Organisation of the Human Genome

Question 1

What is the human genome made up of?

Answer 1

3 billion base pairs.

23 pairs of linear chromosomes.

And mitochondrial genome = 16,569 base pairs, circular DNA

Question 2

What is a way to analyse a genome

Answer 2

DNA Melt-Reassociation study.

Denature DNA = single-stranded DNA fragments.

Rapid = highly repeated

Intermediate = moderately repeated

Slow = unique

= reannealed double stranded DNA fragments

Question 3

What are the different elements (+%) of the genome?

Answer 3

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%

Question 4

How is the eukaryotic DNA sequence organised?

Answer 4

Single copies.

Gene families.

Tandem gene arrays.

Intermediate repeats (transposable elements).

Simple sequence repetitive DNA.

Question 5

What does single copy DNA do?

Answer 5

= Protein coding genes.

=25% of genome (exons only 1%)

= average gene is 27kb with 9 exons

Question 6

What is the largest gene in the human genome?

Answer 6

DMD (dystrophin) gene

over 2 million base pairs on X chromosome

main mRNA = 14 kb containing 79 exons

Question 7

What is one of the smallest genes in the human genome?

Answer 7

IFNA6 (Interferon alpha 6) gene

around 1.5kb on chromosome 9

is a single exon mRNA (no introns)

Question 8

What does non-protein coding single copy DNA do?

Answer 8

24% of genome = intron

15% of genome = single copy NOT part of protein-coding gene

function = most is transcribed to RNA

Question 9

What is the function of non-coding DNA?

Answer 9

Most of the genome can be transcribed.

22,219 non-coding genes.

Question 10

What are examples of structural RNAs?

Answer 10

rRNAs, tRNAs, snRNAs

Question 11

What are microRNAs (miRNAs) involved in?

Answer 11

Gene regulation.

Roles in development.

Can cause cancer when dysregulated.

Question 12

What do long non-coding (lnc) RNAs do?

Answer 12

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

Question 13

What are some examples of human gene families? (+number of genes)?

Answer 13

alpha-globulins = 4

beta-globulins = 5

actin = 15

keratin type 1 = 19

beta-tubulin = 19

alpha-tubulin = 10

Question 14

What is a pseudogene?

Answer 14

A non functional, inactive copy of a gene

Question 15

What are the 2 classes of eukaryotic transposable elements?

Answer 15

Retrotransposons. (retroposons).

DNA-DNA transposable elements.

Question 16

What is the role of eukaryotic transposable elements in genome evolution?

Answer 16

They are a source of regulatory elements, sites of recombination.

Insertion can cause disease.

Question 17

What do retrotransposons do?

Answer 17

Transpose via an RNA intermediate.

Can be viral:
retrovirus like = endogenous retrovirus
LINE-like = LINE1 + LINE2

Can be non-viral:
SINEs
Processed pseudogenes

Question 18

What do DNA-DNA transposable elements do?

Answer 18

Transpose directly from DNA to DNA.

Similar to bacterial transposons.

(NOT active in human genome).

Question 19

What is the transposable element composition of the human genome? (30%)

Answer 19

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%

Question 20

What is the retrovirus / retrotransposon life cycle?

Answer 20

Question 21

What is the structure of viral retrotransposons?

Answer 21

= 250-260 bp

Question 22

What is the structure of the LINE-1 element (L1)?

Answer 22

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

Question 23

What is the timing and tissue specificity of L1 transposition

Answer 23

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.

Question 24

What are non-viral elements?

Answer 24

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

Question 25

What are Alu sequences?

Answer 25

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)

Question 26

What are SVAs (SINE-VNTR-Alu)?

Answer 26

Non-autonomous hominid-specific retrotransposons.

Several subtypes.

Can be transcribed.

Mobilise by LINE L1 retrotransposase.

Associated with disease in humans.

Question 27

What are examples of SVA-associated diseases?

Answer 27

Question 28

What is simple sequence repetitive (satellite) DNA?

Answer 28

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)

Question 29

What is mini/ micro sattelite DNA?

Answer 29

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

Question 30

What can mini / microsatellite DNA be used for?

Answer 30

Can be used in paternity and forensic analysis, gene mapping. (VNTR Analysis by PCR).