Chapter 9

Identifying Genes
Instructor: Anne Simon

FINAL EXAM
Thursday April 28

9:00 AM until noon

Where: TBD (To Be Determined)

INVITED SPEAKER
Wednesday
Dr. Jeremy McNeil

At the end of the session, you will:

See examples of GXE
MAO A
Serotonin transporter serotonin-transporter-linked
polymorphic region (5-HT TLPR)
(presented in last tutorials)

G X E interaction: The effect of a

polymorphism in the MAOA gene

G X E interaction: The effect of a

polymorphism in the 5-HTTLPR
Serotonin (5-HT) transporter linked polymorphic region

Monoamine oxidase A (MAOA)

Enzyme that degrades amine
neurotransmitters, such as dopamine,
norepinephrine, and serotonin.
The protein localizes to the outer
mitochondrial membrane.
Alternatively spliced transcript variants
encoding multiple isoforms have been
observed.

What are these genes encoding?

Lets look at a monoaminergic synapse

Synapse
Transporter
removal from the
extracellular space,
terminating the actions of
neurotransmitters

Synapse
Membrane Transporter
removal from the
extracellular space,
terminating the actions of
neurotransmitters

Vesicular Transporter
Load the neurotransmitter
in the synaptic vesicule

Celladhesion
molecules
maintain synapse
structure

Monoamines at rush hour

Noradrenalin

Dopamine

Attention
Blood pressure

Reward, Addiction

Serotonin

Histamine

Appetite, Mood,
Anxiety
Gastrointestinal
motility

Gastric acid release

Immune response

Adapted from Hakeem Lawal, 2010

ww.redbubble.com/people/andykazie/art/231042...

Monoamine oxidase A (MAOA)

Enzyme that degrades amine neurotransmitters, such as
dopamine, norepinephrine, and serotonin.
The protein localizes to the outer mitochondrial membrane.
Alternatively spliced transcript variants encoding multiple
isoforms have been observed.
Its encoding gene is adjacent to a related gene (MAOB)

Pre and postsynaptic players:

Example: monoaminergic synapse
Vesicular monoamine

Biosynthesis enzyme

Transporter (VMAT)
Metabolizing enzymes
monoamine oxidase (MAO)

Monoamine reuptake
transporter
Monoamine receptors

Pre and postsynaptic players:

Example: monoaminergic synapse
Vesicular monoamine

Biosynthesis enzyme

Transporter (VMAT)

Nerve
impulse

Metabolizing enzymes
monoamine oxidase (MAO)

Monoamine reuptake
transporter
Monoamine receptors

Many psychostimulants target the proteins

at the dopaminergic synapse
Methylphenidate
(Ritalin)
Cocaine

Amphetamine
Meth

DAT
DAT

Many antidepressant target the proteins

at the serotonergic synapse

Metabolizing enzymes
monoamine oxidase (MAO)

Serotonin reuptake
transporter

Many antidepressant target the proteins

at the serotonergic synapse

5-HTTLPR: serotonin re-uptake transporter

5-HTTLPR: localized effect of this specific

transporter

fMRI

Brain region specific S allele amygdale reactivi

Quantitative genetics and molecular genetics

To
identif
y
genes!

Problem
There is a genetic basis to most behavioral traits in
human.
Linkage mapping has been extremely successful in
mapping genes and gene variants affecting
Mendelian traits (e.g., single - gene disorders)
But these traits rarely are single-gene
They also have variable penetrance

Solution
Association mapping between a phenotype
(trait) and a genotype (DNA marker)
Linkage disequilibrium
Analysis of Quantitative Trait Loci (QTL)
Genome-Wide Association Studies (GWAS)

DNA markers are also known as

polymorphisms
Which kind of polymorphisms
exist and how do they appear?

Genetic variations

chromosomal variations

Chromosomal variations

Not used traditionally to map gene

What is a SNP?

Or
Functional
SNP

Think/Pair/Share
Where do SNPs come from?
Spontaneous or mutagens induced mutation
single-base pair substitutions

How do they occur?

Single Nucleotide Polymorphisms: SNPs

HapMap (short for haplotype map)

--> catalog of the 10 millions SNPs
Difference between individuals:
every 1 in 1000 nt
Very few has effect on diseases
Very few are new in the species

tp://www.dnalc.org/view/553-Whole-Genome-Association.html

For more on SNPs and Haplotypes

http://learn.genetics.utah.edu/content/variatio
n/haplotype/

CNVs (copy number variants):

Most dynamic form of human genetic
variation
Rate of mutation higher than for SNPs
>50,000 CNVariations

Database of genomic variants

>Cover >10% of the genome

tp://www.dnalc.org/view/553-Whole-Genome-Association.html

www.sanger.ac.uk/humgen/cnv/data/

How are polymorphisms detected?

SNPS:
Hybridization techniques
including microarrays and dot blots
Direct sequencing
Structural variants:
Cytogenetic detection
Array-based, genome-wide methods
Multiplex PCR-based methods

Several methods to detect specific

nucleotide changes (polymorphisms)

Allele specific oligonucleotides

hybridization

Conformational methods

Heteroduplex
Analysis:

denaturing
gradient
electrophoresis
and
HPLC

Base mismatch cleavage

Enzymatic
Chemical analysis
Cleavage
revealed by
gel
electrophoresis

Sequencing

Most labor
intensive
Terminated strands
at different length
detected using
fluorescence
(capillary

Cytogenetic detection and confirmation

of structural variants

Cytogenetic detection and confirmation

of structural variants

Array-based, genome-wide methods

Quantitative multiplex PCR of short

fluorescent fragments (QMPSF)

What to remember
The dopaminergic and serotonergic synapses
How do MAOA and 5-HTTLPR affect the synapse
function
What kind of polymorphisms exists
Which ones are used for linkage and QTL analysis,
and GWAS
How the polymorphisms can be detected

Next class
Reading assignment:
Chap 9: identifying genes