1. Genomics
Chapter 18

2. Mapping Genomes Maps of genomes can be divided into 2 types:
-Genetic maps
-Abstract maps that place the relative location of genes on chromosomes based on recombination frequency.
-Physical maps
-Use landmarks within DNA sequences, ranging from restriction sites to the actual DNA sequence.

3. Physical Maps
Distances between “landmarks” are measured in base-pairs.
-1000 basepairs (bp) = 1 kilobase (kb)
Knowledge of DNA sequence is not necessary.
There are three main types of physical maps:
-Restriction maps (constructed use restriction enzymes)
-Cytological maps (chromosome-banding pattern)
-Radiation hybrid maps (using radiation to fragment chromosomes)

4. Restriction maps
-The first physical maps;
-Based on distances between restriction sites;
-Overlap between smaller segments can be used to assemble them into a contig
-Continuous segment of the genome.

5. Physical Maps Cytological maps
-Employ stains that generate reproducible patterns of bands on the chromosomes
-Divide chromosomes into subregions
-Provide a map of the whole genome, but at low resolution
-Cloned DNA is correlated with map using fluorescent in situ hybridization (FISH)

6. Physical Maps Radiation hybrid maps
-Use radiation to fragment chromosomes randomly;
-Fragments are then recovered by fusing irradiated cell to another cell
-Usually a rodent cell
-Fragments can be identified based on banding patterns or FISH.

7. Genetic Maps
Most common markers are short repeat sequences called, short tandem repeats, or STR loci:
-Differ in repeat length between individuals;
-13 form the basis of modern DNA fingerprinting developed by the FBI;
-Cataloged in the CODIS database to identify criminal offenders

8. Genetic Maps Genetic and physical maps can be correlated:
-Any cloned gene can be placed within the genome and can also be mapped genetically.

9. Genetic Maps
All of these different kinds of maps are stored in databases:
-The National Center for Biotechnology Information (NCBI) serves as the US repository for these data and more;
-Similar databases exist in Europe and Japan

10. Whole Genome Sequencing
The ultimate physical map is the base-pair sequence of the entire genome.
- Requires use of high-throughout automated sequencing and computer analysis.

11. Whole Genome Sequencing
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 use to clone large pieces of DNA:
-Yeast artificial chromosomes (YACs)
-Bacterial artificial chromosomes (BACs)
-Human artificial chromosomes (HACs)
-Are circular, at present

12. Whole Genome Sequencing
Clone-by-clone sequencing
-Overlapping regions between BAC clones are identified by restriction mapping or STS analysis.
Shotgun sequencing
-DNA is randomly cut into smaller fragments, cloned and then sequenced;
-Computers put together the overlaps.
-Sequence is not tied to other information.

14. The Human Genome Project
Originated in 1990 by the International Human Genome Sequencing Consortium;
Craig Venter formed a private company, and entered the “race” in May, 1998;
In 2001, both groups published a draft sequence.
-Contained numerous gaps

15. 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;
-99% of euchromatic sequence;
-Error rate = 1 per 100,000 bases

16. 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.

17. 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.

18. Finding Genes
BLAST
-A search algorithm used to search NCBI databases for homologous sequences;
-Permits researchers to infer functions for isolated molecular clones
Bioinformatics
-Use of computer programs to search for genes, and to assemble and compare genomes.

19. Genome Organization Genomes consist of two main regions -Coding DNA
-Contains genes than encode proteins
-Noncoding DNA
-Regions that do not encode proteins

20. Coding DNA in Eukaryotes
Four different classes are found:
-Single-copy genes: Includes most genes.
-Segmental duplications: Blocks of genes copied from one chromosome to another.
-Multigene families: Groups of related but distinctly different genes.
-Tandem clusters : Identical copies of genes occurring together in clusters.

21. 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.

22. Noncoding DNA in Eukaryotes
Noncoding DNA within genes:
-Protein-encoding exons (less than 1.5%) are embedded within much larger noncoding introns (about 24%).
Structural DNA:
-Called constitutive heterochromatin;
-Localized to centromeres and telomeres.
Simple sequence repeats (SSRs):
-One- to six-nucleotide sequences repeated thousands of times. (SSRs can arise from DNA replication errors. About 3%).

23. Noncoding DNA in Eukaryotes
Segmental duplications:
-Consist of 10,000 to 300,000 bp that have duplicated and moved either within a chromosome or to a nonhomologous chromosome.
Pseudogenes:
-Inactive genes that may have lost function because of mutation.

24. Noncoding DNA in Eukaryotes
Transposable elements (transposons)
-Mobile genetic elements
- Able to move from one location on a chromosome to another.
-Four types:
-Long interspersed elements (LINEs) (21%)
-Short interspersed elements (SINEs) (13%)
-Long terminal repeats (LTRs) (8%)
-Dead transposons (3%)
TOTAL OF 45% OF THE GENOME!!!!

25. Genomics
Comparative genomics, the study of whole genome maps of organisms, has revealed similarities among them:
-Over half of Drosophila genes have human counterparts;
- Humans and mouse: only 300 genes that have no counterparts in the genome.
Synteny refers to the conserved arrangements of DNA segments in related genomes;
-Allows comparisons of unsequenced genomes.

26. Genomic Alignment (Segment Rearrangement)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Rice
Sugarcane
Corn
Wheat

27. 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.

28. Proteomics Proteomics is the study of the proteome:
-All the proteins encoded by the genome.
- A single gene can code for multiple proteins using alternative splicing.
Although all the DNA in a genome can be isolated from a single cell, only a portion of the proteome is expressed in a single cell or tissue.
The transcriptome consists of all the RNA that is present in a cell or tissue.

29. Proteomics
Proteins are much more difficult to study than DNA because of:
-Post-translational modifications
-Alternative splicing.
However, databases containing the known protein structural exist:
-These can be searched to predict the structure and function of gene sequences.

30. Applications of Genomics
The genomics revolution will have a lasting effect on how we think about living systems;
The immediate impact of genomics is being seen in diagnostics:
-Identifying genetic abnormalities;
-Identifying victims by their remains;
-Distinguishing between naturally occurring and intentional outbreaks of infections.

31. Applications of Genomics

32. Applications of Genomics
Genomics has also helped in agriculture.
-Improvement in the yield and nutritional quality of rice.
-Doubling of world grain production in last 50 years, with only a 1% cropland increase.

33. 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?