Organisation of the Genome

Question 1

What forms the human genome

Answer 1

3 billion base pairs spread over 23 pairs of linear chromosomes (51Mbp-245Mbp)

Question 2

Size of mitochondrial genome

Answer 2

16,569bp, circular DNA

Question 3

What percentage of the human genome encodes for proteins

Answer 3

~1%

Question 4

Size of E. coli genome

Answer 4

4.6Mbp, 4288 protein-encoding genes

Question 5

Size of mouse genome

Answer 5

2,800Mbp, ~23,000 protein encoding genes

Question 6

C-value paradox

Answer 6

Human genome is smaller than mudpuppy genome, but human genome has a greater percentage of protein encoding genes

Question 7

Explain DNA Melt-Reassociation

Answer 7

Denatured ssDNA fragments -> rapid reassociation -> highly repeated reannealed dsDNA fragments

Denatured ssDNA fragments -> intermediate reassociation -> moderately repeated reannealed dsDNA fragments

Denatured ssDNA fragments -> slow reassociation -> Unique reannealed dsDNA fragments

Question 8

Eukaryotic DNA sequence organisation

Answer 8

Single copy

Gene families

Tandem gene arrays

Intermediate repeat (transposable elements)

Simple sequence repetitive DNA

Question 9

Single copy DNA in genome

Answer 9

• Forms ~25% of genome but exons only 1%

Question 10

Size of average gene

Answer 10

27kb with 9 exons

Question 11

Smallest gene

Answer 11

SRY on Y chromosome

0.9kb formed from 1 exon which is 850bp

Question 12

Larger genes

Answer 12

DMD

Encodes for dystrophin

2400kb formed from 79 exons which are 180bp - introns are 30,770bp

Question 13

Non-protein-coding single copy DNA

Answer 13

24% of genome is intron

15% of genome is single copy but not a part of a protein-coding gene

Question 14

Function of single-copy non-coding DNA

Answer 14

• Most of this part is functional - over 80% has ≥1 biochemical activity
• Majority can be transcribed

22,219 non-coding genes

rRNAs, tRNAs, snRNAs

miRNAs - involved in gene regualtion (2,588 identified)

long non-coding (lnc)RNAs (14,727) - some known to be functional, e.g. Xist
Target regulatory proteins
Disease markers eg. DD3/PCA3 (prostate cancer)
Possible causative agents in disease (BACE1)

Question 15

Human gene families

Answer 15

a-globins - 4 genes

b-globins - 5 genes

Actin - 15 genes

Keratin type 1 - 19 genes

b-tubulin - 19 genes

a-tubulin - 10 genes

Question 16

What are tandemly arrayed genes (TAGs)

Answer 16

• Gene clusters created by tandem duplications
• One gene duplicated, copy next to original
• Can encode large numbers of genes at a time (2-100’s)
• 14-17% of human, mouse and rat coding genomes

Question 17

Tandem clusters of rRNA encoding genes

Answer 17

Human embryo has 5-10 million ribosomes

Cell number doubles within 24 hours

Single RNA gene may not be able to provide enough RNA, but tandem repeats allows sufficient RNA production

Question 18

What are the different eukaryotic transposable elements

Answer 18

Retrotransposons (retroposons):
Transpose via an RNA intermediate
Viral: retrovirus like e.g endogenous retroviruses or LINE like e.g. LINE1 and LINE2
Non-viral: SINEs or processed pseudogenes

DNA-DNA transposable elements:
Transpose directly from DNA to DNA
Similar to bacterial transposons - Not active in human genome

Question 19

What are eukaryotic transposable elements important for

Answer 19

Genome evolution - Source of regulatory elements, site of recombination. Insertions can cause disease

Question 20

Viral retrotransposons

Answer 20

Gag - Group antigens (viral core structure, RNA binding)
Pol - reverse transcriptase
Env - Envelope protein

Question 21

LINE-1 element

Answer 21

> 500,000 copies in human genome
1-6kb in length
Only 40-50 active

Open reading frames:
ORF1:1137bp - homology to gag
ORF2: 3900bp - homology to pol

No LTRs

Question 22

Timing and tissue specificity of L1 transposition

Answer 22

• 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 a unique mosaic

Question 23

What percentage of the human genome has transposable element composition

Answer 23

~30%

Question 24

Non-viral elements

Answer 24

SINEs (13% of genome)
- Genomic copies of small RNAs
- Mostly 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

150-300bp 1 million copies, 10% of genome Found in other vertebrates Occur every 6kb Transcribed to give RNA Transpose using LINE reverse transcriptase Sites of recombination (hotspots) Insertions cause inherited disease

Question 26

SVAs: SINE-VNTR-Alu

Answer 26

non-autonomous hominid-specific retrotransposons Don’t exist in Old World monkeys Several subtypes Can be transcribed Mobilize by LINE L1 retrotransposase Associated with disease in humans

Question 27

Highly repetitive DNA: Tandem repeat DNA

Answer 27

simple sequence repeat DNA ~8% of genome Repeat length 2-200bp Total array length up to 5 x 10^6 bp (alphoid DNA) Short tandem repeats Minisatellite and microsatellite DNAs

Question 28

Short tandem repeats

Answer 28

5% of genome Repeat unit length 1-6 bp Total array length up to 100bp Length variations can affect gene expression is some hereditary diseases e.g. HD, autism, schizophrenia Maybe by directly (weakly) binding transcription factors – STRs are enriched in (some) TF binding regions

Question 29

What do short tandem repeats influence?

Answer 29

Transcription factor protein binding at core gene regulatory sequences Binding of TFs to STRs is weaker than to core regulatory sequences but stronger than it is to genomic sequences

Question 30

Minisatellites

Answer 30

Repeat unit length 15-100bp 0.5-30kbp Array length variable - Variable number tandem repeats (VNTRs) or short tandem repeats Can be used in paternity and forensics

Question 31

Microsatellites

Answer 31

2-5bp - Repeat unit length 60-200bp - Total array length Array length variable - Variable number tandem repeats (VNTRs) or short tandem repeats Can be used in paternity and forensics