1. Genomics & Proteomics What is genomics? GOALS of Genomics
How are genomes mapped?
Methods for sequencing genomes
The Human Genome Project
Finding answers w/advanced technology!
Bioinformatics
Comparative genomics & model organisms
DNA chips aka microarrays
Proteomics

2. I. What is genomics?
Genome = the total genetic composition of an organism.
Genomics = the molecular analysis of the entire genome of a species.
Genome mapping = Segments of chromosomes are cloned and analyzed in progressively smaller pieces, the locations of which are known on the intact chromosomes
Ultimately leads to the determination of the complete DNA sequence, and understanding of that sequence
Genomes sequenced so far: 800+ organisms
sequenced or in progress…

3. Hemophilus influenzae – first bacterial genome sequenced in 1995
Hemophilus influenzae – first bacterial genome sequenced in Composed of 1.83 bp circular chromosome, 1,743 genes.

4. A. GOALS of Genomics Compile the genomic sequences of organisms
Establish the location of all genes and annotate the gene set in a genome
Find ORFs (start codon – stop codon)
Tells us the spatial relationships among genes
Establish the function of all genes
Generate gene expression profiles for cells under differing conditions
Compare genes and proteins between organisms to establish evolutionary relationships

5. Genomics has 3 subfields:
Structural genomics = genetic mapping, physical mapping, and sequencing of entire genomes
Functional genomics = comprehensive analysis of the functions of genes and nongene sequences in genomes
Comparative genomics = comparison of genomes of different species to determine the function of each genome and understand evolutionary relationships

6. B. How are genomes mapped?
Cytogenetic mapping
FISH

7. 2) Linkage mapping Testcross & Pedigree analysis
Molecular markers = segment of DNA found at a specific site along a chromosome, can be recognized using molecular tools, provides higher resolution.
RFLPs (restriction fragment length polymorphisms)
VNTR (variable number of tandem repeats)
STR (short tandom repeats)
SNP (single nucleotide polymorphism)
The distance between two linked markers can be determined by making crosses and analyzing the offspring (parentals v. nonparentals)

8. 3) Physical mapping
Physical map of a chromosome is constructed by creating a contiguous series of overlapping clones from a chromosome-specific library
Contig = collection of clones, found as overlapping regions within a group of vectors
The contigs are arranged relative to each other by comparing restriction maps & DNA markers
(YACs, BACs) can carry large genomic inserts
Genomic library generated, clone individually isolated and arranged to a grid pattern
Identify adjacent members that contain overlapping regions
Southern blotting
Molecular markers

9. YAC

11. A comparison of linkage, cytogenetic & physical maps

12. C. Methods for sequencing genomes
Clone by clone method (“top-down”)
Construction of genomic libraries of fragments covering the total DNA of an organism. Then using genetic markers, overlapping clones are assembled to establish maps that encompass the entire genome
Shotgun method
Genomic libraries are prepared and randomly selected clones are sequenced until all clones in library are analyzed. Software packages organize the nucleotide sequences.

13. overlapping clones are assembled to establish maps

14. libraries are prepared and randomly selected clones are sequenced
Compiling the sequence = genome sequenced multiple times to ensure the sequence is accurate

15. D. The Human Genome Project
International research effort to characterize the genome of the human, GOALS:
Complete mapping and sequencing of the DNA
Identify all the genes & store this information in a public database
Develop technologies for genome analysis & transfer these tools to the private sector
Examine ethical, legal and social implications of human genetics research
In U.S., Funded by NSF, global cooperative effort (GB, France, and Japan) – additionally, Celera (Craig Ventor) was involved:

16. Human Genome Project
Began in 1990… as of 2003, 99% of the euchromatic region was published: October issue of Nature
2.85 billion nucleotides
~45% of the genome consists of repetitive DNA
At least 50% is derived from transposable elements
< 5% protein coding genes
20,500 known protein-coding genes and a further 4,000 additional sections of DNA predicted to be putative protein-coding genes
Chromosome 19 has the highest gene density, 55.8 million bases ~1500 genes; the Y chromosome the lowest (78 genes)

17. II. Finding answers w/advanced technology!
Annotation = identifying genes, their regulatory sequences, their function + identifying non-protein coding regions
A. Bioinformatics = Annotating genomes
Emerging field concerned with the development and
application of computer software to the acquisition,
storage, analysis and visualization of biological
information
identifying protein coding genes (ORFs = open reading frames)
identifying non-protein coding regions
Characterizing Mobile elements
Analyzing homologous regions – comparative genomics
BLAST = basic local alignment search tool, computer program that allows you to start with a DNA or protein sequence and then locate homologous sequences in a huge database.

18. B. Comparative genomics & model organisms
So far, confirmed a common ancestor, similar gene sets for basic cellular functions
Can study inherited disorders, gene interactions and environment
To date: Yeast, Drosophila, C. elegans, mouse, dog
Orthologous = descended from a common anscestral gene, have same function
240 between M. genitalium and H. influenzae
Paralogous – arise from a gene duplication event
w/ dog, humans share 400 single gene disorders, sex chromosome anueploidies, multifactorial diseases
Dogs share many genetic disorders w/humans

19. Pan troglodytes & Homo sapiens
Last common ancestor = 6mya, we’ve been diverging ever since!
Chromosome 22 – 24, only a 1.44% difference, however there are 68,000 indels
Tissue expression patterns differed – several genes found to be expressed in either one or the other, but not both
patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles

20. C. DNA chips aka microarrays
Functional genomics seeks to understand the function of genes and how they determine phenotypes.
C. DNA chips aka microarrays
Analyzing genome wide expression patterns in different tissues
studying genome-wide patterns of gene expression
Can view cells as an array of expressed genes
DNA complementary to genes of interest are generated and laid out in microscopic quantities on a slide
Sample cDNA binds to complement, presence of bound DNA is detected by fluorescence

21. identify the genes that are active within a cell and help identify mutated genes

22.
A hand-held DNA Chip device, (Nanogen, Inc). The circles at the top are sample ports. The wires guide electric fields over the DNA array, located on the light blue diamond.

23. III. Proteomics Genomics 1st step…
Proteomics = the cataloging and analysis of a the proteome (a complete set of expressed proteins in a cell at a particular time) to determine when a protein is expressed, how much is made, and with what other proteins the protein can interact.
Goals: to identify every protein in the proteome, to determine the sequences of each protein, and to analyze globally protein levels in different cell types and at different stages in development.

24. Dot matrix can compare the degree of similarity between two primary sequences.
Regions of homology are recognized, gaps can be inserted to align sequences.
Too simple for very long sequences, dynamic programming methods used instead: Multiple sequence alignment.

25. Proteomics, big challenge!
Proteome – larger than the genome,
Changes in pre-mRNA structure may affect the primary sequence of a protein
Alternative splicing
RNA editing
Post-translational modifications
Methods:
Two-dimensional gel electrophoresis, used to separate cellular proteins
Mass spectrometry – used to identify proteins
Protein microarrays, protein expression & function