Summary Oxford University FHS revision notes: Genome Structure
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Course
Genetics and Evolution
Institution
Oxford University (OX)
My Oxford University notes for the FHS exam in Genetics and Evolution. Useful for Biology, Biomedical Sciences and Human Sciences. I achieved a first and multiple academic prizes. Includes descriptions of concepts and key references/experiments.
How is the human genome more than genes and junk?
Why is a genome sequence not enough to predict a phenotype?
COMPLEX TRAITS
Complex trait: bell-shaped
Extreme phenotypes lead to clinical conditions/disease traits
Variation due to age, sex, environmental factors (e.g. diet) and genetic variation
May be an effect of multiple common variants that slightly alter normal physiological processes
The complex path from genotype to phenotype complicates the identification of disease genes
Complex traits are defined as any trait which does not follow mendelian inheritance patterns, and
as such almost all traits can be considered complex traits, not only are they often polygenic, but
also there are often strong gene-environment interactions which affect the expressed phenotype
Three types:
o Continuous (e.g. height or weight)
o Semi-continuous (e.g. clutch size)
o Threshold (e.g. diabetes)
It is how we USE our genes (both coding and non-coding) that makes us unique
Temporal and spatial gene expression during development
Regulation of gene expression to specialise cells
Epigenetic effects
Environment
GENOME OVERVIEW
The human genome
22 autosomes + 2 different sex chromosomes = nuclear genome (2.3Gb)
Mitochondrial genome (16.5kb)
Architecture of the human genome
≈1% protein coding
≈24% introns and regulatory regions
≈15% unique non-coding
Repetitive DNA (including transposable elements and related sequences)
Repetitive DNA (NOT including transposable elements and related sequences)
Function overview
30% not transcribed
63% transcribed but not stable (e.g. introns)
6% stably transcribed but non-coding
1% stably transcribed and coding (NOTE the majority of the genome that is stable transcribed is
NOT coding)
ENCODE project: identifying which regions of the genome we can assign a function to
Findings from 2012 phase: 80.4% of the genome is functional
Size -> Complexity?
, The C-value
Amount of DNA (in picograms pg) in a haploid nucleus
Often used interchangeably with genome size but NOTE in polyploids the C-value may represent
two or more genomes contained within the same nucleus
The C-value paradox: eukaryotic genome size fails to correlate well with apparent complexity
o Genome size does not reflect gene number in eukaryotes since most of their DNA is non-
coding and therefore does not consist of genes. The human genome, for example,
comprises less than 2% protein-coding regions, with the remainder being various types of
non-coding DNA
BUT even gene number is not a reliable predictor of complexity
Why? Some genes may encode multiple proteins and gene regulation may be more important than
gene number, which means that constructing a complex organism does not require a large number
of genes any more than it requires a large genome
EXAMPLE OF NON-CODING DNA: REPETITIVE DNA
Transposable elements and relatives
SINES: short interspersed nuclear elements (13%)
o Fragments of genes that were previously rRNA, tRNA and snRNA
o These have been reverse transcribed and reintegrated back into the genome
o Depend on LINES for their replication
o Most common = Alu sequence
LINES: long interspersed nuclear elements (21%)
o Have a promoter and encode a reverse transcriptase and an integrase
LTR retrotransposons
DNA transposons
How LINES move:
Repetitive DNA sequences NOT related to transposable elements
Segmental duplications (≈6%)
Microsatellites (≈3%)
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