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BB30055: Genes and genomes. Genomes - Dr. MV Hejmadi ([email protected]). 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 - PowerPoint PPT Presentation
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BB30055: Genes and genomesGenomes - Dr. MV Hejmadi ([email protected])
Lecture 2 – Repeat elements
Repetitive elementsSignificanceEvolutionary ‘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
locationSatellite 5-171 bp > 100kb centromeric
heterochromatinminisatellite 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 repeatsA.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
16.93.2
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 opthalmoplegiaPtosisAtaxiaCataract 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