Organisation of the Human Genome Flashcards
What is the human genome made up of?
3 billion base pairs.
23 pairs of linear chromosomes.
And mitochondrial genome = 16,569 base pairs, circular DNA
What is a way to analyse a genome
DNA Melt-Reassociation study.
Denature DNA = single-stranded DNA fragments.
Rapid = highly repeated
Intermediate = moderately repeated
Slow = unique
= reannealed double stranded DNA fragments
What are the different elements (+%) of the genome?
Repetitive DNA including transposable elements = 44%
Introns / regulatory sequences = 24%
Unique noncoding DNA = 15%
Repetitive DNA unrelated to transposable elements = 15%
Exons (protein coding) = 1.5%
How is the eukaryotic DNA sequence organised?
Single copies.
Gene families.
Tandem gene arrays.
Intermediate repeats (transposable elements).
Simple sequence repetitive DNA.
What does single copy DNA do?
= Protein coding genes.
=25% of genome (exons only 1%)
= average gene is 27kb with 9 exons
What is the largest gene in the human genome?
DMD (dystrophin) gene
over 2 million base pairs on X chromosome
main mRNA = 14 kb containing 79 exons
What is one of the smallest genes in the human genome?
IFNA6 (Interferon alpha 6) gene
around 1.5kb on chromosome 9
is a single exon mRNA (no introns)
What does non-protein coding single copy DNA do?
24% of genome = intron
15% of genome = single copy NOT part of protein-coding gene
function = most is transcribed to RNA
What is the function of non-coding DNA?
Most of the genome can be transcribed.
22,219 non-coding genes.
What are examples of structural RNAs?
rRNAs, tRNAs, snRNAs
What are microRNAs (miRNAs) involved in?
Gene regulation.
Roles in development.
Can cause cancer when dysregulated.
What do long non-coding (lnc) RNAs do?
Some are known to be functional.
e.g. Xist:
Can target regulatory proteins.
Can be disease markers - DD3/PCA3 prostate cancer
Possible causative agents in disease - BACE1
What are some examples of human gene families? (+number of genes)?
alpha-globulins = 4
beta-globulins = 5
actin = 15
keratin type 1 = 19
beta-tubulin = 19
alpha-tubulin = 10
What is a pseudogene?
A non functional, inactive copy of a gene
What are the 2 classes of eukaryotic transposable elements?
Retrotransposons. (retroposons).
DNA-DNA transposable elements.
What is the role of eukaryotic transposable elements in genome evolution?
They are a source of regulatory elements, sites of recombination.
Insertion can cause disease.
What do retrotransposons do?
Transpose via an RNA intermediate.
Can be viral:
retrovirus like = endogenous retrovirus
LINE-like = LINE1 + LINE2
Can be non-viral:
SINEs
Processed pseudogenes
What do DNA-DNA transposable elements do?
Transpose directly from DNA to DNA.
Similar to bacterial transposons.
(NOT active in human genome).
What is the transposable element composition of the human genome? (30%)
Non - mobile element (ME) sequence = 33%
ME + repeat remnants = 21%
LINE-1 = 17.6%
LINE-2 = 3.5%
Alu = 10.7%
SVA = 0.1%
(H)ERV = 8.9%
DNA = 3.4%
Other MEs = 0.7%
Non-ME repeats = 2%
What is the retrovirus / retrotransposon life cycle?
What is the structure of viral retrotransposons?
= 250-260 bp
What is the structure of the LINE-1 element (L1)?
Over 500,000 copies in human genome.
1-6 kb in length.
Only 40-50 are active.
Has 2 open reading frames:
ORF1 = 1137 bp - homology to gag
ORF2 = 3900 bp - homology to pol
No LTRs
What is the timing and tissue specificity of L1 transposition
Mostly repressed (methylation).
Demethylation and increased transposition in tumours.
Germ cells (many unique new insertions).
Early embryos (somatic cells).
Neural progenitor cells during childhood.
Each human is unique - can be neuronal differences.
What are non-viral elements?
A class of retrotransposons.
SINEs (13% of genome)
= genomic copies of small RNAs
= most belong to Alu family (7SL RNA)
= also copies of snRNAs and tRNAs
Processed pseudogenes
= genomic copies of mRNAs
What are Alu sequences?
150-300 bp
1 million copies, 10% of human genome
occur approx. every 6 kb
transcribed to give RNA
transpose using LINE reverse transcriptase
sites of recombination (hotspots)
What are SVAs (SINE-VNTR-Alu)?
Non-autonomous hominid-specific retrotransposons.
Several subtypes.
Can be transcribed.
Mobilise by LINE L1 retrotransposase.
Associated with disease in humans.
What are examples of SVA-associated diseases?
What is simple sequence repetitive (satellite) DNA?
Makes up 3% of genome.
Short repeating sequence.
Repeat unit length usually 5-10 bp (can be 2-200bp)
Total array length up to 5 x 106 bp (alphaloid DNA)
What is mini/ micro sattelite DNA?
Minisatellite and microsatellite DNAs = shorter repeats and array lengths.
Mini:
Repeat unit length = 15-100 bp
Total array length = 0.5-30 kbp
Micro:
Repeat unit length = 2-5 bp
Total array length = 60-200 bp
Array length is variable:
VNTRs = variable number tandem repeats
STRs = short tandem repeats
What can mini / microsatellite DNA be used for?
Can be used in paternity and forensic analysis, gene mapping. (VNTR Analysis by PCR).
