resources tools.neb.com/NEBcutter2/index.php
NEBcutter—a tool created by New England BioLabs that allows you to create restriction enzyme maps of DNA sequences, even allowing you to analyze DNA sequences by GenBank accession number.
DNALC: Cycle Sequencing—an interactive tutorial dealing with the Sanger DNA sequencing technique.
The Protein Data Bank—a repository of over 24,000 three dimensional protein structures. Also provides educational information on nucleic acids and proteins.
iubio.bio.indiana.edu
IUBio Archive for Biology—hosted by Indiana University, this is a searchable Web site containing biology data and software, primarily in the area of molecular biology.
Genome Biology—a collection of information regarding the genomes of many organisms, ranging from nematodes to bacteria to humans.
bip.weizmann.ac.il
The Weizmann Institute of Bioinformatics—hosted by the Weizmann Institute of Science, this site provides many bioinformatics tools, including “GeneCards,” which is essentially an encyclopedia of human genes.