Maps and Tour guides

Question 1

Briefly describe maps in genomics

Answer 1

Maps tell us where things are in relation to other things. In genomics, maps have been essential in revealing the organization of the hereditary material.
Different types of maps describe different types of observation:
>Linkage maps of genes
> Banding patterns of chromosomes
> Restriction maps- DNA cleavage fragment patterns
> DNA sequences

Question 2

What is the crucial idea that emerged from mapping

Answer 2

The crucial idea that emerged from mapping is that the organization of hereditary information is linear. The first steps proved that, within any chromosome, linkage maps are one-dimensional arrays. All the types of maps are one-dimensional and co-linear.

Question 3

What don’t genome sequences tell us

Answer 3

Genome sequences describe the hereditary information of organisms in only one-dimensional and static form. What they don’t tell us is:
> how much information is implemented in space and time
> how gene expression is choreographed by orderly developmental programmes
> the influence of surroundings and experience and epigenetics on the structure and activities of the organism, beyond the genome itself.

Question 4

What are linked traits

Answer 4

Mendel did not report that, in some cases, genes for different traits do not show independent assortment but are linked- their alleles are co-inherited. Linked traits are governed by genes on the same chromosome. However, in many cases linkage is incomplete. During gamete formation, alleles on different chromosomes of a homologous pair can recombine. This occurs as a result of crossing over - the exchange of material between homologous chromosomes during copying in meiosis.

Question 5

Explain Thomas Hunt Morgan’s observation

Answer 5

Thomas Hunt Morgan observed varying degrees of linkage in different pairs of genes. He suggested that the extent of recombination could be a measure of the distance between genes on a chromosome. Morgan’s student Alfred Sturtevant, then an undergraduate, made a crucial observation: the data were consistent with a linear distribution of genes. What he found was that genetic distance, as measured by crossing-over frequency, was additive. Consider 3 genes- A, B, and C. Suppose that the distance from A-B is 5 and B-C is 3, then A-C will be 5+3=8. The observations are consistent with a linear additive structure with the gene order A-B-C.

Question 6

What did Strutevant’s analysis make it possible to determine

Answer 6

Sturtevant’s analysis made it possible to determine the order of genes along each chromosome and to plot them along a line at positions consistent with the distances between them. The unit of length in a gene map is the Morgan, defined by the relation that 1cM corresponds to a 1% recombination frequency. In humans, 1cM is 10^6 bp, but it varies with the location of the genome, the distance between the genes, and the gender of the parent- for males 1cM is about 1.05Mb and for females, it’s about 0.88Mb.

Question 7

Discuss crossing over at different regions in the chromosome

Answer 7

Crossing over is reduced at pericentromeric regions and telomeric regions. Other regions are ‘hot spots’ for crossing over. It is estimated that around 80% of genetic recombination takes place in no more than 25% of our genome.

Question 8

Explain how linkage guides the search for genes

Answer 8

To identify the gene responsible for a disease, look for a marker of known location that tends to be co-inherited with the disease phenotype. The target gene is then likely to be on the same chromosome, at a position near to the marker.

Question 9

Explain linkage and linkage disequilibrium

Answer 9

Linkage and linkage disequilibrium are closely related, but distinct concepts. Linkage is about the distribution of loci among chromosomes and linkage disequilibrium is about the distribution of allelic patterns in populations.

Question 10

Explain the effect that the linkage of genes has on the LD

Answer 10

Close linkage of two loci on a chromosome is a common source of long-term persistence of LD. Two genes at the opposite ends of the same chromosome may not show significant LD. Conversely, it is possible(rare) to observe LD between two genes on different chromosomes. This can happen in two ways:
> a community of immigrants imports a particular set of SNPs into a larger population and they preferentially intermarry for many generations
> theoretically by interactions between gene products that permit only certain combinations of alleles to be viable. (epistatic interactions)

Question 11

Why is LD a better tool for localizing a target gene

Answer 11

Classical linkage maps typically involved markers no less than 1cM apart(1Mb in humans). LD is detectable between markers that are 0.01-0.02cM apart (10-20kb). Therefore LD is a much finer tool for localizing a target gene.

Question 12

Explain figure 3.2- Suppose that M is a mutation that occurred in a human population 50 generations ago. A and B are known phenotypic traits and x and y are closely spaced markers.

Answer 12

The markers are 0.1cM from M. It is highly likely that the markers are co-inherited with M- the probability of recombination between x or y with M is 0.1%(1cM= 1%), so 0.001. The probability of recombination in 50 generations is 50 x 0.001= 0.05 (low=unlikely to be separated). It is highly likely that the markers A and B will be separated by recombination. The probability of recombination between A or B with M is 1%(1cM=1%) so 0.01. The probability of recombination in 50 generations is 50 x 0.01= 0.5. Therefore markers x and y will be good candidates for localizing the target gene in which M occurs, through the analysis of human pedigrees for genetic markers and disease occurrence. For humans, we do not have access to 50 generations of records and DNA samples (take about 100 years). However, the effects of recombination during the 50 generations can be deduced since the mutation filters out all, except the most closely-linked genes from the co-inheritance pedigree. Haplotype groupings simplify the identification of gene-marker correspondences.

Question 13

Explain chromosome banding pattern maps

Answer 13

Banding patterns are visible features on a chromosome. The most commonly used pattern is G-banding, produced by a Giemsa stain. The bands reflect base composition and chromosome loop structure. The darker regions tend to contain highly condensed heterochromatin of relatively low GC/AT ratio and sparse in gene content.

Question 14

What is a karyotype

Answer 14

The karyotype of an individual comprises the structures of the individual chromosomes. The karyotype is largely consistent within a species but varies between species. This is the result of chromosome rearrangement during evolution. The inability of most cells with incongruent karyotypes to pair chromosomes properly is one barrier to fertility that contributes to species separation. Although most individuals have the same karyotype, occasionally aberrant chromosomes appear. Some of them are lethal and others are correlated with disease, eg. Down Syndrome and Prader-Willi or Angelman syndromes. Studies of chromosome banding patterns support several types of investigations.

Question 15

Discuss the nomenclature of chromosome bands

Answer 15

In many organisms, chromosomes are numbered in order of size, 1 being the largest. The two arms of human chromosomes are called the p(petite= short) and q(queue) arm. Regions within the chromosome are numbered p1,p2…..and q1,q2….. outward from the centromere. There are also additional digits for subdivisions p1.1, p1.2 or q1.1, q1.2…
Refer to box 3.2- certain bands on the q arm of human chromosome 15 are labelled 15q11.1, 15q11.2. Deletions in the region 15q11-13 are associated with Prader-Willi and Angelman syndromes. Genomic imprinting- one of the chromosomes are silenced in Prader-Willi it’s the paternal and in Angelman its the maternal.

Question 16

Discuss the correlation between linkage maps and chromosome structure

Answer 16

Chromosome aberrations include deletions, translocations(the transfer of material from one chromosome to another), and inversions. The genetic consequences of a short deletion in only one of a pair in homologous chromosomes (only one instead of 2 for traits that map to the deleted region) allowed for direct mapping of genes to positions on chromosomes. In this way, the abstract genetic linkage maps could be superimposed onto the chromosome. This was 1st done in the 1930s after the discovery of the very large chromosomes in the Drosophila melanogaster salivary glands. The correlation of the chromosome aberrations with changes in the genetic linkage map proved that they are colinear. Together with the mapping of sex-linked traits to the X-chromosome, the genetic consequences of chromosomal deletions confirmed that chromosomes carry hereditary information.

Question 17

What is the modern technique for mapping genes onto chromosomes

Answer 17

Fluorescent in situ hybridization (FISH)- a probe oligonucleotide sequence labelled with a fluorescent dye is hybridized to a chromosome. The location where the probe is bound shows up directly in a photograph of the chromosome. The typical resolution is 10^5 bp, but specialized new techniques can achieve high resolution down to 1 kb. Simultaneous FISH with two probes can detect linkage and even estimate gene distances. FISH can also detect chromosomal abnormalities. The use of chromosome-specific dyes of different colours visualises the karyotype by ‘chromosome painting’.

Question 18

Discuss the studies of evolutionary change in karyotype

Answer 18

If we compare our chromosomes with a chimpanzee’s, we see that large-scale rearrangements have taken place, eg. human chromosome 2 is split into 2 separate chromosomes in the chimpanzee. However, most regions in the corresponding chromosomes of the two species show conservation of banding patterns. Such regions are called syntenic blocks. For humans and chimpanzees, full genome sequences are available. They confirm that the relationships suggested by comparison of the banding patterns reflect conservation at the level of DNA sequences.

Question 19

Explain, how genomes were seen previously vs. today

Answer 19

Formerly, genomes were only seen by the reflected light of phenotypes. Now, markers are no longer limited to genes with phenotypically observable effects. The ability to integrate DNA sequences directly means that any features that vary among individuals can serve directly as markers.

Question 20

What was the 1st genetic marker

Answer 20

The first genetic marker was based directly on DNA sequences rather than on phenotypic traits, were restriction fragment length polymorphisms. The genetic marker is the size of the restriction fragments that contain a particular sequence within them. A restriction endonuclease is an enzyme that cuts the DNA at a specific sequence, typically 4,6 or 8 bp long. Many specificity sites for REs are palindromic sequences. The fragment length can be estimated using 4^n.

Question 21

What are other useful markers

Answer 21

> Variable number tandem repeats (also called minisatellites)- VNTRs contain regions 10-100 bp long, repeated a variable number of times(the same sequence is repeated, but a different number of sequences per locus). In any individual repeats with the same motif, many appear once in the genome or several times, with different lengths on different chromosomes. The distribution of the sizes of repeats is the marker. Inheritance of VNTRs can be followed in a family and correlated with a disease phenotype like any other trait. VNTRs were the first genetic sequence data used for personal identification- genetic fingerprints- in paternity and in criminal cases.
Short tandem repeat polymorphisms (also called microsatellites) STRPS are regions of about 2-5 bp, but repeated many times, typically 10-30 consecutive copies. They have several advantages as markers over VNTRs. one is that they are even more distributed over the human genome. There is no reason why these markers need to lie within expressed genes and usually, they do not, except for the CAG repeats in Huntington’s disease and certain other disease genes.

Question 22

Name some of the applications of markers

Answer 22

> medical applications include their use in tissue typing to identify compatible donors for transplants, detection of disease susceptibility, and prediction of individual drug-response variation (pharmacogenomics)
anthropologists use them to trace migrations and relationships among populations
the DNA sequence itself can also be used as a marker. Collection and application of sequence data directly formerly made use of mtDNA or haplotypes. Now whole-genome sequencing is replacing many older techniques.

Question 23

Explain restriction maps

Answer 23

When you cut along DNA molecule,e.g the DNA in an entire chromosome, into fragments of convenient size for cloning and sequencing, you will require additional maps to report the order of the fragments so that the entire chromosome can be reconstructed from the fragments.
Cutting the DNA with a restriction enzyme produces a set of fragments. Cutting the same DNA with different restriction enzymes(with different specificities) produces overlapping fragments. From the size of the fragments produced from the individual REs and in combination, it is possible to construct a restriction map, stating the order and distance between the RE cleavage sites.
REs can produce fairly large pieces of DNA. Cutting the DNA into smaller pieces, which are clones and ordered by sequence overlaps, produces a finer dissection of DNA.
In the past, connections between chromosomes, genes, and DNA sequences were essential for identifying the molecular deficits underlying inherited diseases, like Huntington’s disease or CF. Sequencing of the human genome has revolutionized these investigations.