1. Today… Review a few items from last class
Next week Presentations on Thurs!
Guest Speaker
In-Class #9

2. What is genomics? Field of genetics that studies whole genomes Content
Organization
Function
Evolution

3. What started the field of genomics?
1997 Svante Paabo sequenced 379 bp region of mtDNA from Neanderthal fossil

4. What genomes were the first to be sequenced?
1995 Haemophilus influenzae (1.8 Mb)
1996 Saccharomyces cerevisiae (12 Mb)
1998 C. elegans (100 Mb)
2000 Drosophila melanogaster (180 Mb)
2001 First draft of Human genome (3000 Mb)
2005 First draft of Chimpanzee
2007 Craig Venter’s Genome Released; Jim Watson’s Genome Sequenced Using High-Throughput Methods

5. Map of H. influenzae

6. Creating a Map of the Genome
Break genome into pieces
Read sequences of small segments
Computationally find areas of overlap
Assemble contigs

7. Genome Sequencing is Automated

8. Two Strategies for Sequencing Whole Genomes:
Whole-genome shotgun (WGS)
Sequence first, map later
Ordered-clone sequencing
Map first, sequence later

9. WGS: Begin with Reads from Inserts
Primers are used to sequence 600 bp of insert
If both ends of the clone are sequenced paired-end reads are generated

10. WGS worked well for bacterial genomes….what about eukaryotes?
How do we figure out the location of sequences with lots of repetition??

11. Overview of WGS

12. Ordered Clone Approach

13. Once we had the sequence…
The field of bioinformatics was born!
What information is found in the DNA???
Goal: Annotate the genome!

14. First look at the Proteome
How do we find gene regions in the DNA?
Open reading frames (ORFs)
Analyze mRNA by creating cDNA
Expressed sequence tags (ESTs)

15. Lots of binding sites to focus on! (from consensus motifs)

16. Different ways to make gene predictions

17. Structure of the Human Genome
Only 3% codes for proteins
60% of current proteins have splice variations
Estimate about 20,000 genes
19,000 pseudogenes

18. Cytogenetic Map of Chromosome 7
Mapped physical break points related to disease
1600 rearrangement breakpoints have been mapped, 440 have been sequenced

19. Comparative Genomics
Assume that natural selection rejects mutations that decrease fitness
Also see conserved sequences over long periods of evolution
Genes are conserved from one species to another

20. Comparative Genomics Used to study evolution of genes across species
Used to study conserved sequences among vertebrates
Used to study strains of bacteria (E. coli K12 and E. coli O157:H7)

21. Compare Genomes of Bacteria
Common backbone in blue
O157:H7 in red
K12 in green

22. What’s with all the -ogs?
Homologs: closely related genes
Orthologs: homologs that evolved from a common ancestor
Paralogs: genes related by gene duplication in the genome

23. Oh give me a Ome Besides the genome there are new -omes Transcriptome
Proteome
Interactome
PROTEOME SAMPLER from Yeast. shows 1,458 yeast proteins (circles) and their 1,948 interactions (lines). Removing proteins has different effects on the yeast: lethal (red); nonlethal (green); slowed growth (orange); unknown (yellow).  Hawoong Jeong; University of Notre Dame.

24. DNA Microarrays DNA chips have “spots” of DNA bound to slide
One chip can have an entire genome
Expose chip to sample of labeled RNA from a cell…RNA will hybridize to areas of complementary DNA

25. DNA Microarrays

26. Ways to Study the Interactome
Two-hybrid test
Detects the physical interaction between proteins
Chromatin Immunoprecipitation Assay (ChIP)
Study proteins that bind to DNA

27. Ways to Study the Interactome
Two-hybrid test
Detects the physical interaction between proteins
Chromatin Immunoprecipitation Assay (ChIP)
Study proteins that bind to DNA

28. Reverse Genetics
Disrupt gene function and then study the phenotype in native conditions
Random mutagenesis
Targeted mutagenesis
Phenocopying

29. Phenocopying RNA interference Chemical genetics
Generate dsRNA with sequences homologous to gene you want to study
Chemical genetics
Reduce the activity of target gene by binding inhibitory molecule

30. Welcome……..our guest speaker
Dr. Michael Schlador
Illumina
Regional Manager, Field Applications