BB30055: Genes and genomesGenomes - Dr. MV Hejmadi (bssmvh@bath.ac.uk)

Lecture 2 – Repeat elements

• What are repeat elements?

• How did they originate?

• Why are they important?

Lecture 2 Lecture 2 Repeat elementsRepeat elements

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

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

Broadly divided into 3 types based on size and location

HMG3 – Chap 9 pp 265-270

Which of the classes of tandem repeats are likely to be found in a mRNA and which are unlikely?

SatellitesLarge arrays of

repeats

Some examplesSatellite 1,2 & 3Sat Alphoid DNA) - found in all

chromosomesSat satellite

ICF syndromeICF syndrome (Immunodeficiency- Centromeric instability-Facial anomalies syndrome)Caused by hypomethylation of Sat in chromosomes 1,9,16

Coutesy: Evani Viegas-Pequignot

MinisatellitesModerate sized arrays of repeats

Some examplesHypervariable minisatellite DNA

- core of GGGCAGGAXG- found in telomeric regions- used in original DNA fingerprinting technique by Alec Jeffreys

MicrosatellitesVNTRs - 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 genomea single pair of PCR primers will produce different sized products for each of the different length microsatellites

Genotype test in a large family Genotype test in a large family using (CA)/(TG) marker D17S800using (CA)/(TG) marker D17S800

Samples

Alleles

1 (3,6)2 (1,5) 3 (3,5)4 (2,5)5 (3,6) etc

What is the genotype of sample 10, 13, 16 ?What is the genotype of sample 10, 13, 16 ?

Why do you get the shadow bands?Why do you get the shadow bands?

Suggested to be due to replication slippageSuggested to be due to replication slippage

strand slippage during replication

Fig 11.5 HMG3 by Strachan and Read pp 330

How are tandem repeats generated in the genome?

strand slippage during replication

2) Interspersed repeatsA.k.a. Transposon-derived repeats~ 45% of genomeArise mainly as a result of transposition either through DNA or RNA

See lecture 3 for transposition

retrotransposons (retroposons)‘copy and paste’ DNA transposons (‘cut & paste’)

Classes of transposable elementsClasses of transposable elements

Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

Interspersed repeats (transposon-derived)

class family size Copy numbe

r

% 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

major types

* Updated from HGP publications HMG3 by Strachan & Read pp268-272

Repeat elements in the human genome 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 duplicationsSegmental duplications in chromosome 22

How did they originate?

Tandem repeats – replication slippage etc

Interspersed repeats – transposition events

Segmental duplications – strand exchange,

recombination events

Repeat elementsRepeat elements

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

Repeat elementsRepeat elements

Why are they important?

Pathogenic potential of Short Tandem Repeats (STR)

Reduction or expansion of STR can be pathogenic

Large expansions outside Large expansions outside coding sequencescoding sequences

Modest expansions within Modest expansions within coding sequencescoding 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

1) Unstable expansion of short tandem repeats 1) Unstable expansion of short tandem repeats Characterised by anticipationCharacterised by anticipation

HMG 3 Chapter 11 pp 337 - 344

2) Unstable deletions of STRs2) Unstable deletions of STRs

STRs tend to be deletion hotspotsSTRs tend to be deletion hotspots

Interspersed repeats are susceptible to Interspersed repeats are susceptible to deletions/duplicationsdeletions/duplications

External opthalmoplegia

Ptosis

Ataxia

Cataract Common 4977bp deletion in mt DNA

E.g. Kearns-Sayre syndrome- encephalomyopathyE.g. Kearns-Sayre syndrome- encephalomyopathy

Pathogenic potential of segmental duplicationsPathogenic potential of segmental duplications

Nature Reviews Genetics 2, 791-800 (2001)

STRs are… 

A) microsatellite sequences.

B) generally highly polymorphic.

C) Useful markers along the chromosome.

D) a and b

E) b and c

F) 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 FalseTrue or False

All Repetitive DNA elements in the human genome arose through a common

mechanism

Match the columnsMatch the columns

A. Recombination events

B. Replication slippage

C. Transposition events

1. Tandem repeats

2. Interspersed repeats

3. Segmental duplications

ReadingReading

Chapter 9: HMG 3 by Strachan & Read

Repeat elements and diseaseRepeat elements and disease

Nature Reviews Genetics 2, 791-800 (2001)

CpG islands

Significance of CpG islands1) Non-methylated CpG islands associated with

the 5’ ends of genes2) Usually overlap the promoter region3) 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

CpG Methyl CpG TpG

methylated at C Deamination

CpG islands show no methylation

C T

Inheritance of CpG methylationInheritance of CpG methylation