Topic 7: Genomics Part 2

Question 1

What are transposable elements

Answer 1

Aka transposons. Sequences that can move about the genome. They are of viral origin

Question 2

How repetitive are TEs

Answer 2

Moderately

Question 3

Features of TEs

Answer 3

• transposase (enzyme responsible for excising, relocating)
• direct repeats
• inverted repeats
• reverse transcriptase

Question 4

What is transposition

Answer 4

Movement of the transposons

Question 5

Three steps of transposition, performed by tranposase

Answer 5

1. Staggered breaks are made in the target DNA site
2. Transposable element is joined to single stranded ends of the target
3. DNA is replicated at the single stranded gaps

Question 6

What are direct repeats

Answer 6

Not part of the TE, but are generated by transposition

Question 7

What are inverted repeats

Answer 7

Are part of the TE, direct the tranposase

Question 8

Two main classes of TE

Answer 8

Class 1 - retrotransposons: work through an RNA intermediate (copy/paste)
Class 2 - DNA transposons: cut/paste mechanism, non-replicative

Question 9

Describe class 1 transposable elements

Answer 9

Retrotransposons
Copy/paste mechanism (replicative)
Encode a reverse transcriptase that can create and integrate cDNAs into the genome

Question 10

Examples of class 1 TE

Answer 10

SINE and LINE short and long interspersed elements
Alu element: 300 bases long

Question 11

Slide 8

Answer 11

Retrotransposons

Question 12

What is metagenomics? Examples

Answer 12

Sequencing all DNA from an environment to find out which species or genes are present
Ex soil biome, gut microbiome, lake/ocean sample

Question 13

Why do metagenomics?

Answer 13

Most microorganisms are unculturable in lab setting, may be crucial to understanding ecosystem

Allows sequencing of all the genomes present in a sample

Question 14

Metagenomics can determine..

Answer 14

species present (biodiversity) or genes present (biome function)

Question 15

What is genome wide association mapping

Answer 15

Involves detecting statistical associations between single nucleotide polymorphism markers and phenotypes (genotype-phenotype association) using a large sample of unrelated individuals

Question 16

Example of genome-wide association mapping

Answer 16

Collect a large dataset of mapped SNPs in
1. 1000 ppl with particular type of cancer
2. 1000 people without cancer
^ phenotype

Are there SNP alleles that most of the ppl with cancer have but few of the ppl without cancer have?

Question 17

Why use genome-wide association mapping? (4)

Answer 17

1. Some species cannot be mutagenized and studied in lab (humans)
2. some species can not be crossed and studied in lab (whale)
3. some phenotypes involve many genes (no good/clear phenotypes when knocked out)
4. many scientists interested in natural variation/mutations and how they evolve

Question 18

Slides 13-15**

Answer 18

Genome-wide association mapping

Question 19

Who got the nobel prize for discovering transposable elements

Answer 19

Barbara McClintock