Topic 7: Genomics Part 2 Flashcards
What are transposable elements
Aka transposons. Sequences that can move about the genome. They are of viral origin
How repetitive are TEs
Moderately
Features of TEs
- transposase (enzyme responsible for excising, relocating)
- direct repeats
- inverted repeats
- reverse transcriptase
What is transposition
Movement of the transposons
Three steps of transposition, performed by tranposase
- Staggered breaks are made in the target DNA site
- Transposable element is joined to single stranded ends of the target
- DNA is replicated at the single stranded gaps
What are direct repeats
Not part of the TE, but are generated by transposition
What are inverted repeats
Are part of the TE, direct the tranposase
Two main classes of TE
Class 1 - retrotransposons: work through an RNA intermediate (copy/paste)
Class 2 - DNA transposons: cut/paste mechanism, non-replicative
Describe class 1 transposable elements
Retrotransposons
Copy/paste mechanism (replicative)
Encode a reverse transcriptase that can create and integrate cDNAs into the genome
Examples of class 1 TE
SINE and LINE short and long interspersed elements
Alu element: 300 bases long
Slide 8
Retrotransposons
What is metagenomics? Examples
Sequencing all DNA from an environment to find out which species or genes are present
Ex soil biome, gut microbiome, lake/ocean sample
Why do metagenomics?
Most microorganisms are unculturable in lab setting, may be crucial to understanding ecosystem
Allows sequencing of all the genomes present in a sample
Metagenomics can determine..
species present (biodiversity) or genes present (biome function)
What is genome wide association mapping
Involves detecting statistical associations between single nucleotide polymorphism markers and phenotypes (genotype-phenotype association) using a large sample of unrelated individuals
Example of genome-wide association mapping
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?
Why use genome-wide association mapping? (4)
- Some species cannot be mutagenized and studied in lab (humans)
- some species can not be crossed and studied in lab (whale)
- some phenotypes involve many genes (no good/clear phenotypes when knocked out)
- many scientists interested in natural variation/mutations and how they evolve
Slides 13-15**
Genome-wide association mapping
Who got the nobel prize for discovering transposable elements
Barbara McClintock
