Transcript DNA and Gene Expression

Pathways between Genes and
Behaviour
Functional Genomics
• Understanding the pathways between genes
and behaviours (i.e., mechanisms of genes
affecting behaviour)
• Levels of analysis
DNA
RNA
Protein
Genome Transcriptome Proteome
Brain
Neurome
Mind
Behaviour
Phenome
Levels of Analysis
• Functional genomics
– Bottom up
– Start at level of cells, molecular biology
– Work up to more complex systems
• Behavioural genomics
– Top down
– Identify relevant/interesting behaviour
– Reductionism towards genes
• Between level relationships correlational until proven causal
– E.g., behaviour can change brain structure, just as structural changes
can alter behaviour
Transcriptome
• Gene expression throughout the genome
• Gene expression beginning point for gene to
behaviour pathway
• Housekeeping genes
– Expressed at steady rate; most cells, most times
• “Special purpose” genes
– Only expressed when needed, at particular
developmental points, when activated by other genes or
environmental stimulus…
Factors on Expression
• Altering rate of transcription initiation
• Alteration of RNA transcript
– Passage of mRNA out of nucleus
– Protection/degradation of RNA transcript in
cytoplasm
• Rate of translation
• Posttranslational modification of protein
Gene Expression Profiling
• DNA permanent
• RNA ephemeral and specific
• RNA microarrays
– 1000s of genes simultaneously monitored
– Study effects of treatments, diseases,
developmental stages on gene expression
– “Snapshots” of gene expression throughout
genome
Brain Mapping
• Can create an atlas of
localized patterns of gene
expression
• Need brain tissue, so
limited in humans and
issues of pathology
• Mouse brain atlas
• Such maps are functional,
because genes only
detected if expressed
Genetical Genomics
• Emphasizes links between genome and
transcriptome
• Treats gene expression as phenotypic trait
• Aim is to find expression QTLs (eQTLs)
associated with gene expression
• Primarily with rodent models
Gene Expression & Environment
• Individual differences in gene expression
• Not necessarily highly heritable
• Gene expression responds to intra- and extracellular environmental variation
• Environmental influence at transcript level quite
significant
• Consider gene expression as a phenotype
• Epigenesis: gene-gene effects and environmentgene effects
The Proteome
• Refers to entire compliment of proteins
• Complexity increase from transcriptome
– Many more proteins than genes
– Post-translation from mRNA, amino acid
sequences can be modified, changing their
function
– Protein function is affected by other proteins;
they work in complexes
Analysis
• Like transcriptome, consider proteome as a
phenotype
• Hence, gene and environmental interaction
• Useful, given high individual differences in
protein function in different tissues
– Protein trait: differences in quantity of protein in
different tissues
• Protein microarrays
– Antibodies detect specific proteins
– Limited capacity (100s of proteins on array)
Early Protein Microarray Findings
• Most proteins show linkage to several
regions
• Chromosomal positions often differed from
those of the genes that code for the proteins
• Suggests multiple genes affect individual
protein traits
The Neurome
• Another step up in complexity
• Trillions of synapses vs. only billions of
DNA base pairs
• 100s of neurotransmitters
• Brain phenotypes called endophenotypes
Circadian Rhythm
• Approximately daily periodicity
• Endogenously generated, although
modifiable by external cues
• From prokaryotic cyanobacteria to humans
Period
• Konopka & Benzer (1971)
• Fruit fly
• Three mutant lines of flies showed shorter, longer,
and no circadian rhythm
• All mutations mapped to same gene, named period
• Conservative gene
– Responsible for Familial Advanced Sleep Phase
Syndrome in humans
• Not the only gene involved; interactions between
many genes
PER Genes
• Per1, Per2, Per3
• Members of period family of genes
• Expressed in suprachiasmatic nucleus
– Bilateral brain region, located in anterior
hypothalamus; controls circadian rhythms
– E.g., rats with SCN damage have no circadian
rhythm; they sleep the same amount, but
polyphasically for random lengths
Mice
• Per2 and Bmal1 work in opposition
• Per2 peaking for sleep
• Bmal1 peaking for wakefulness
Humans
• Per2 and Bmal1 work together
• Both peak around the same time
Lark vs. Owl
• Genes influencing morning or night person
• Per2 produces high RNA levels around 4AM;
associated with sleeping
• Food influences gene expression; Per2 has small
peak after food intake (post-lunch “slump”)
• REV-ERB works in opposition to Per2, peaking its
expression around 4PM; associated with
wakefulness
• Recent research looking to see if environmental
factors (e.g., shift work) can permanently alter
gene expression
Pleiotropy
• Clock genes have many functions
• Period found to have role in long term
memory
• Per genes may be involved in influencing
effect and abuse of drugs like cocaine
• Disruption of genes linked to bipolar
disorder, cardiovascular disease, effects of
drug toxicity
Learning and Memory
• Short-term memory
• Long-term memory
• Long-term potentiation
– Long-term synaptic changes
Drosophila
• Dunce and rutabaga: first
learning and memory
mutants
• Disrupts STM, but LTM
works fine
• Encode components of an
intracellular signaling
pathway involving cAMP,
protein kinase A, and a
transcription factor (CREB)
<en.wikipedia.org/wiki/Image:Drosophila_
melanogaster_-_side_%28aka%29.jpg>
Mouse
• Targeted mutations
• Hippocampus
• Knocked out -CaMKII
– Increased difficulty learning
spatial tasks
• Well over 20 genes known
to affect learning and
memory in mice
– Change strength of synaptic
connections
<en.wikipedia.org/wiki/Image:MorrisWaterMaze.jpg>
Long-Term Potentiation
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•
•
•
Genes drive long-term potentiation
But not an easy mechanism to understand
1000s of protein components involved
Numerous systems
– Glutamate receptor, NMDA receptor, CREB, etc., etc., etc.
• None of the fly or mouse genes and signaling molecules
involved are exclusive to learning processes
• Many necessary for basic cell functions
– Is memory being regulated by modulating background function of
cells involved in memory encoding?