Repetitive elements Significance 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
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Repetitive elements Significance Evolutionary signposts Passive markers for mutation assays Actively reorganise gene organisation by creating, shuffling.
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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,
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 & 3
- found in all chromosomes
Alphoid DNA) 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
Fig 7.7 HMG3 by Strachan and Read pp 190
The most common way to detect microsatellites is to design PCR primers that are unique to one locus in the genome and that base pair on either side of the repeated portion
Therefore, a single pair of PCR primers will work for every individual in the species and produce different sized products for each of the different length microsatellites
Microsatellite genotyping.
CA repeat genotyping.
Fig 7.8 HMG3
A B C D E Allele typesA (3,6)B (1,5)C (3,5)D (2,5)E (3,6)
Marker D17S800
N.B. ‘stutters’ or shadow bands
Caused by strand slippage
strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330
Fig 11.5 HMG3 by Strachan and Read pp 330
strand slippage during replication
2) Transposon-derived repeats
A.k.a. interspersed repeats45% of genomeArise mainly as a result of transposition either through a DNA or a RNA intermediate
4 main typesLINES, SINES, LTRs and DNA transposons
Repetitive elements…
Most ancient of eukaryotic genomes Autonomous transposition (reverse
trancriptase) ~6-8kb long Internal polymerase II promoter and 2 ORFs 3 related LINE families in humans
– LINE-1, LINE-2, LINE-3.
Believed to be responsible for retrotransposition of SINEs and creation of processed pseudogenes
LINEs (long interspersed elements)
Transposon-derived repeats…
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.
HMG3 by Strachan & Read pp268-272
SINEs (short interspersed elements)
Transposon-derived repeats…
Nature (2001) pp879-880
LINES 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