1. CO 10

2. The entire collection of genes encoded by a
Genome:
The entire collection of genes encoded by a
particular organism.
Determination of a entire genome sequence
is a prerequisite to understanding the complete
biology of an organism.

3. Genomics: Structural: construction of sequence data and gene map.
Functional: functions of genes, and their regulation
and products.
Comparative: compare genes from different genomes
to elucidate functional and evolutional
relationship.

4. History 1990: International Human Genome project begins.
To generate physical, genetic, and sequence map of the human genome.
To sequence the genome of a variety of model organisms.
To develop improved technologies for mapping and sequencing.
To develop computational tools for capturing, storing, analyzing,
displaying, and distributing map and sequence information.

5. History 1990: International Human Genome project begins.
5. To sequence EST (expressed-sequence tag) fragments of
cDNA, and eventually full-length cDNA in different cell types of human and mice.
6. To consider the ethical, social, and legal challenges posted
by genomic information.

6. Fig. 10.1

7. What in this chapter? Challenges and strategies of genome analysis
Major insights emerging from complete genome sequences
High throughput tools for analyzing genome and their products.

8. The genomes of living Organisms vary enormously in size
Table 10.1
The genomes of living Organisms vary enormously in size

9. Sequences and polymorphisms
Challenges and strategies of genome analysis
Sequences and polymorphisms
Sequence error rate: 1% per sequence read
Good genomic sequence errors: 1/10,000
Polymorphisms: 1/500 bp.
Repeated sequences may be hard to place
Unclonable DNA cannot be sequenced

10. A divide and conquer strategy
Fig. 10.2
A divide and conquer strategy

11. 10-fold sequence coverage
Sequencing of every chromosomal region from 10 independent inserts can generate an error rate of less than 1/10000.
Random sequence error:1/10 sequence fragments
Polymorphisms: 5/10 sequence fragments

12. Major techniques in genome characterization
Cloning
hybridization
PCR amplification
sequencing
Computational tool

13. Three types of maps used in the analysis of human genome
Linkage map (DNA markers)
Physical map (divide and conquer)
Sequence map
Human genome: 3X109

14. The making of large-scale linkage maps
Fig. 10.3
The making of large-scale linkage maps
Two common types of polymorphisms used or mapping
(expand or contract during replication)
DNA markers

15. Genomewide identification of genetic markers
Identification of SSR by specific pairs of PCR primers

16. Human Linkage Map
20,000 SSRs, 4 million SNPs.

17. Physical Maps Overlapping DNA fragments that are ordered and oriented
Fig. 10.4
Physical Maps
Overlapping DNA fragments that are ordered and oriented
and span each of the chromosomes in a genome
The molecular counterparts of linkage maps
In human: 1 cM= 1 Mb
In mice: 1 cM= 2 Mb

18. How to build the long-range physical maps: Bottom-up and Top-Down approaches

19. A Hypothetical physical map generated by the analysis of sequence tagged sites
STS: sequence tagged sites

20. metaphase Dark band: gene poor, AT rich Light band: gene rich, CG rich
Fig. 10.5
metaphase
Dark band: gene poor, AT rich
Light band: gene rich, CG rich

21. Chromosome 7 at three levels
of banding resolution

22. FISH (fluorescent in situ hybridization)
Fig. 10.6
FISH (fluorescent in situ hybridization)

23. Advantages of FISH compared to linkage mapping
All clones can be mapped by FISH, but those that detect polymorphisms can be mapped by linkage analysis.
FISH can be done on any clone locus in isolation, but linkage requires
the analysis of one locus in relation to another.
3. FISH requires only a single sample, linkage requires genotype information from a large cohort of individuals.
Disadvantages: low resolution, 4-8 Mb

24. A sequencing map is the highest-resolution
genomic map
Hierarchical shotgun approach
Whole-genome shotgun approach

25. Hierarchical shotgun approach
Fig
Hierarchical shotgun approach
200kbX10/2Kb=1000
10X coverage across
The BAC insert
minimal
overlapping
BACs

26. Whole genome shotgun approach
Fig
Whole genome shotgun approach
10-fold sequence
coverage
3X109X6/2000

27. Whole genome shotgun approach
Advantages: no construction of physical map.
Disadvantage: some genomic sequences can not be cloned.

28. The human genome project has changed the practice of
Biology, genetics, and genomics
Gene finding and gene-function analyses:
Through comparative genomics, Identification of genes
and gene functions in second genome is facilitated by
sequence homology.
Genes often encodes one or more protein domains. These
information provide insights into the functions of a
protein.

29. Fig

30. Fig
Syntetic
blocks

31. Major insights from the Human and model organism
genome sequence
There are approximately 30,000 human genes.
Genes encodes either noncoding RNAs or proteins
Non-coding RNAs:
tRNA,
snoRNA (small nucleolar RNAs)
snRNA (small nuclear RNAs)

32. 3. Higher complexity of proteome in human: more genes, more paralogous, alternative splicing.
Homologous genes: genes with enough sequence similarity to be
evolutionarily related.
Orthologous genes: defined by their sequence similarities, are
genes in two different species that arose
from the same gene in the two species’
common ancestor.
Paralogous genes: arise by duplication within the same species.

33. Major insights from the Human and model organism
genome sequence
4. More Domain architecture:

34. 5. Chemical modification of proteins
400 different chemical modification
1 million different proteins

35. Major insights from the Human and model organism
genome sequence
6. Repeated sequences constitute more than 50% of the
human genome.
Transposon-derived repeats, pseudogenes, or simple sequence repeats

36. Major insights from the Human and model organism
genome sequence
6. The genome contains distinct types of gene organization
A). gene family: multiple related genes
olfactory gene family (1000 genes), histones, hemoglobins,

37. Olfactory receptor gene family
Fig
Olfactory receptor gene family
One gene undergoes duplication to generate 20 paralogs.
Massive duplication created 30 sites of the original 20-paralog family.

38. B). Gene rich region 60 genes/700 kb C). Gene deserts
Fig
B). Gene rich region
70% DNA is transcribed
60 genes/700 kb
C). Gene deserts
82 gene deserts: no identifiable gene within a megabase

39. Combinational strategies may amplify genetic
Fig
Combinational strategies may amplify genetic
Information and generate diversity
at DNA level
Antibody or T-cell receptor genes: VDJ recombination

40. Combinational strategies may amplify genetic
Fig
Combinational strategies may amplify genetic
Information and generate diversity
At the RNA level

41. High throughput genomic and proteomic platforms
permit the global analysis of gene product

42. Sanger sequencing scheme
Fig
Sanger sequencing scheme

43. DNA arrays Macroarray: cDNA on nylon membrane
Microarray: PCR amplified
product on glass-slide
Oligonuclotide array:
chemically synthesized 20-
60 nt of DNA or RNA

44. Two-color DNA microarray
Fig
Two-color DNA microarray
Normal
tumor
Normal
tumor

45. Fig
Protein analyses
Mass/charge
ratios

46. MPSS: methods to identify transcriptome
Fig
MPSS: methods to identify transcriptome
(multiple parallel signature sequencing)

47. Protein-protein interaction: affinity purification and
Fig
Protein-protein interaction:
affinity purification and
mass spectrometry

48. Fig
The yeast two-hybrid

49. System Biology
Global study of multiple components of biological systems and their simultaneous interaction

50. System Biology approaches
Formulate a computer-based model based on current understanding.
To define as many of the system’s element as possible by discovery
science.
Perturb the system either genetically or environmentally and measure changes.

51. Perturb the system and measure changes
Fig
Perturb the system and measure changes

52. Fig

53. 4. Integrate the biological information, and compare
Fig
4. Integrate the biological information, and compare
these data against prediction of the model

54. 5. Formulate hypothesis to explain disparities between
experimental data and the model, and use these hypothesis as the basis for a second round of perturbation
6. Refine the model until model and experiment are in accord with one another.

55. TABLES

56. Table 10.2a

57. Table 10.2b

58. Table 10.3

59. Fig. 10.9b

60. Fig

61. Fig

62. Fig

63. Fig

64. Fig

65. Fig

66. Basic procedures in building a whole chromosome physical map
Fig. 10.7
Basic procedures in building a whole chromosome physical map