1. Genomics and Proteomics
Benjamin A. Pierce
GENETICS
A Conceptual Approach
SIXTH EDITION
CHAPTER 20
Genomics and Proteomics
© 2017 W. H. Freeman and Company

2. Photo of yeast and of the Johns Hopkins students who were part of the artificial chromosome project coming soon. [Micrograph: Thomas Deerinck, NCMIR/Science Source.]

3. 20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes
Structural genomics: organization and sequence of genetic information contained within a genome
Genetic maps
(Linkage map) approximate locations of genes, relative to the location of other genes, based on the rates of recombination
Limitations
Low resolution or detail
Do not correspond to physical distances between genes

4. 20. 1 Genetic maps are based on rates of recombination
20.1 Genetic maps are based on rates of recombination. Shown here is a genetic map of human chromosome 1.

5. 20.2 Genetic and physical maps may differ in relative distances and even in the position of genes on a chromosome. Genetic and physical maps of yeast chromosome III reveal such differences.

6. 20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes
Physical map: based on the direct analysis of DNA, places genes in relation to distances measured in bp, kbp, and mbp
Higher resolution and more accurate than genetic maps

7. 20. 3 Physical maps are often used to order cloned DNA fragments
20.3 Physical maps are often used to order cloned DNA fragments. A part of a physical map of a set of overlapping YAC clones from one end of the human Y chromosome.

8. 20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes
Sequencing the entire genome
The Human Genome Project
Map-based sequencing
Whole-genome shotgun sequencing

9. 20.4 The bacterium Haemophilus influenzae was the first free-living organism to be sequenced.

10. 20.5 Map-based approaches to whole-genome sequencing rely on detailed genetic and physical maps to align sequenced fragments.

11. 20.6 Whole-genome shotgun sequencing uses sequence overlap to align sequenced fragments.

12. 20.7 Craig Venter (left), president of Celera Genomics, and Francis Collins (right), director of the National Human Genome Research Institute, NIH, announce the completion of a rough draft of the human genome at a press conference in Washington, D.C., on June 26, [Alex Wong/Newsmakers/Getty Images.]

13. Concept Check 1 A contig is _____.
a set of molecular markers used in genetic mapping
a set of overlapping fragments that form a continuous stretch of DNA
a set of fragments generated by a restriction enzyme
a small DNA fragment used in sequencing

14. Concept Check 1 A contig is _____.
a set of molecular markers used in genetic mapping
a set of overlapping fragments that form a continuous stretch of DNA
a set of fragments generated by a restriction enzyme
a small DNA fragment used in sequencing

15. 20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes
Single-nucleotide polymorphisms
A site in the genome where individual members of a species differ in a single base pair
Haplotype: the specific set of SNPs and other genetic variants observed on a chromosome
Linkage disequilibrium
Genome-wide association studies

16. 20.8 A haplotype is a specific set of SNPs and other genetic variants observed on a single chromosome or part of a chromosome. Chromosomes 1a, 1b, 1c, and 1d represent different copies of a chromosome that might be found in a population.

17. 20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes
Copy-number variations (CNV)
The number of copies of DNA sequences varies among people
Expressed-sequence tags (ESTs)
Markers associated with DNA sequences that are expressed as RNA
Bioinformatics
Molecular biology + computer science

18. Concept Check 2
The ab initio approach finds genes by looking for _____.
common sequences found in most genes
similarity in sequences with known genes
mRNA with the use of in situ hybridization
mutant phenotypes

19. Concept Check 2 The ab initio approach finds genes by looking
for _____.
common sequences found in most genes
similarity in sequences with known genes
mRNA with the use of in situ hybridization
mutant phenotypes

20. 20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes
Metagenomics: sequencing genomes of entire communities of organisms
Synthetic biology: the creation from scratch of novel organisms

21. 20.2 Functional Genomics Determines the Functions of Genes by Using Genomic-Based Approaches
characterizes what the sequences do
Transcriptome: all the RNA molecules transcribed from a genome
Proteome: all the proteins encoded by the genome

22. 20.2 Functional Genomics Determines the Functions of Genes by Using Genomic-Based Approaches
Predicting function from sequence
Homologous
Genes that are evolutionarily related
Orthologs
Homologous genes in different species that evolved from the same gene in a common ancestor
Paralogs
Homologous genes arising by duplication of a single gene in the same organism

23. 20. 9 Homologous genes are evolutionarily related
20.9 Homologous genes are evolutionarily related. Orthologs are homologous genes found in different species; paralogs are homologous genes in the same species.

24. Concept Check 3 What is the difference between orthologs and paralogs?
Orthologs are homologous sequences; paralogs are analogous sequences.
Orthologs are more similar than paralogs.
Orthologs are in the same organism; paralogs are in different organisms.
Orthologs are in different organisms; paralogs are in the same organism.

25. Concept Check 3 What is the difference between orthologs and paralogs?
Orthologs are homologous sequences; paralogs are analogous sequences.
Orthologs are more similar than paralogs.
Orthologs are in the same organism; paralogs are in different organisms.
Orthologs are in different organisms; paralogs are in the same organism.

26. 20.2 Functional Genomics Determines the Functions of Genes by Using Genomic-Based Approaches
Gene expression and microarrays
Nucleic acid hybridization: using a known DNA fragment as a probe to find a complementary sequence
Gene expression and reporter sequences
Reporter sequence: encoding an easily observed product used to track the expression of a gene of interest
Genome-wide mutagenesis
Mutagenesis screen

27. 20.10 Microarrays can be used to examine gene expression associated with disease progression. Each row in the microarray represents a tumor from one patient. [Reprinted by permission from Macmillan Publishers Ltd. Van’t Veer, Laura J., et al., “Gene expression profiling predicts clinical outcome of breast cancer,” Nature 415:532. © 2002.]

28. 20.11 Microarrays have been used to compare the expression of miRNAs in cancerous cervical cells with that in normal cervical cells. [Adapted from Wang X., Tang S., Le S.-Y., Lu R., Rader J. S., et al. (2008) Aberrant Expression of Oncogenic and Tumor-Suppressive MicroRNAs in Cervical Cancer Is Required for Cancer Cell Growth. PLoSONE 3(7): e2557. doi: /journal.pone ]

29. 20. 12 RNA sequencing can be used to determine the expression of genes
20.12 RNA sequencing can be used to determine the expression of genes. Cellular RNA is isolated, converted to cDNA, and sequenced, providing information on the RNA transcripts present in a cell.

30. 20. 13 A reporter sequence can be used to examine expression of a gene
20.13 A reporter sequence can be used to examine expression of a gene. Expression of the neural-specific beta-tubulin gene in the
brain of a tadpole is revealed by green fluorescent protein. [Photo by Miranda Gomperts, Courtesy Enrique Amaya, the Amaya Lab.]

31. 20.14 Genes affecting a particular characteristic or function can be identified by a genome-wide mutagenesis screen. In this illustration, M1 represents a dominant mutation and m2 represents a recessive mutation.

32. 20.3 Comparative Genomics Studies How Genomes Evolve
Prokaryotic genomes
Genome size and number of genes
Horizontal gene transfer
Exchanging genetic information from closely related or distantly related species over evolutionary time
Function of genes

33. Size (Millions of Base Pairs) Number of Predicted Genes
TABLE 20.1
Characteristics of representative prokaryotic genomes that have been completely sequenced
Species
Size (Millions of Base Pairs)
Number of Predicted Genes
Archaea
Archaeoglobus fulgidus
2.18
2407
Methanobacterium thermoautotrophicum
1.75
1869
Nanoarchaeum equitans
0.490
536
Eubacteria
Bacillus subtilis
4.21
4100
Bradyrhizobium japonicum
9.11
8.317
Escherichia coli
4.64
4289
Haemophilus influenzae
1.83
1709
Mycobacterium tuberculosis
4.41
3918
Mycoplasma genitalium
0.58
480
Staphylococcus aureus
2.88
2697
Vibrio cholerae
4.03
3828
Source: Data from the Genome Atlas of the Center for Biological Sequence Analysis,

34. 20.3 Comparative Genomics Studies How Genomes Evolve
Eukaryotic genomes
Genome size and number of genes
Segment duplications and multigene families
Noncoding DNA
Transposable elements
Protein diversity
Homologous genes
Collinearity between related genomes

35. Genome Size (Millions of Base Pairs) Number of Predicted Genes
TABLE 20.2
Characteristics of representative eukaryotic genomes that have been completely sequenced
Species
Genome Size (Millions of Base Pairs)
Number of Predicted Genes
Saccharomyces cerevisiae (yeast) 12
6,144
Physcomitrella patens (moss)
480
38,354
Arabidopsis thaliana (thale-cress plant)
125
25,706
Zea mays (corn)
2,400
32,000
Hordeum vulgare (barley)
5,100
26,159
Caenorhabditis elegans (nematode)
103
20,598
Drosophila melanogaster (fruit fly)
170
13,525
Anopheles gambiae (mosquito)
278
14,707
Danio rerio (zebrafish)
1,465
22,409
Takifugu rubripes (tiger pufferfish)
329
22,089
Xenopus tropicalis (clawed frog)
1,510
18,429
Anolis carolinensis (anole lizard)
1,780
17,792
Mus musculus (mouse)
2,627
26,762
Pan troglodytes (chimpanzee)
2,733
22,524
Homo sapiens (human)
3,223
~20,000
Source: Data from the Ensembl Web site: and plants.ensembl.org/index.html.

36. TABLE 20.3
Percentages of eukaryotic genomes consisting of interspersed repeats derived from transposable elements
Organism
Percentage of Genome
Arabidopsis thaliana (thale-cress plant)
10.5
Zea mays (corn)
85.0
Caenorhabditis elegans (nematode)
6.5
Drosophila melanogaster (fruit fly)
3.1
Takifugu rubripes (tiger pufferfish)
2.7
Homo sapiens (human)
44.4

37. Number of estimated protein domains encoded by some eukaryotic genomes
TABLE 20.4
Number of estimated protein domains encoded by some eukaryotic genomes
Organism
Number of Predicted Protein Domains
Saccharomyces cerevisiae (yeast)
851
Arabidopsis thaliana (thale-cress plant)
1012
Caenorhabditis elegans (nematode)
1014
Drosophila melanogaster (fruit fly)
1035
Homo sapiens (human)
1262
Source: Number of genes and protein-domain families from the International
Human Genome Sequencing Consortium, Initial sequencing and analysis of
the human genome, Nature 409:860–921, Table 23, 2001.

38. 20.15 Collinear relationships among blocks of genes found in rice, sorghum, and Brachypodium (wild grass). Each colored band represents a block of genes that is collinear between chromosomes of the three species.

39. 20.3 Comparative Genomics Studies How Genomes Evolve
Comparative Drosophila genomics
The human genome

40. Average characteristics of genes in the human genome
TABLE 20.5
Average characteristics of genes in the human genome
Characteristic
Average
Number of exons
8.8
Size of internal exon
145 bp
Size of intron
3,365 bp
Size of 5' untranslated region
300 bp
Size of 3' untranslated region
770 bp
Size of coding region
1,340 bp
Total length of gene
27,000 bp

41. 20.16 The introns of genes in humans are generally longer than the introns of genes in nematodes and fruit flies.

42. 20. 17 Functions for many human genes have yet to be determined
20.17 Functions for many human genes have yet to be determined. Proportion of the circle occupied by each color represents the proportion of genes affecting various known and unknown functions.

43. 20.4 Proteomics Analyzes the Complete Set of Proteins Found in a Cell
Determination of cellular proteins
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)
Mass spectrometry

44. 20.18 Two-dimensional acrylamide gel electrophoresis (2D-PAGE) can be used to separate cellular proteins. [After G. Gibson and S. Muse A Primer of Genome Science, 2e. Sinauer Associates, Inc. p. 274, Fig. 5.4.]

45. 20.19 Mass spectrometry is used to identify proteins.

46. 20.4 Proteomics Analyzes the Complete Set of Proteins Found in a Cell
Affinity capture
Interactome
Protein microarrays
Structural proteomics

47. 20.20 Protein microarrays can be used to examine interactions among proteins. (a) A microarray containing 4400 proteins found in yeast. (b) The array was probed with an enzyme that phosphorylates proteins to determine which proteins serve as substrate for the enzyme. Dark spots represent proteins that were phosphorylated
by the enzyme. Proteins that phosphorylate themselves (autophosphorylate) are included in each block of the microarray (shown in blue boxes) to serve as reference points. [From D. Hall, J. Ptacek, and M. Snyder Mechanisms of Aging and Development. 128 (2007) 161–167. © 2006, with permission from Elsevier.]