Genomes & Sequencing

Question 1

What are transposons & how do they work?

Answer 1

Jumping genes
Can replicate & insert into other parts of the genome.
Some transpose via mRNA (retrotransposon) eg LINES

Question 2

Who discovered transposons & when?

Answer 2

Discovered by Barbara McClintock in 1940s from maize.

Question 3

Give the 2 categories of transposons.

Answer 3

DNA transposons
-form most of the mobile elements in bacteria
-can also occur in eukaryotes
Retrotransposons
-form most of the mobile units in eukaryotes

Question 4

How are genomes sequenced?

Answer 4

Very small fragments

Sequences assembled in silico by bioinformatics

Question 5

Give the features of 1st generation sequencing.

Answer 5

amplify DNA via PCR or cloning

• in vitro DNA synthesis
• base specific chain-terminating inhibitors
• typical length of sequences <1000 bases

Question 6

Give the features of 2nd generation sequencing.

Answer 6

amplify DNA through multiple PCR ‘clusters’ on a glass slide

• massive parallel in vitro DNA synthesis
• typical length of sequences 75-300 bases

Question 7

Give the features of 3rd generation sequencing.

Answer 7

amplify DNA not needed

• a strand of DNA is passed through a nanopore. The current is changed as the bases G, A, T & C pass through the pore in different combinations
• typical length of sequences 10s of Kbs of fragments bases

Question 8

Monozygotic twins have no genomic differences, but have a few…

Answer 8

epigenetic differences.

Question 9

Give the types of genetic variation.

Answer 9

• single nucleotide polymorphisms (SNPs)
• indels (insertions & deletions)
• copy number variations (CNVs)
• structural rearrangements

Question 10

Give the definition of an allele.

Answer 10

Broad term used to describe alternative forms of a heritable trait.

Question 11

Give the definition of a polymorphism.

Answer 11

Variation within a population of a given trait.

Question 12

What is an SNP & its significance in the human genome?

Answer 12

• differences at a single nucleotide
• Dr James Watson’s genome contained 3.3 million SNPs relative to the human genome project reference, ~0.1% of the genome differed
• approx. 10 million common SNPs in humans
• SNP rate versus chimpanzee ~1%

Question 13

What is an indel & its significance in the human genome?

Answer 13

• insertion or deletion of 1 or a few nucleotides
• ~4 x 105 indel polymorphisms identified in human genome, ~30% of these are tandem repeat expansion polymorphisms
• can be analysed by PCR & gel electrophoresis
• short tandem repeats are multi-allelic
• used in genetic profiling

Question 14

Give the phenotypic effects of genetic variation.

Answer 14

• intergenic region has often no phenotypic effect

- non-coding regulatory regions may have effects on gene expression