1. Genomics: Sequencing Is the Basis for Identifying and Mapping All Genes in a Genome
Genomics, the study of genomes, encompasses structural genomics, functional genomics, and comparative genomics.
Several hundred genomes from both prokaryotes and eukaryotes have been sequenced, and more than 1000 genome sequencing projects are under way.

2. Approaches to genome sequencing include the clone-by-clone method and the shotgun method. The shotgun method is the favored method and was used to generate the first genome sequence.
In genome sequencing, the genome is sequenced several times over to ensure accuracy.

3. Figure 20-1a (a) In the clone-by-clone method, clones from a genomic library are organized into genetic and physical maps of each chromosome. After the clones are arranged into physical maps, they are broken into smaller, overlapping clones that cover each chromosome. Each smaller clone is sequenced, and the genomic sequence is assembled by stringing together the nucleotide sequence of the clones. (b) In the shotgun method, a genomic library is constructed from fragments of genomic DNA. Clones are selected from the library at random and sequenced. The sequence is assembled by looking for sequence overlaps between clones from different libraries. This is done with a computer, using assembler software designed for genomic analysis.

4. Figure 20-1b (a) In the clone-by-clone method, clones from a genomic library are organized into genetic and physical maps of each chromosome. After the clones are arranged into physical maps, they are broken into smaller, overlapping clones that cover each chromosome. Each smaller clone is sequenced, and the genomic sequence is assembled by stringing together the nucleotide sequence of the clones. (b) In the shotgun method, a genomic library is constructed from fragments of genomic DNA. Clones are selected from the library at random and sequenced. The sequence is assembled by looking for sequence overlaps between clones from different libraries. This is done with a computer, using assembler software designed for genomic analysis.

5. An Overview of Genomic Analysis (“annotation”)
Analysis of genome sequences includes identifying open reading frames (ORFs); finding promoter sites and transcription and translation initiation sites; finding splice sites, introns, and exons in eukaryotic genomes; and translating the DNA sequences into protein sequences. The predicted protein sequences are analyzed to predict protein function.

6. Functional Genomics Classifies Genes and Identifies Their Functions
Functional genomics classifies ORFs by function. In any genome, some ORFs have known function, some show homology to ORFs of known function from other organisms, and some have no known or proposed function.

8. The Human Genome Project
What did they do?
Why did they do it?
What will it mean for humankind?

9. Brief history of the work…
Proposed in 1985
1988. Initiated and funded by NIH and US Dept. of Energy ($3 billion set aside)
1990. Work begins.
The human genome was sequenced by both the National Institutes of Health and an international consortium, as well as by the private company Celera
First draft published in Science and Nature in February, 2001

10. Goals of HGP
Create physical map of the 24 human chromosomes (22 autosomes, X & Y)
Identify the entire set of genes & map them all to their chromosomes
Determine the nucleotide sequence of the estimated 3 billion base pairs
Analyze genetic variation among humans
Map and sequence the genomes of model organisms

11. Model organisms Bacteria (E. coli, influenza, several others)
Yeast (Saccharomyces cerevisiae)
Plant (Arabidopsis thaliana)
Roundworm (Caenorhabditis elegans)
Fruit fly (Drosophila melanogaster)
Mouse (Mus musculus)

12. Goals of HGP (cont’d)
Develop new laboratory and computing technologies to make all this possible
Disseminate genome information
Consider ethical, legal, and social issues associated with this research

16. The Beginning of the Project
Most the first 10 years of the project were spent improving the technology to sequence and analyze DNA.
Scientists all around the world worked to make detailed maps of our chromosomes and sequence model organisms, like worm, fruit fly, and mouse.

19. What did they find?

20. 5000 bases per page
CACACTTGCATGTGAGAGCTTCTAATATCTAAATTAATGTTGAATCATTATTCAGAAACAGAGAGCTAACTGTTATCCCATCCTGACTTTATTCTTTATG AGAAAAATACAGTGATTCC
AAGTTACCAAGTTAGTGCTGCTTGCTTTATAAATGAAGTAATATTTTAAAAGTTGTGCATAAGTTAAAATTCAGAAATAAAACTTCATCCTAAAACTCTGTGTGTTGCTTTAAATAATC
AGAGCATCTGC TACTTAATTTTTTGTGTGTGGGTGCACAATAGATGTTTAATGAGATCCTGTCATCTGTCTGCTTTTTTATTGTAAAACAGGAGGGGTTTTAATACTGGAGGAACAA
CTGATGTACCTCTGAAAAGAGA AGAGATTAGTTATTAATTGAATTGAGGGTTGTCTTGTCTTAGTAGCTTTTATTCTCTAGGTACTATTTGATTATGATTGTGAAAATAGAATTTATCC
CTCATTAAATGTAAAATCAACAGGAGAATAGCAAAAACTTATGAGATAGATGAACGTTGTGTGAGTGGCATGGTTTAATTTGTTTGGAAGAAGCACTTGCCCCAGAAGATACACAAT
GAAATTCATGTTATTGAGTAGAGTAGTAATACAGTGTGTTCCCTTGTGAAGTTCATAACCAAGAATTTTAGTAGTGGATAGGTAGGCTGAATAACTGACTTCCTATC ATTTTCAGGTT
CTGCGTTTGATTTTTTTTACATATTAATTTCTTTGATCCACATTAAGCTCAGTTATGTATTTCCATTTTATAAATGAAAAAAAATAGGCACTTGCAAATGTCAGATCACTTGCCTGTGGT
CATTCGGGTAGAGATTTGTGGAGCTAAGTTGGTCTTAATCAAATGTCAAGCTTTTTTTTTTCTTATAAAATATAGGTTTTAATATGAGTTTTAAAATAAAATTAATTAGAAAAAGGCAA
ATTACTCAATATATATAAGGTATTGCATTTGTAATAGGTAGGTATTTCATTTTCTAGTTATGGTGGGATATTATTCAGACTATAATTCCCAATGAAAAAACTTTAAAAAATGCTAGTGA
TTGCACACTTAAAACACCTTTTAAAAAGCATTGAGAGCTTATAAAATTTTAATGAGTGATAAAACCAAATTTGAAGAGAAAAGAAGAACCCAGAGAGGTAAGGATATAACCTTACC
AGTTGCAATTTGCCGATCTCTACAAATATTAATATTTATTTTGACAGTTTCAGGGTGAATGAGAAAGAAACCAAAACCCAAGACTAGCATATGTTGTCTTCTTAAGGAGCCCTCCCCT
AAAAGATTGAGATGACCAAATCTTATACTCTCAGCATAAGGTGAACCAGACAGACCTAAAGCAGTGGTAGCTTGGATCCACTACTTGGGTTTGTGTGTGGCGTGACTCAGGTAATCT
CAAGAATTGAACATTTTTTTAAGGTGGTCCTACTCATACACTGCCCAGGTATTAGGGAGAAGCAAATCTGAATGCTTTATAAAAATACCCTAAAGCTAAATCTTACAATATTCTCAAG
AACACAGTGAA ACAAGGCAAAATAAGTTAAAATCAACAAAAACAACATGAAACATAATTAGACACACAAAGACTTCAAACATTGGAAAATACCAGAGAAAGATAATAAATAT
TTTACTCTTTAAAAATTTAGTTAAAAGCTTAAACTAATTGTAGAGAAAA AACTATGTTAGTATTATATTGTAGATGAAATAAGCAAAACATTTAAAATACAAATGTGATTACTTAAAT
TAAATATAATAGATAATTTACCACCAGATTAGATACCATTGAAGGAATAATTAATATACTGAAATACAGGTCAGTAGAATTTTTTTCAATTCAGCATGGAGATGTAAAAAATGAAAA
TTAATGCAAAAAATAAGGGCACAAAAAGAAATGAGTAATTTTGATCAGAAATGTATTAAAATTAATAAACTGGAAATTTGACATTTAAAAAAAGCATTGTCATCCAAGTAGATGTG
TCTATTAAATAGTTGTTCTCATATCCAGTAATGTAATTATTATTCCCTCTCATGCAGTTCAGATTCTGGGGTAATCTTTAGACATCAGTTTTGTCTTTTATATTATTTATTCTGTTTACTAC
ATTTTATTTTGCTAATGATATTTTTAATTTCTGACATTCTGGAGTATTGCTTGTAAAAGGTATTTTTAAAAATACTTTATGGTTATTTTTGTGATTCCTATTCCTCTATGGACACCAAGGCT
ATTGACATTTTCTTTGGTTTCTTCTGTTACTTCTATTTTCTTAGTGTTTATATCATTTCATAGATAGGATATTCTTTATTTTTTATTTTTATTTAAATATTTGGTGATTCTTGGTTTTCTCAGCC
ATCTATTGTCAAGTGTTCTTATTAAGCATTATTATTAAATAAAGATTATTTCCTCTAATCACATGAGAATCTTTATTTCCCCCAAGTAATTGAAAATTGCAATGCCATGCTGCCATGTGG
TACAGCATGGGTTTGGGCTTGCTTTCTTCTTTTTTTTTTAACTTTTATTTTAGGTTTGGGAGTACCTGTGAAAGTTTGTTATATAGGTAAACTCGTGTCACCAGGGTTTGTTGTACAGATCA
TTTTGTCACCTAGGTACCAAGTACTCAACAATTATTTTTCCTGCTCCTCTGTCTCCTGTCACCCTCCACTCTCAAGTAGACTCCGGTGTCTGCTGTTCCATTCTTTGTGTCCATGTGTTCTC
ATAATTTAGTTCCCCACTTGTAAGTGAGAACATGCAGTATTTTCTAGTATTTGGTTTTTTGTTCCTGTGTTAATTTGCCCAGTATAATAGCCTCCAGCTCCATCCATGTTACTGCAAAGAA
CATGATCTCATTCTTTTTTATAGCTCCATGGTGTCTATATACCACATTTTCTTTATCTAAACTCTTATTGATGAGCATTGAGGTGGATTCTATGTCTTTGCTATTGTGCATATTGCTGCAAG
AACATTTGTGTGCATGTGTCTTTATGGTAGAATGATATATTTTCTTCTGGGTATATATGCAGTAATGCGATTGCTGGTTGGAATGGTAGTTCTGCTTTTATCTCTTTGAGGAATTGCCATG
CTGCTTTCCACAATAGTTGAACTAACTTACACTCCCACTAACAGTGTGTAAGTGTTTCCTTTTCTCCACAACCTGCCAGCATCTGTTATTTTTTGACATTTTAATAGTAGCCATTTTAACT
GGTATGAAATTATATTTCATTGTGGTTTTAATTTGCATTTCTCTAATGATCAGTGATATTGAGTTTGTTTTTTTTCACATGCTTGTTGGCTGCATGTATGTCTTCTTTTAAAAAGTGTCTGTT
CATGTACTTTGCCCACATTTTAATGGGGTTGTTTTTCTCTTGTAAATTTGTTTAAATTCCTTATAGGTGCTGGATTTTAGACATTTGTCAGACGCATAGTTTGCAAATAGTTTCTCCCATTC
TGTAGGTTGTCTGTTTATTTTGTTAATAGTTTCTTTTGCTATGCAGAAGCTCTTAATAAGTTTAATGAGATCCTGATATGTTAGGCTTTGTGTCCCCACCCAAATCTCATCTTGAATTATA
TCTCCATAATCACCACATGGAGAGACCAGGTGGAGGTAATTGAATCTGGGGGTGGTTTCACCCATGCTGTTCTTGTGATAGTGAATGAGTTCTCACGAGATCTAATGGTTTTATGAGG
GGCTCTTCCCAGCTTTGCCTGGTACTTCTCCTTCCTGCCGCTTTGTGAAAAAGGTGCATTGCGTCCCTTTCACCTTCTTCTATAATTGTAAGTTTCCTGAGGCCTTCCCAGCCATGCTGAA
CTTCAAGTCAATTAAACCTTTTTCTTTATAAATTACTCAGTCTCTGGTGGTTCTTTATAGCAGTGTGAAAATGGACTAATGAAGTTCCCATTTATGAATTTTTGCTTTTGTTGCAATTGCTT
TTGACATCTTAGTCATGAAATCCTTGCCTGTTCTAAGTACAGGACGGTATTGCCTAGGTTGTCTTCCAGGGTTTTTCTAATTTTGTGTTTTGCATTTAAGTGTTTAATCCATCTTGAGTTGA
TTTTTGTATATTGTGTAAGGAAGGGGTCCAGTTTCAATCTTTTGCATATGGCTAGTTAGTTATCCCAGTACCATTTATTGAAAAGACAGTCTTTTCCCCATCGCTCGTTTTTGTCAGTTTT
ATTGATGATCAGATAATCATAGCTGTGTGGCTTTATTTCTGGGTTCTTTATTCTGTTCTATTGGTTTATGTCCCTGTTTTTGTGCCAGTACCATGCTGTTTTGGTTAACATAGCCCTGTAGT
ATAGTTTGAGGTCAGATAGCCTGATGCTTCCAGCTTTGTTCTTTTTCTTAAGATTGCCTTGGCTATTTGGCCTCTTTTTTGGTTCCACATGAATTTTAAAACAGTTGTTTCTAGTTTTTGAA
GAATGTCATTGGTAGTTTGATAGAAATAGCATTTAATCTGTAAATTGATTTGTGCAGTATGGCCTTTTAATGATATTGATTCTTCCTATCCATGAGCATGATATGTTTTCCATTTTGTTTG
TATCCTCTCTGATTTCTTTGTGCAGTGTTTTGTAATTCTCAT TGTAGAGATTTTTCACCTCCCTGGTTAGTTGTATTTTACCCTAGATATTT TATTCTTTTTGTGAAAATTGTGAATGGGAT
TGCCTTCCTGATTTGACTGC CAGCTTGGTTACTGTTGGTTTATAGAAATGCTAGTGATTTTTGTACATTG ATTTTCTTTCTAAAACTTTGCTGAAGTTTTTTTTATTAGCAGAAGGAGCT
TTGGGGCTGAGACTATGGGGTTTTCTAGATATAGAATCATGTCAGCTTCAAATAGGGATAATTTTACTTCCTCTCTTCCTATTTGGATGCCCTTTATTTCTTTCTCTTGCCTGATTACTCTG
GCTGGGATTTCCTATGTTGAATAGGAGT CATGAGAGAGGGCATCAAATCTACACATATCAAATACTAACCTTGAATGTCTAGATATTT TATTCTTTTTGTGAAAATTGTGAATGGGAT

21. How much data make up the human genome?
3 pallets with 40 boxes per pallet x 5000 pages per box x 5000 bases per page = 3,000,000,000 bases!
To get accurate
sequence requires
6-fold coverage.
Now: Shred 18 pallets
and reassemble.

22. Human genome content 1-2 % codes for protein products
24% important for translation
75% “junk”
Repetitive elements
Satellites (regular, mini-, micro-)
Transposons
Retrotransposons
Parasites
BOOK THAT WROTE ITSELF

23. The Continuing Project
The sequence of all human chromosomes has been published in a special Nature issue in Now Annotation is the main ongoing goal.
Proteomics is studying the structure and function of groups of proteins. Proteins are really important, but we don’t really understand how they work.
Comparative Genomics is the process of comparing different genomes in order to better understand what they do and how they work. Like comparing humans, chimpanzees, and mice that are all mammals but all very different.
Annotation: includes, for example, not only the genes, but the proteins the genes makes and what diseases they are associated with.
Proteins are really important for drug development and discovery.

25. Comparative Genomics

26. Yeast 70 human genes are known to repair mutations in yeast
Nearly all we know about cell cycle and cancer comes from studies of yeast
Advantages:
fewer genes (6000)
few introns
31% of yeast genes give same products as human homologues

27. Drosophila
nearly all we know of how mutations affect gene function come from Drosophila studies
We share 50% of their genes
61% of genes mutated in 289 human diseases are found in fruit flies
68% of genes associated with cancers are found in fruit flies
Knockout mutants
Homeobox genes

28. C. elegans 959 cells in the nervous system
131 of those programmed for apoptosis
apoptosis involved in several human genetic neurological disorders
Alzheimers
Huntingtons
Parkinsons

29. Mouse known as “mini” humans Very similar physiological systems
Share 90% of their genes