Lecture 07

Question 1

Box 1.12

Discuss Moderately repetitve DNA (2)(3)

Answer 1

Box 1.12

Moderately repetitive DNA
a. functional
- dispersed gene families, created by gene duplication + divergence (e.g., actin,
globin)
- tandem gene family arrays (250 rRNA genes, 50 sites of 10 – 100 tRNA genes,
histone genes)

b. without known function
- SINES – 100,000s Alu copies (200 – 300 bp) scattered around genome
- LINES – 10 – 10,000 copies of 1 – 5 kb long
- pseudogenes

Question 2

Highly repetitive DNA
a. List the 3 types of highly repetitive DNA(3)

b. Discuss each of the above by giving its characteristics(3)

Answer 2

a. Minisatellites,microsatellites and telomeres

b.Characteristics
Minisatellites
- repeat arrays of 14 – 500 bp, scattered around genome; 1 – 5 kb long

Microsatellites
- repeat arrays up to 13 bp, 100s of kb long, ~106 copies per genome mainly as heterochromatin around centromeres

Telomeres
- typically comprise a 6 bp repeat (e.g., TTAGGG in humans, TTGGGG in Paramecium, TAGGG in Trypanosomes and TTTAGGG in Arabidopsis) that occurs 250 – 1,000x per chr end

Question 3

Dynamic components of genomes

a. What are transposable elements?(1)
b. Discuss the mechanisms of transposition(4)
c. Discuss the other features of TEs(2)

Answer 3

Dynamic components of genomes

a. Transposable Elements (TEs) – Fig. 1.15
* skittish segments of DNA, found in all organisms, that move around the genome

b.Mechanisms of transposition – Table 1.3
* retrotransposons (class I) – replicate via an RNA intermediate (RTase) and
thus use a ‘copy-and-paste’ mode; e.g., LINES (L1) and SINES (Alu)
* transposons (class II) – produce DNA copies without an intermediate RNA stage; encode transposase, which recognizes sequences within the
transposon itself, cuts it out, and inserts it elsewhere
* often the excision is sloppy, leaving a mutation at the original site (i.e. ‘cut-and-paste’ mode)
* at times, a bit of the surrounding sequence adheres to and accompanies the transposed material

c. TEs – other features
* contain inverted repeats at their ends (Fig. 1.16, Box 1.13), targets of excision machinery
* two juxtaposed TEs are capable of moving all the genetic material that occurs between them (e.g., E. coli Tn3 transposon used in DNA cloning)

Question 4

List the 5 biological effects of TEs(5)

Discuss each of the above 5 biological effects(5)

Answer 4

TEs – biological effects

Sequence broadcasting
* multiple copies distributed to various locations in the genome (genetic markers!)

Alter gene properties
* non-functional gene product (i.e. ‘knockout’ effect); affect gene regulation (TEs in promoters) even when in introns (slow down RNA pol) or alter its splicing pattern

Serve as an important engine of evolution
* gene evolution by fusion or exon shuffling; generate species-specific alternative
splicing patterns leading to protein isoforms; change reading frame leading to
truncated proteins, and thus, diseases

Cause chr rearrangement
* mispairing of chr’s during cell division (e.g., inversions, translocations, transpositions
and duplications) and deletions (mutation in TE sequence; e.g., Prader-Willi and
Angelman syndromes)

Leakage of epigenetic modification
* TEs are offensive squatters!; natural defence – methylate or regulate TEs using
siRNAs; TE silencing can also affect neighbouring genes; hypomethylation lead to
transcriptional reactivation of TEs due to cancers and other diseases!