1. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CHAPTER 18 LECTURE SLIDES

2. Whole Genome Sequencing The ultimate physical map is the base-pair sequence of the entire genome Automation of this process increased the rate of sequence generation Genome sequencing is one case in which technology drove the science, rather than the other way around 2

3. Sequencers provide accurate sequences for DNA segments up to 800 bp long To reduce errors, 5–10 copies of a genome are sequenced and compared Vectors used to clone large pieces of DNA –Yeast artificial chromosomes (YACs) –Bacterial artificial chromosomes (BACs) 3

4. The Human Genome Project Originated in 1990 by the International Human Genome Sequencing Consortium –Goal of this publicly funded effort was to use a clone- by-clone approach to sequence the human genome Craig Venter formed a private company and entered the “race” in May, 1998 –Using shotgun-sequencing In 2001, both groups published a draft sequence Gaps in sequence still being filled Still being revised 4

5. 5 The Human Genome Project In 2004, the “finished” sequence was published as the reference sequence (REF-SEQ) in databases -3.2 gigabasepairs -1 Gb = 1 billion basepairs -Contains a 400-fold reduction in gaps -Error rate = 1 per 100,000 bases

6. 6 Characterizing Genomes The Human Genome Project found fewer genes than expected -Initial estimate was 100,000 genes -Number now appears to be about 25,000! In general, eukaryotic genomes are larger and have more genes than those of prokaryotes -However, the complexity of an organism is not necessarily related to its gene number

7. 7 Characterizing Genomes

8. 8 Finding Genes Genes are identified by open reading frames -An ORF begins with a start codon and contains no stop codon for a distance long enough to encode a protein Sequence annotation -The addition of information, such as ORFs, to the basic sequence information

9. 9 Noncoding DNA in Eukaryotes Each cell in our bodies has about 6 feet of DNA stuffed into it -However, less than one inch is devoted to genes! Six major types of noncoding human DNA have been described

10. 10 Noncoding DNA in Eukaryotes Noncoding DNA within genes -Protein-encoding exons are embedded within much larger noncoding introns Structural DNA -Called constitutive heterochromatin -Localized to centromeres and telomeres Simple sequence repeats (SSRs) -One- to six-nucleotide sequences repeated thousands of times

11. 11 Noncoding DNA in Eukaryotes Segmental duplications -Consist of 10,000 to 300,000 bp that have duplicated and moved Pseudogenes -Inactive genes

12. 12 Noncoding DNA in Eukaryotes Transposable elements (transposons) -Mobile genetic elements -Four types: -Long interspersed elements (LINEs) -Short interspersed elements (SINEs) -Long terminal repeats (LTRs) -Dead transposons

13. 13 Noncoding DNA in Eukaryotes

14. 14 Expressed Sequence Tags ESTs can identify genes that are expressed -They are generated by sequencing the ends of randomly selected -But how can 25,000 human genes encode three to four times as many proteins? -Alternative splicing yields different proteins with different functions

15. 15 Alternative Splicing

16. 16 Variation in the Human Genome Single-nucleotide polymorphisms (SNPs) are sites where individuals differ by only one nucleotide -Must be found in at least 1% of population

17. 17 Genomics Functional genomics is the study of the function of genes and their products DNA microarrays (“gene chips”) enable the analysis of gene expression at the whole-genome level -DNA fragments are deposited on a slide -Probed with labeled mRNA from different sources -Active/inactive genes are identified

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20. 20 Genomics

21. 21 Genomics

22. 22 Genomics

23. 23 Genomics

24. 24 Proteomics Proteomics is the study of the proteome -All the proteins encoded by the genome The transcriptome consists of all the RNA that is present in a cell or tissue

25. 25 Applications of Genomics Genome science is also a source of ethical challenges and dilemmas -Gene patents -Should the sequence/use of genes be freely available or can it be patented? -Privacy concerns -Could one be discriminated against because their SNP profile indicates susceptibility to a disease?