Transcript BB30055: Genes and genomes

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
Chromosome structure and dynamics
Provide 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
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 265-268
Satellites
Large arrays of repeats
Some examples
Satellite 1,2 & 3
a (Alphoid DNA)
- found in all
chromosomes
b satellite
HMG3 by Strachan and Read pp 265-268
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
HMG3 by Strachan and Read pp 265-268
Microsatellites
VNTRs - Variable Number of Tandem Repeats,
SSR - Simple Sequence 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)
Individual genotype
HMG3 by Strachan and Read pp 265-268
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
How are tandem repeats generated in the genome?
strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330
strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330
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)
major types
class
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
mariner
~0.25kb
1-2x104
2.8
DNA
transposon
family
* Updated from HGP publications
HMG3 by Strachan & Read pp268-272
LINEs (long interspersed elements)
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)
Nature (2001) pp879-880
HMG3 by Strachan & Read pp268-272
SINEs (short interspersed elements)
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.
100-300bp
1,500,000
13%
Alu repeats evolved from processed copies
of the 7SL RNA gene
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
http://www.geneticorigins.org/geneticorigins/
pv92/intro.html
Long Terminal Repeats (LTR)
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
Nature (2001) pp879-880
HMG3 by Strachan & Read pp268-272
DNA transposons (lateral transfer?)
DNA transposons
Inverted repeats on both sides of element
e.g. ATGCNNNNNNNNNNNCGTA
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 duplications
Interchromosomal segments
duplicated among non
homologous chromosomes
Prone to deletions/ duplications
Nature Reviews Genetics 2, 791-800 (2001);
Intrachromosomal
duplications occur within a
chromosome / arm
Prone to translocations
Segmental
duplications
in chromosome 22
Segmental
duplications
Segmental duplications - chromosome 7.
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
Unstable deletions of STRs?
STRs tend to be deletion hotspots
Interspersed repeats are susceptible to
deletions/duplications
E.g. Kearns-Sayre syndrome- encephalomyopathy
External opthalmoplegia
Ptosis
Ataxia
Common 4977bp deletion in mt DNA
Cataract
Pathogenic 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 339-348
Genetics from genes to genomes by
Hartwell et al (2/e)
3) Nature (2001) 409: pp 879-891