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

Lecture 2 – Repeat elements

Repetitive elements

Significance

Evolutionary ‘signposts’ Passive markers for mutation assays Actively reorganise gene organisation by

creating, shuffling or modifying existing genes

Chromosome structure and dynamicsProvide tools for medical, forensic,

genetic analysis

Repetitive elements

Main classes based on origin

Tandem repeats

Interspersed repeats

Segmental duplications

1) Tandem 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

HMG3 by Strachan and Read pp 265-268

Broadly divided into 4 types based on size

SatellitesLarge arrays of

repeats

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

chromosomes satellite

HMG3 by Strachan and Read pp 265-268

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

HMG3 by Strachan and Read pp 265-268

MicrosatellitesVNTRs - Variable Number of Tandem Repeats, SSR - Simple Sequence Repeats 1-13 bp repeats e.g. (A)n ; (AC)n

HMG3 by Strachan and Read pp 265-268

2% of genome (dinucleotides - 0.5%)Used as genetic markers (especially for disease mapping)

Individual genotype

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

strand slippage during replication

Fig 11.5 HMG3 by Strachan and Read pp 330

How are tandem repeats generated in the genome?

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 a DNA or a RNA intermediate

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

Most ancient of eukaryotic genomes Autonomous transposition (reverse trancriptase) ~6-8kb long, located mainly in euchromatin Internal polymerase II promoter and 2 ORFs 3 related LINE families in humans

– LINE-1, LINE-2, LINE-3.LINE-1 still active (~17% of human genme)

Believed to be responsible for retrotransposition of SINEs and creation of processed pseudogenes

LINEs (long interspersed elements)

LINEs (long interspersed elements)

Nature (2001) pp879-880 HMG3 by Strachan & Read pp268-272

Non-autonomous (successful freeloaders! ‘borrow’ RT from other sources such as LINEs)

~100-300bp long Internal polymerase III promoter No proteins Share 3’ ends with LINEs 3 related SINE families in humans

– active Alu, inactive MIR and Ther2/MIR3.

SINEs (short interspersed elements)

100-300bp 1,500,000 13%

Alu repeats evolved from processed copies Alu repeats evolved from processed copies of the 7SL RNA geneof the 7SL RNA gene

LINES and SINEs have preferred insertion sitesLINES and SINEs have preferred insertion sites

• In this example, yellow represents the distribution of mys (a type of LINE) over a mouse genome where chromosomes are orange. There are more mys inserted in the sex (X) chromosomes.

Try the link below to do an online experiment which shows how an Alu insertion polymorphism has been used as a tool to reconstruct the human lineage

http://www.geneticorigins.org/geneticorigins/pv92/intro.html

Repeats on the same orientation on both sides of element e.g. ATATATnnnnnnnnnnnnnnATATAT• contain sequences that serve as transcription promoters as

well as terminators. • These sequences allow the element to code for an mRNA

molecule that is processed and polyadenylated. • At least two genes coded within the element to supply

essential activities for the retrotransposition mechanism. • The RNA contains a specific primer binding site (PBS) for

initiating reverse transcription. • A hallmark of almost all mobile elements is that they form

small direct repeats formed at the site of integration.

Long Terminal Repeats (LTR)

Autonomous or non-autonomous Autonomous LTR encode retroviral genes gag, pol genes

e.g HERV Non-autonomous elements lack the pol and sometimes

the gag genes e.g. MaLR

Long Terminal Repeats (LTR)

Nature (2001) pp879-880 HMG3 by Strachan & Read pp268-272

DNA transposons Inverted repeats on both sides of elemente.g. ATGCNNNNNNNNNNNCGTA

DNA transposons (lateral transfer?)

Nature (2001) pp879-880 From GenesVII by Levin

3) Segmental duplications

Closely related sequence blocks at different genomic loci

Transfer of 1-200kb blocks of genomic sequence

Segmental duplications can occur on homologous chromosomes (intrachromosomal) or non homologous chromosomes (interchromosomal)

Not always tandemly arranged Relatively recent

Segmental duplicationsInterchromosomal segments

duplicated among non homologous chromosomes

Prone to deletions/ duplications

Intrachromosomal duplications occur within a chromosome / armProne to translocations

Nature Reviews Genetics 2, 791-800 (2001);

Segmental duplicationsSegmental duplications in chromosome 22

Segmental duplications - chromosome 7.

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

Unstable deletions of STRs?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)

References

1) Chapter 9 pp 265-268 HMG 3 by Strachan and

Read

2) Chapter 10: pp 339-348Genetics from genes to genomes by Hartwell et al (2/e)

3) Nature (2001) 409: pp 879-891