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Genomics
Chapter 18
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.
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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)
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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.
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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)
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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.
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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
criminal offenders
identify
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Genetic Maps
Genetic and physical maps can be correlated:
-Any cloned gene can be placed within the genome and can
also be mapped genetically.
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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
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Whole Genome Sequencing
The ultimate physical map is the base-pair sequence of the
entire genome.
- Requires use of highthroughout automated
sequencing and computer
analysis.
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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
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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.
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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
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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
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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.
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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.
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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.
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Genome Organization
Genomes consist of two main regions
-Coding DNA
-Contains genes than encode proteins
-Noncoding DNA
-Regions that do not encode proteins
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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.
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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.
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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%).
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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.
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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!!!!
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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.
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Rice
Sugarcane
Corn
Wheat
Genomic Alignment (Segment Rearrangement)
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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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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.
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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.
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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.
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Applications of Genomics
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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.
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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?
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