Download presentation
Presentation is loading. Please wait.
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
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.