1. Lecture 2 – Repeat elements
BB30055: Genes and genomes
Genomes - Dr. MV Hejmadi
Lecture 2 – Repeat elements

2. Lecture 2 – Repeat elements
What are repeat elements?
How did they originate?
Why are they important?

4. Repetitive elements Main classes based on origin Tandem repeats
Interspersed repeats
Segmental duplications

5. 1) Tandem repeats Blocks of tandem repeats at subtelomeres
pericentromeres
Short arms of acrocentric chromosomes
Ribosomal gene clusters

6. Tandem / clustered repeats
Broadly divided into 4 types based on size
class
Size of repeat
Repeat block
Major chromosomal location
Satellite
5-171 bp
> 100kb
centromeric
heterochromatin
minisatellite
9-64 bp
0.1–20kb
Telomeres
microsatellites
1-13 bp
< 150 bp
Dispersed
HMG3 by Strachan and Read pp

7. Satellites Large arrays of repeats Some examples Satellite 1,2 & 3
a (Alphoid DNA)
- found in all chromosomes
b satellite
Alphoid contains centromere binding protein CENPB
HMG3 by Strachan and Read pp

8. 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
Similar to ecoli chi sequence – hotspot for recombination
HMG3 by Strachan and Read pp

9. 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)
A father might have a genotype of 12 repeats and 19 repeats, a mother might have 18 repeats and 15 repeats while their first born might have repeats of 12 and 15.
Individual genotype
HMG3 by Strachan and Read pp

10. 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 .

11. 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’)
See lecture 3 for transposition

12. Interspersed repeats (transposon-derived)
major types
class
family
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
DNA
transposon
mariner
~0.25kb
1-2x104
2.8
* Updated from HGP publications
HMG3 by Strachan & Read pp

13. Classes of transposable elements
Classes of mobile elements. DNA transposons, e.g., Tc-1/mariner, have inverted terminal inverted repeats (ITRs) and a single open reading frame (ORF) that encodes a transposase. They are flanked by short direct repeats (DRs). Retrotransposons are divided into autonomous and nonautonomous classes depending on whether they have ORFs that encode proteins required for retrotransposition. Common autonomous retrotransposons are (i) LTRs or (ii) non-LTRs (see text for a discussion of other retrotransposons that do not fall into either class). Examples of LTR retrotransposons are human endogenous retroviruses (HERV) (shown) and various Ty elements of S. cerevisiae (not shown). These elements have terminal LTRs and slightly overlapping ORFs for their group-specific antigen (gag), protease (prt), polymerase (pol), and envelope (env) genes. They produce target site duplications (TSDs) upon insertion. Also shown are the reverse transcriptase (RT) and endonuclease (EN) domains. Other LTR retrotransposons that are responsible for most mobile-element insertions in mice are the intracisternal A-particles (IAPs), early transposons (Etns), and mammalian LTR-retrotransposons (MaLRs). These elements are not present in humans, and essentially all are defective, so the source of their RT in trans remains unknown. L1 is an example of a non-LTR retrotransposon. L1s consist of a 5'-untranslated region (5'UTR) containing an internal promoter, two ORFs, a 3'UTR, and a poly(A) signal followed by a poly(A) tail (An). L1s are usually flanked by 7- to 20-bp target site duplications (TSDs). The RT, EN, and a conserved cysteine-rich domain (C) are shown. An Alu element is an example of a nonautonomous retrotransposon. Alus contain two similar monomers, the left (L) and the right (R), and end in a poly(A) tail. Approximate full-length element sizes are given in parentheses
Science 12 March 2004: Vol no. 5664, pp

14. 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

15. Segmental duplications
Interchromosomal segments
duplicated among non homologous chromosomes
Prone to deletions/ duplications
Intrachromosomal
duplications occur within a chromosome / arm
Prone to translocations
Nature Reviews Genetics 2, (2001);

16. Chromosome rearrangements originate from double strand break repair or homologous recombination between repeat sequences

17. Segmental duplications
Segmental duplications in chromosome 22

18. Repeat elements How did they originate?
Tandem repeats – replication slippage etc
Interspersed repeats – transposition events
Segmental duplications – strand exchange, recombination events

19. strand slippage during replication
How are tandem repeats generated in the genome?
strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330

20. strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330

21. Alu repeats (type of SINE) evolved from processed copies of the 7SL RNA gene

22. Repeat elements Why are they important? Evolutionary ‘signposts’
Passive markers for mutation assays
Actively reorganise gene organisation by creating, shuffling or modifying existing genes
Chromosome structure and dynamics
Provide tools for medical, forensic, genetic analysis

23. 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
Anticipation – lower age of onset and/or severity is worse over subsequent generations
FA – Freidrich’s ataxia HD
10-30 CAG repeats – non pathogenic
repeats – unstable repeats cause huntingtin protein to aggregate and kill cells
Pg 477 HMG3

24. Unstable deletions of STRs?
STRs tend to be deletion hotspots
Pg 358-HMG3

25. Interspersed repeats are susceptible to deletions/duplications
E.g. Kearns-Sayre syndrome- encephalomyopathy
External opthalmoplegia
Ptosis
Ataxia
Cataract
Common 4977bp deletion in mt DNA
External opthalmoplegia
Ptosis
Ataxia
Cataract
Mt is recombination deficient therefore such deletions could arise due to replication slippage just like the STR

26. Pathogenic potential of segmental duplications
Nature Reviews Genetics 2, (2001)

27. References Chapters 9 and 11 Chapter 10: pp 339-348
HMG 3 by Strachan and Read
Chapter 10: pp
Genetics from genes to genomes by Hartwell et al (2/e)
Nature (2001) 409: pp