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Lifestyle Genomics nutr 3360 > Module 1 - Genetics of Obesity > Flashcards

Module 1 - Genetics of Obesity Flashcards

1
Q

What is a genome? (3)

A
  1. genetic material of an organism
  2. hereditary information
  3. “coding and non-coding info
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2
Q

C-value paradox

A

organisms complexity not correlated with genome size

humans:
25,000 genes (small - coding region)
2.9 billion base pairs (large - includes non-coding)

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3
Q

Use genomic information for…

A

4 P’s

  • prediction
  • prevention
  • personalization
  • participation
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4
Q

Personalized medicine (nutrition) vs precision medicine (nutrition)

A

Personalized
- not feasible

Precision

  • considers similar individuals
  • targets specific need (ex. low iron absorption)
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5
Q

Common (older) method for sequencing genome

A

Sanger method (1980) aka dideoxy method

  • amplify DNA
  • 4 reacting mixtures
  • primed DNA to be sequenced, DNA polymerase, nucleotides, 1 of 4 labeled chain terminating nucleotide
  • chain build and ends at random
  • gel electrophoresis determines length (smallest travels furthest - read bottom to top - smallest to largest - 5’ to 3’)
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6
Q

DNA name

A

deoxyribonucleic acid

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7
Q

2 groups who sequenced the genome

  • goal
  • primary difference between approaches
A

Public Consortium (human genome project)

  • sequence ALL 3billion BP using BACs
  • coding and non-coding

Private Consortium (celera genomics)

  • sequence all genes shotgun method
  • coding only
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8
Q

what is a BAC

A

bacterial artificial clone

- circular bacterial plasmid and gene of interest ligated (bond together)

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9
Q

of BPs used in shotgun and BAC

A 
BAC = 150,000bp
Shotgun = 2000bp, 10000bp
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10
Q

BAC approach advantages (2)

A

1 - Reduce chance to misassemble because location is better known
2 - sequencing step is quick, dont need to sequence both ends of DNA

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11
Q

BAC approach disadvantages (2)

A

1 - laborious and time consuming

2 - bioinformatically heavy

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12
Q

Shotgun approach advantages (1)

A

experimentally quicker

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13
Q

shotgun approach disadvantages (2)

A

1 - experimentally quicker (sequenced from both ends)

2 - major problems dealing with “repeat sequences”

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14
Q

BAC method DNA sequencing steps

A

1) Form BACs
- approximately 150,000bp
- 30,000 formed)
2) create BAC library (amplify in bacteria / ecoli)
3) sequence landmarks (200-500bp)
- dna postal codes
- overlap and create a map
4) form M13 library
- smaller pieces fit into specific BAC
5) sanger sequencing of M13
6) sequence alignment

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15
Q

Shotgun method of DNA sequencing steps

A

1) restriction enzymes cut DNA into 2000 and 10,000 bp
2) form base plasmid library
* skip steps 3 and 4
5) sanger sequencing
- dont know which piece belongs to which gene or chromosome
6) sequence alignment
- align 2000bp to 10,000bp
- huge problems with repeats - requires powerful computer

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16
Q

Importantance of studying DNA (4)

A
  • inter-individual variability in disease phenotype and response to intervention (pharmacogenomics/nutrigenomics)
  • infuence gene expression and function (gene dosage/ more copies)
  • genes underlying common diseases (genetic targets for pharma - SNPs)
  • how disease is passed between generations (transgenerational effect)
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17
Q

% genetic component of obesity

A

40-80% (strong!)

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18
Q

best method to study if environmental impact depends on genes

A

Twin studies (genetically identical)

  • intervention, control for environmental factors
  • similar impact on twins, huge variance between individuals
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19
Q

microscopic structural variations in genomes (2)

A

aneuploidy
- abnormal # of chromosomes

heteromorphism
- visible region of a chromosome that varies in size or morphology

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20
Q

small-scale variations in the genome (5)

A

1) non-coding DNA (junk DNA)
2) copy number variants (CNVs) and segmental duplications (SDs)
3) inversions
- DNA segment reverse orientation to rest of chromosome
4) translocations
- DNA portion changes position w/o changing sequence
5) single nucleotide polymorphisms (SNPs)
- single bp changes

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21
Q

non-coding dna regulation of protein-coding dna (3)

A

1) non-coding functional RNA’s (tRNAs, rRNAs, siRNAs, etc)
2) promotor/repressor seq.
3) sequence recognition during meiosis (centromeres)

22
Q

Difference between segmental duplications and copy-number varients

A

SDs spread out

CNV side by side

23
Q

potential issue when studying SDs and CNVs

A

reference genomes are only as good as the people in that pool
- highly variable between populations, geographically, etc

24
Q

how do CNVs and SDs arise?

A

recombination within a chromosome
recombination between non-homologous chromosomes (maternal/paternal)

*happens in part due to repeat sequences in the genome

25
Q

SD size

A

> 1kb

  • 90% sequence identity (not perfect match but very similar)
  • constitutes 5% of genome
26
Q

SD location (is it random?)

A

spread over a persons genome

  • not random
  • 2% of SDs on chrome 3, 12% on chromosome 22
  • still unclear why
27
Q

Cause of SD formation

A

Replication errors or non-allelic homologous recombination (high sequence similarity but are not alleles)

  • what determines where they occur still unclear
28
Q

SD direct effects on phenotype

A 
gene expression (dosage sensitive genes)
- specifically genes involved with immunity (mean not random
29
Q

SD indirect effect on phenotype

A

structural rearrangements within chromosomes

- can be positive or negative

30
Q

major example of SD

- how does it work

A

CCL31L

  • increases # cause reduction in susceptibility to HIV infection and progression of AIDS
  • protein product competes with HIV binding site (CCR5 - chemokine receptor type 5)

*controversial

31
Q

CCL31L - SD

  • HIV-1/AIDS more common in smaller # of duplications
  • why might # of duplications be higher in a places with higher disease prevalence?
A

possible adaptation due to environmental pressures

  • reason still unclear
  • controversial
32
Q

CNV size

- proportion of genome?

A

1kb - 1mb

- constitutes 12% of the genome

33
Q

CNV location

A

CNVs found side by side on chromosomes

34
Q

CNV contribution to variations in genome

A

randomly selected genomes
- differ by atleast 1% due to CNVs

  • relevance
  • humans are 99% similar (not 99.9% - old theory)
  • very common in human genome
35
Q

cause of CNV formation

A

replication errors or non-allelic homologous recombination (high sequence similarity but not alleles)

  • what determines where they occur still unclear
  • same as SDs
36
Q

Distribution and frequency of CNVs

A

prevalent across genome

- 10% of protein coding genes have CNVs

37
Q

CNV direct effect on phenotypes

A

effect gene expression (dosage sensitive genes)
- enriched in regions where genes are involved with immune function and defence responses to bacteria

provide redundancy

  • organisms can evolve new or modified functions
  • 2 copies, 1 mutates – HUGE effect
  • multiple copies, 1 mutates – small/no effect
  • translocation, deletion or duplication events can affect exons, proteins aquire diff structure and function
38
Q

CNV major example

A

AMY1 (alpha amylase)

  • high # reported in populations consuming high carbohydrate (starch) diets
  • more copies, more amylase in saliva to break down starch
  • relevance
  • shows potential effect of environmental pressures of #
39
Q

CNVs involved with obesity

A

**AMY1 - alpha amylase

Others:
Chromosome 4
- UCP1 (thermogenesis)
- IL5 (inflammation)

Chromosome 16

  • large CNV regions (28 genes) rare varient
  • duplications – extreme leanness
  • deletions – morbid obesity
40
Q

Effect of large copy # of AMY1 (alpha amylase)

A

more copies, more protein, lower BMI

  • found in saliva and blood
  • link between ability to digest and body weight
41
Q

Imprinted genes

A
  • sex specific imprints (methylation)
  • only receive one copy of gene
  • certain genes always silenced from mom, others from dad during formation of egg and sperm
  • silenced throughout life, reset sex-specific imprints and totipotency during egg/sperm formation
  • necessary for normal development
42
Q

Imprinted genes effect on health risk

A

protection from diploidy no longer exists

  • mutation in the only copy, gene no longer expressed
  • ex. Prader-Willi syndrome
43
Q

Genetic conflict theory (imprinting)

A
  • males try to maximize use of maternal resources so offspring become stronger and healthier
  • females minimize use of maternal resources so all offspring survive
  • imprinting (methylation) causes battle for nutrients
44
Q

Imprinted genes and obesity

A
  • controls resetting of parental imprints during gametogenesis (chromosome 15)
  • equal occurrence in males, females and all ethnicities
  • Prader-Willi Syndrome (PWS)
  • Angelman Syndrome (AS)
  • together most common cause for life threatening obesity in children
45
Q

Pradaer Willi syndrome (PWS)

  • cause (gene)
  • clinical signs
A

4Mb deletion/silencing of ‘paternal’ chromosome 15 (70% of cases)

  • multiple genes in this region
  • SNRPN (gene encoding component of mRNA splicing)
  • obesity, excessive hunger, hypergonadism, sleep apnea, behavioural problems, mild/moderate retardation
    remember: P - paternal
46
Q

Angelman Syndrome (AS)

  • cause (gene)
  • clinical signs
A

Deletion UBE3A on ‘maternal’ chromosome 15 (70% of cases)
- ubiquitin pathway

  • severe mental retardation, absence of speech, smaller heads
  • but no obesity**
47
Q

Allele

A

alternate form of a gene at a given locus on a chromosome

48
Q

Single Nucleotide Polymorphisms (SNPs)

- amount and frequency

A

10million SNPs within human population

  • 1 every 300 nucleotides
  • most frequent source of polymorphic changes
  • variation based on geographic location
  • 14000 people only 200,000 SNPs
  • can tell with 50% accuracy where people are from (Europe study)
49
Q

SNPs associated with obesity

A

FTO and MC4R

  • 6 others less significant
  • 8 SNPs together explain
50
Q

FTO gene

A
  • highly expressed in hypothalamus
  • anorexigenic (appetite surpressing)
  • demethylase (animal / in vitro)
  • potential adipocyte development (white vs brown fat) and thermogenesis

SNP ‘risk’ allele

  • weighed 3kg more on average
  • consumed 200kcal more on average
51
Q

Direct to consumer (DTC) genetic tests vs traditional predictors

  • as predictors of obesity
  • SNP (FTO or top 32) vs family
A

childhood obesity and parental obesity prediction
- 75% accuracy
genetic prediction (FTO or top 32)
- 57% accuracy

relevance**
- more SNPs found that associate with obesity, but

Lifestyle Genomics nutr 3360 (4 decks)

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