Topic 7- Genomics-Part 2

Transposable elements (TEs) - 45% human genome

also called transposons, jumping genes

Barbara mclintoch discovered TEs in Zea maize (aka corn)

Can be cut out and “jump” around within genome, cause mutations

Dr. Kate St.Onge – Biol 207

 Learning Outcomes

At the end of this topic you will be able to:

ü Define: transposable element, transposition, replicative vs
non-replicative, direct repeat, inverted repeat, cDNA, reverse
transcriptase
ü Describe how transposition generated direct repeats
ü Describe how retrotransposons transpose
ü Explain what is meant by the term metagenomics
ü Describe the basic procedure of a genome-wide association
mapping study
ü Analyze a manhattenplot

Dr. Kate St.Onge – Biol 207

 Topic 7 Genomics

• Transposable elements
• Association Mapping
• Metagenomics

Dr. Kate St.Onge – Biol 207

 Transposable Elements
Transposable elements ______:
TEs sequences that can move about
the genome. Viral origin

• Part of the moderately repetitive sequence class

_________________:
Transpositions
movement of the transposons

Discovered by Barbara McClintock -1983 Nobel prize

work done in 40s

Features
Transposase - enzyme that transposes the transposons

Direct repeats - not part of TE, but generated by transposition

Inverted repeats - part of TE, direct transposase (where to do cutting/pasting)

Reverse transcriptase (retrotransposon) also called “selfish genetic elemen

Dr. Kate St.Onge – Biol 207

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

formed from
filling gaps in
sticky ends

Dr. Kate St.Onge – Biol 207

 Transposition
1. Staggered breaks are made in
the target DNA site terminal inverted repeats
2. Transposable element is joined recognized by transposase and directs transposition
to single stranded ends of
target
3. DNA is replicated at the single PART of the TE
stranded gaps

Dr. Kate St.Onge – Biol 207

 Transposable Elements
There are two main classes of TE:
most TEs in humans
Class I- Retrotransposons- works through an RNA intermediate
• Transposition mechanism: copy/paste —> replicative
SINE and LINE
_________________________– short and long interspersed elements

_____________________~300
Alu element bases long. Found between 300,000
and one million times in the human genome! all over theplace

Class II-DNA transposons- only DNA

• Transposition mechanism: cut/paste

*some can copy/paste

Dr. Kate St.Onge – Biol 207

 Retrotransposons
Retrotransposons encode a reverse transcriptase that can create and integrate
cDNAs into the genome RNA —> cDNA (copy)

• This copy and paste mechanism is hard to select against and causes
bloating of the genome

translation generates
reverse transcriptase +
transposase
makes copy DNA

cDNA

Dr. Kate St.Onge – Biol 207

 Metagenomics
Sequence all DNA from an environment to find out which
species or genes are present filter to sort by size
Example: soil biome, gut microbiome, water sample

Why do metagenomics?
Most microorganisms are unculturable in a lab
DNA extraction
setting but still may be crucial to the understanding
of an ecosystem

Metagenomics allows the sequencing of all the (clone)

genomes present in a sample

1. assembly to determine species that are present —> biodiversity

2. assembly to determine genes that are present —> biome function sequence

assembly

Dr. Kate St.Onge – Biol 207

 Metagenomics
Sequence all DNA from an environment to find out which
species or genes are present
Example:

Why do metagenomics?
Most microorganisms are unculturable in a lab
setting but still may be crucial to the understanding
of an ecosystem B, C, D

diversity
function

Dr. Kate St.Onge – Biol 207

 Genome-wide Association Mapping
single nucleotide polymorphism

• Association mapping involves detecting statistical

associations between SNP markers and phenotypes using
a large sample of unrelated individuals.
genotype to phenotype association

~500k
• Example: collect a large dataset of mapped SNPs in genotype

1. 1000 people with a particular type of cancer

2. 1000 people without cancer phenotype

Ask-> is are there SNP alleles that most of the people with
cancer have but few of the people without cancer have?

Dr. Kate St.Onge – Biol 207

 Genome-wide Association Mapping
Why use this method?
• Some species can not be mutagenized and studied in the lab
eg. humans

• Some species can not be crossed and studied in the lab

eg. whales

• Some phenotypes involve many genes

don’t give good/clear phenotypes when knocked out
quantitative traits ex. human height

• Many scientist are interested in natural variation/mutations

and how they evolve
mutation - source of all natural variation that evolution acts on

Dr. Kate St.Onge – Biol 207

 NNCNNN
alleles
NNTNNN

Genome-wide Association Mapping

C/C C/C T/T T/T C/T T/T

C/C C/T T/T T/T

C/T C/T

SNP 1 C T
Blue 8 4 p-value 0.013
Yellow 2 10 < 0.05
statistically significant in a chi sq.
phenotype

this SNP is in/ near gene that causes this phenotype

Dr. Kate St.Onge – Biol 207

 Genome-wide Association Mapping
C/C G/C G/G G/G C/G C/C

C/G C/G G/G C/C

C/G C/G

SNP2 C G
Blue 6 6 p-value <0.05
>0.05
Yellow 6 6

not significant

Dr. Kate St.Onge – Biol 207

 Genome-wide Association Studies
• Manhattan plot shows geno/phenotype association

each dot is a SNP

most closely associated with given phenotype

log p value

5 loci significantly associated

p-val threshold

Dr. Kate St.Onge – Biol 207