Module 6 - Genomics, Proteomics, Epigenetics

Question 1

What are genetic maps?

Answer 1

• (also called linkage maps) provide information about the relative locations of genes to each other
• genetic map distances are based on recombination frequencies between genetic loci. Two loci on the same chromosome are said to belong to the same linkage group, and the recombination frequency will be less than 50%. If the recombination frequency between two loci equals 50%, then they belong to different linkage groups (i.e. on different chromosomes).
• 1 cM or map unit = 1% recombination between two loci

Question 2

Limitations of genetic maps

Answer 2

• limited resolution (detail) of positions
• because of certain characteristics, genetic distances don’t always correspond to physical distances between genes

Question 3

What are physical maps?

Answer 3

• based on direct analysis of DNA
• relative locations of genes are measured in # of base pairs (kb/Mb)
• physical maps generally give better resolution than genetic maps
• typically, a set of clones (inserts in vector backbone such as YAC, BAC, or cosmid) are available that correspond to regions of the physical map

Question 4

What is a contig?

Answer 4

• a contig is a set of two or more overlapping DNA fragments that covers a continuous stretch of a chromosome

Question 5

What is restriction mapping?

Answer 5

• DNA is split into different aliquots: one sample is cut with one restriction enzyme, and a second sample is cut with another restriction enzyme. A third sample is cut with both restriction enzymes.
• DNA fragments of each digest are run out by agarose gel electrophoresis
• overlap/patterns of fragments are used to position each restriction enzyme on the original DNA molecule
• other types of mapping include sequencing

Question 6

How do you sequence an entire genome?

Answer 6

• the difficulty of the task depends on the size and complexity of the genome (it is more difficult with large genomes, in regions of repetitive DNA, in centromeres, and telomeres)
• sequencing has improved vastly in terms of efficiency and the cost has been dramatically reduced for the past 20+ years since model organisms and humans were published

Question 7

What are the two general approaches when it comes to sequencing a human genome?

Answer 7

1. map-based sequencing:
   - initially, detailed genetic and physical maps of the gene of interest are created
   - clones are analyzed and contigs are assembled
   - finer mapping is done followed by sequencing of contigs
2. shotgun sequencing:
   - clones are sequenced at random (i.e. without being ordered first)
   - super computer finds overlapping sequences and orders them
   - requires more computing power

Question 8

What is epigenetics?

Answer 8

• potentially heritable traits that can’t be explained by changes in DNA sequences
• involves changes in chromatin structure which leads to changes in gene expression
• the three major molecular mechanisms are:
  i. methylation of DNA
  ii. histone modifications
  iii. RNA molecules

Question 9

Epigenetics and the rats experiment

Answer 9

• rats who are nurtured by their mother (highly licked/groomed) showed signs of a lower stress response and less fear. As opposed to a lower-licked/groomed rat who showed signs of a higher stress response and fear.
• highly groomed rats have distinct DNA methylation and histone acetylation; Glutacorticoid receptor (GR) which is one gene that plays a role in stress response
• a test was done with both rats:
• the lower-licked/groomed rat was infused with a drug to remove the methyl group and it showed signs of a lower stress response and less fear
• the highly licked/groomed rat was infused with methionine (methyl group) and it showed signs of an increased stress response and and was more anxious