Genomics

Chapter 9 in Modern Genetic Analysis, 2nd Edition

What is Genomics?
Study of complete set of genes
Global vs local
Genome Projects (Table)
Structural vs. Functional genomics

Steps in Whole Genome Mapping:

High resolution genetic mapping
Physical mapping
DNA sequencing

Applications of the Complete DNA Sequence

Functional Genomics
Bioinformatics

High Resolution Genetic Mapping

used to place molecularly defined differences on linkage maps or cytogenetic maps
provide molecular landmarks for building higher resolution physical and sequencing maps
builds on low-resolution genetic maps

DNA polymorphisms: molecularly defined differences between individuals

Mapping Techniques Used to Determine Position of DNA Marker on a

Chromosome:
1) Meiotic Recombination Maps
based on analyzing recombinant frequency in dihybrid and multihybrid crosses
done more easily in Saccharomyces cerevisiae, Ceanorhabiditis elegans, Drosophila melanogaster etc.
due to ease of controlled experimental crosses
Not as easy for humans since crosses are harder to obtain and progeny sizes are too small
measurements of loci with known phenotypic effect showed intervals in between genes which contain vast
amounts of DNA
To fill in these gaps, various kinds of polymorphic DNA markers need to be exploited

Examples of polymorphic DNA markers (RFLPs, SSLPs, and RAPDs):

 a) RFLPs

Restriction Fragment Length Polymorphism

Restriction enzyme recognition sites present in some strains but not in others (presence/absence)

b) SSLPs

Simple Sequence Length Polymorphisms

Advantages over RFLPs include larger number of alleles as well as higher levels of heterozygosity

Types of SSLPs:

i) Minisatellite markers

based on VNTRs: Variable Number of Tandem Repeats

VNTRs are 1 - 5 kb sequences of repeating units that are 15 - 100 nucleotides long
When genome cut by restriction enzymes, and there are no recognition sites located within VNTRs,
Southern blot analysis reveals a large number of different sized fragments bound by VNTR probe.
Due to high variability in number of tandem repeats from person to person, set of fragments revealed
is highly individualistic.
Often called DNA fingerprints

ii) Microsatellite markers

based on variable number of dinucleotides repeated in tandem

CA with complementary GT most common
Use PCR to make probes for DNA flanking marker. First digest the DNA with a restriction enzyme
such as Alu1. Clone the fragments into a sequencing vector and then identify those containing the
CA/GT repeats with a CA/GT probe. Sequence these vectors and create PCR primer pairs. These
primers are designed to recognize single copy DNA sequences flanking the marker. Use these
primers with genomic DNA in PCR amplification. Gel electrophoresis can be used to determine size
differences.

c) RAPDs

Randomly Amplified Polymorphic DNA

based on random PCR amplification
A single PCR primer is designed at random and used to amplify different regions of the genome.

Also SNPs should be mentioned.

SNPs are Single Nucleotide Polymorphisms

many due to neutral variation, such as third codon position
There is one SNP difference every 1000 base pairs of human DNA. Since the human genome is about 3
billion base pairs long there are 3 million differences between any two of our genomes. A very rich source
of variation!

2) Cytogenetic Maps
produced by relating locations of DNA markers to cytogenetic landmarks such as chromosome bands and
puffs
 Ways to do this:

a) In Situ Hybridization Mapping

if a cloned DNA sequence is available for area of interest, label it as a probe and use it to hybridize to
chromosomes in situ
individual chromosomes are recognizable through morphology differences such as size, banding
pattern, centromere location
map the probe sequence to approximate position on chromosome
labels used for probes: FISH - Fluorescent In Situ Hybridization

b) Rearrangement Breakpoint Mapping

based on using DNA breakpoints as molecular landmarks
when cloned DNA spanning a breakpoint has been identified, breakpoints are easily detected on
Southern blots as two bands of hybridization, while in normal chromosomes you would only see one
band

c) Radiation Hybrid Mapping

does not require marker heterozygosity

irridate cells with Xray fragments to break up the chromosomes (human)
insert these fragments into rodent cells
fragmented human chromosomes fuse to chromosomes of rodent cells
create a series of clones each containing a different random assortment of fragments of human
chromosomes
isolate and denature DNA from each cell line
introduce a labeled human DNA probe to identify positions of human DNA homologous to probe
analyze the data from many probe hybridizations to determine co-retention of DNA markers
co-retention of different human markers allows high-resolution mapping of the chromosonal loci of
the DNA markers

Physical Mapping
Physical mapping is an intermediate step in sequencing the entire genome
(genetic map > physical map > sequence map)
A complete physical map of the genome includes:
maps for each chromosome in the haploid chromosome set
for each chromosome, continuous overlapping cloned genomic DNA segments extending from one
telomere of the chromosome to the other

Vector - plasmid or phage chromosome used to carry cloned DNA segment (or insert) Chapter 8, MGA
Main types used: YAC (Yeast Artificial chromosomes) or Cosmids
BAC (Bacterial Artificial Chromosomes)
PAC (Phage P-1 based Artificial Chromosomes)
Contig - set of ordered overlapping clones that constitute a a chromosomal region or a genome

Techniques for Identifying Clone Overlaps:

1) Ordering by Clone Fingerprints
genomic insert (clone) carried by vector has a unique sequence that can be used to generate a DNA
fingerprint
multiple restriction enzyme digestion generates a set bands, unique in number and position, representing
the fingerprint for a particular clone
patterns of bands from multiple clones are read by computer and aligned to determine the degree of
overlap between inserted DNA segments
the proportion of bands shared between two clones indicates whether there is true overlap (usually
20-25%)
important technique in developing physical maps for C. elegans, mouse and human genomes

2) Ordering by STSs
Sequence-Tagged Sites are short unique sequences that can be amplified using defined PCR primers
derive from sequenced regions of the genome so can be used as landmarks for clone classification in
creating physical map
clones that share STSs must overlap; the more STSs they share, the more they overlap
resulting physical map is a STS content map
combination of fingerprinting and STS content mapping has resulted in complete and near-complete
physical maps for many organisms, such as C. elegans

Simplifying Physical Mapping by Subdividing the Genome:

many biological and technical challenges in creating physical maps that are true reflections of the genome
in human genome, there are megabase-size regions that are duplicate copies on two different chromosomes
(biological challenge)
some regions of the genome do not clone efficiently in standard vectors, leaving gaps in the physical map
(technical challenge)
subdividing the genome into smaller working entities can circumvent some biol and tech challenges as the
number of clones required to complete the physical map in a given subregion is much less

1) Chromosome Specific Libraries

separate actual DNA molecules of the genome into those contained within specific chromosomes
library serves as source of clones for fingerprint or STS content physical mapping
individual chromosomes are identified

Techniques:

a) Pulse Field Gel Electrophoresis (PGFE) Chapter 2, MGA

modification of standard gel electrophoresis that adjusts conditions to permit separation of large
DNA molecules
can isolate individual chromosomes if they are small (eg. yeast chromosome)
for large chromosomes, can isolate chromosome fragments by "cutting" with "rare cutter" enzymes
(eg. NotI enzyme cuts every 64,000 bp)

b) Fluorescence-Activated Chromosome Sorting (FACS) or Flow Sorting

cells disrupted to liberate whole metaphase chromosomes into liquid suspension

chromosomes stained with 2 dyes, one binding to AT-rich regions, the other to GC-rich regions
each chromosome has a unique ratio of AT-rich to GC-rich regions, used to distinguish between
different chromosomes
2) Ordering by FISH (Fluorescent In Situ Hybridization)
technique used to confirm physical map order of cloned DNAs
many clones in situ hybridize to the same landmark regions (using human chromosome banding
techniques), thus, FISH puts clones into one of a number of cytogenetic regions within a given
chromosome
clones then evaluated by fingerprint analysis or STS content mapping to produce physical map
provides independent way to corroborate results with the physical maps produces from fingerprint or STS
content mapping
Cytogenetic map of BAC and PAC clones localized by FISH mapping in human genome

DNA Sequencing
Four bases include A, C, T, and G
Human genome equals 3 x 109 base pairs and includes an X and Y chromosome as well as 22 autosomes
All current sequencing techniques are clone based
First make a clone or subclone library and then sequence all or part of inserts of individual clones in the
library. From these sequences form a consensus sequence

There are Two Ways to Assemble a Consensus Sequence:

1) Ordered Clone Sequencing

produce physical map of genome
ordered subset of minimally overlapping clones selected for sequencing
consensus sequence for each clone
assemble in order on physical map

2) Whole Genome Shotgun Sequencing

obtain sequence reads from randomly selected clones from whole genome library
no information on where clones map in genome
homologous sequence allows assembly of sequences into consensus sequence over whole genome

Sequencing Strategies in Bacteria:

bacterial DNA is single copy and only a few megabase pairs in size
due to simple system, whole genome shotgun assembly can be applied
gaps in consensus sequence can be filled in by primer walking
Primer Walking - use of a primer based on a sequenced area of a genome to sequence into a flanking
unsequenced area
shotgun sequencing does not work well in eukaryotic systems since it is not composed entirely of single
copy DNA and may contain repetitive genome sequences

Repeated Genome Sequences:

repeated genome sequences are identical sequence strings present many times in the genome
problematic in eukaryotic systems
 two classes included are tandem repeat arrays and mobile genetic elements

1) Tandem Repeat Arrays

tandem repeats are sequences in multiple copies adjacent to one another, variable in size and number of
repetitions
(Recall: VNTR-minisatellites, microsatellites).

a) Tandemly repeated genes Figure 9-22

b) Non-coding tandem repeats - telomeres and heterochromatin

2) Mobile Genetic Elements: Dispersed Repeats (Summary Table)

dispersed in genome and move to new locations via transposition

a) Transposons
b) Retrotransposons
c) LINE (long interspersed elements)
d) SINE (short interspersed elements)

Tackling Genomes with Repetitive Sequences

1) Assembling a Sequence from Ordered Clones

straightforward assembly of many of the dispersed repeats since they are present only once in the
individual clone
Minimum Tiling Path is a subset of clones with clear but minimal overlap (ie. minimum # of clones that
represent entire genome)
relies on physical map to order and orient the clone sequences

2) Whole Genome Shotgun Assembly

connects the single-copy sequences on either side of the repetitive element but ignores the sequence of the
repetitive element itself.
sequenced clones aligned by their homologous sequence overlaps into contigs (but in no particular order)
paired-end sequences (sequences corresponding to either end of cloned insert) are used to span gaps
between contigs and place them in correct genomic order and orientation
scaffolds - ordered set of contigs in which there are unsequenced gaps connected by paired-end sequence
reads

For a visual comparison of these methods see: Figure 9-29

Functional Genomics
functional genomics includes study of expression and interaction of gene products on a global level, that
is, using genomic approaches to study some aspect of all gene products simultaneously
how molecules cooperate and interact to effect all the processes and phenotypes that make up a biological
system
genome refers to "gene" plus "ome", or the global data set for "all genes"
various other 'ome's are being worked on: transcriptome, proteome, interactome and phenome
 transcriptome - sequence and expression patterns of all transcripts (where, when, how much)
proteome - sequence and expression patterns of all proteins (where, when, how much)
interactome - complete set of physical interactions between: all proteins and all DNA segments; all
proteins and RNA segments; and among all proteins
phenome - description of complete set of phenotypes produced by inactivation of gene function for
each gene in the genome

Studying the Transcriptome and Interactome Using DNA Chips:

DNA chips: chips the size of a microscope cover slip which contain samples of DNA laid out in series

automation and miniaturization of assay methods

contain samples of DNA laid out as a series of microscopic spots bound to a glass "chip"
can contain all genes of complex genome
can assay all gene products in a single experiment
method alternative to mutational analysis; rather than amassing mutations to disrupt a particular process,
chip technology detects the specific mRNAs expressed in that process
can also be used to detect protein-DNA interactions

Constructing DNA Chips:

microscopic droplets of DNA added to slide via a robotic machine (thousands of samples can be
applied to one chip)
DNA dried and treated to bind to glass

1) One protocol detecting which genes are active at a particular stage of development in a cell:
array of known cDNAs from different genes are applied to chip
chip exposed to fluorescently labelled probe, such as, RNA extracted from particular cell at
particular stage of development
binding of probe molecules to homologous DNA spots monitored automatically by laser
beam-illuminated microscope
detect spots on chip where probe binds to determine which genes are active at the particular stage of
interest
Animation

2) Another protocol for building oligonucleotides for detection of active genes:

array of oligonucleotides are chemically synthesized on chip, one nucleotide at a time
chip covered with protecting groups that prevent DNA deposition
mask placed on chip containing holes where sites of deposition are to occur
shine a laser beam on holes where where synthesis will begin, this will knock off protecting groups
bathe chip in first nucleotide to be added (containing protective group to avoid adding dimers)
sequential additions of laser beams, appropriate masks and bathing in nucleotides allow for
construction of oligonucleotide
once this is done, these chips are ready to bind to fluorescent probes isolated at some developmental
stage of interest
chip is analyzed similar to method above
Animation

Studying the Interactome with the Yeast Two-Hybrid System:

investigates interactions between proteins Figure 9-40
uses the yeast GAL4 transcription activator
GAL4 has two domains: a DNA binding domain which binds to site of transcriptional activation and an
 activation domain which is responsible for activating transcription, but cannot do so without the DNA
binding domain
gene for GAL4 is divided between plasmids
gene for protein of interest is spliced next to DNA binding domain of GAL4 = bait
the other protein gene is spliced next to the rest of the GAL4 gene on other plasmid = target
both plasmids introduced into cell or cells of organism together and observed for activation via a reporter
gene (gene for an easily detected protein)

Bioinformatics
deciphering meaning from the raw 4-letter DNA sequence by using computational analysis to predict
mRNA and polypeptide sequences.

Problems with deciphering information content of DNA:

1. Do not know all of the specific DNA sequences that encode the thousands of docking sites for DNA or
RNA-binding regulatory proteins.

2. A given DNA sequence can encode for different things depending on its location within the DNA
ie. if located in coding region, the sequence would code for amino acid, if located in non-coding region,
the sequence would act as binding site for regulatory protein.

3. Two or more different sequences can serve the same function.

Using Bioinformatics to Determine an Organisms Proteome

proteome (complete set of polypeptides encoded by a genome)

Bioinformatics uses several independent sets of information to do this:

1. cDNA sequences (complimentaryDNAs are DNA copies of mRNAs) cDNAs are aligned with genomic
DNA to determine the position of introns and exons.

2. Docking site sequences marking the start and end points for the events in information transfer
(transcription, pre-mRNA splicing, translation).

3. Sequences of related polypeptides. Common statistical tool for aligning proteins is BLAST (Basic Local
Alignment Search Tool)

4. Codon bias - species-specific usage preferences for some codons over other encoding for the same amino
acid. Presence of the preferred codon in predicted mRNA sequence supports the accuracy of the
prediction.

Predictions of mRNA and polypeptide structure from genomic DNA sequence depend on an integration of
information from cDNA sequence, docking site predictions, polypeptide similarities, and codon bias. Summary
Figure