Download BB30055: Genes and genomes

BB30055: Genes and genomes
Genomes - Dr. MV Hejmadi ([email protected])
Lecture 2 – Repeat elements
Lecture 2
Repeat elements
• What are repeat elements?
• How did they originate?
• Why are they important?
Repetitive DNA
Main classes based on origin
 Tandem repeats
Interspersed repeats
 Segmental duplications
1) Tandem repeats/ clustered repeats
Blocks of tandem repeats at
 subtelomeres
 pericentromeres
 Short arms of acrocentric
chromosomes
 Ribosomal gene clusters
Tandem / clustered repeats
Broadly divided into 3 types based on size and location
class
Size of
repeat
Repeat
block
Major
chromosomal
location
Satellite 5-171 bp > 100kb
minisatellite
9-64 bp
centromeric
heterochromatin
0.1–20kb Telomeres
microsatellites
1-13 bp
< 150 bp Dispersed
Which of the classes of tandem repeats are likely
to be found in a mRNA and which are unlikely?
HMG3 – Chap 9 pp 265-270
Satellites
Large arrays of repeats
Some examples
Satellite 1,2 & 3
Sat a (Alphoid DNA)
- found in all
chromosomes
Sat b satellite
ICF syndrome
(Immunodeficiency- Centromeric instabilityFacial anomalies syndrome)
Caused by hypomethylation of Sata in
chromosomes 1,9,16
Coutesy: Evani Viegas-Pequignot
Minisatellites
Moderate sized arrays of repeats
Some examples
Hypervariable minisatellite DNA
- core of GGGCAGGAXG
- found in telomeric regions
- used in original DNA
fingerprinting technique by Alec
Jeffreys
Microsatellites
VNTRs - Variable Number of Tandem Repeats,
SSR - Simple Sequence Repeats /STR – short tandem
repeats
1-13 bp repeats e.g. (A)n ; (AC)n
2% of genome (dinucleotides - 0.5%)
Used as genetic markers (especially for disease
mapping)
Microsatellite genotyping
design PCR primers unique to one locus in the genome
.a single pair of PCR primers will produce different sized products for
each of the different length microsatellites
Genotype test in a large family
using (CA)/(TG) marker D17S800
1 (3,6)
2 (1,5)
3 (3,5)
4 (2,5)
5 (3,6) etc
Alleles
Samples
What is the genotype of sample 10, 13, 16 ?
Why do you get the shadow bands?
Suggested to be due to replication slippage
How are tandem repeats generated in the genome?
strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330
strand slippage during replication
2) Interspersed repeats
A.k.a. Transposon-derived repeats
~ 45% of genome
Arise mainly as a result of
transposition either through DNA or RNA
retrotransposons (retroposons)
‘copy and paste’
DNA transposons (‘cut & paste’)
Classes of transposable elements
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
Interspersed repeats (transposon-derived)
major types
class
size
Copy
%
number genome*
LINE L1 (Kpn family)
L2
~6.4kb
0.5x106
0.3 x 106
16.9
3.2
SINE
Alu
~0.3kb
1.1x106
10.6
LTR
e.g.HERV
~1.3kb
0.3x106
8.3
mariner
~0.25kb
1-2x104
2.8
DNA
transposon
family
* Updated from HGP publications
HMG3 by Strachan & Read pp268-272
Repeat elements in the human genome
3) Segmental duplications
 Closely related sequence blocks (1-200kb)
at different genomic loci

Segmental duplications can occur on
homologous chromosomes
(intrachromosomal) or non homologous
chromosomes (interchromosomal)
 Not always tandemly arranged
 Relatively recent
Segmental
duplications
in chromosome 22
Segmental
duplications
Repeat elements
How did they originate?
Tandem repeats – replication slippage etc
Interspersed repeats – transposition events
Segmental duplications – strand exchange,
recombination events
Repeat elements
Why are they important?
 Evolutionary ‘signposts’
 Passive markers for mutation assays
 Actively reorganise gene organisation by
creating, shuffling or modifying existing
genes
 Provides information on chromosome
structure and dynamics
 Provides tools for medical, forensic, genetic
analysis
Pathogenic potential of Short Tandem Repeats
(STR)
Reduction or expansion of STR can be pathogenic
1) Unstable expansion of short tandem repeats
Characterised by anticipation
Large expansions outside
coding sequences
Modest expansions within
coding sequences
FRAXA, FRAX E
Huntington disease (HD)
Myotonic dystrophy (DM1)
SCA 1,2,3,6,7, 17
Friedrich ataxia (FA)
Kennedy disease
Spinocerebellar ataxia 8,11
HMG 3 Chapter 11 pp 337 - 344
2) Unstable deletions of STRs
STRs tend to be deletion hotspots
Interspersed repeats are susceptible to
deletions/duplications
E.g. Kearns-Sayre syndrome- encephalomyopathy
External opthalmoplegia
Ptosis
Ataxia
Common 4977bp deletion in mt DNA
Cataract
Pathogenic potential of segmental duplications
Nature Reviews Genetics 2, 791-800 (2001)
STRs are…
A)
B)
C)
D)
E)
F)
microsatellite sequences.
generally highly polymorphic.
Useful markers along the chromosome.
a and b
b and c
a and c
Which of the following is not one of the four
classes of transposon-derived repeat
sequences?
A. LINES
B. SINES
C. DNA transposons
D. Long terminal repeat transposons
E. pseudogenes
When repeats of a region lie adjacent to
each other they are called ___________
duplications
________________ gene transfer is the
direct transfer of genes from one species
in the germ line of another species.
True or False
All Repetitive DNA elements in the human
genome arose through a common
mechanism
Match the columns
A. Recombination
events
B. Replication slippage
C. Transposition events
1. Tandem repeats
2. Interspersed repeats
3. Segmental
duplications
Reading
Chapter 9: HMG 3 by Strachan & Read
Repeat elements and disease
Nature Reviews Genetics 2, 791-800 (2001)
C
CpG islands
CpG
Methyl CpG
methylated at C
T
TpG
Deamination
CpG islands show no methylation
Significance of CpG islands
1) Non-methylated CpG islands associated with the
5’ ends of genes
2) Usually overlap the promoter region
3) Aberrant methylation of CpG islands linked to
pathologies like cancer or epigenetic diseases
like Rhett’s syndrome
http://www.sanger.ac.uk/HGP/cgi.shtml
Inheritance of CpG methylation