BB30055: Genes and genomes

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BB30055 Genes and genomes

• Genomes - Dr. MV Hejmadi (bssmvh_at_bath.ac.uk)

Lecture 2 Repeat elements
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(No Transcript)
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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 dynamics
• Provide tools for medical, forensic, genetic
  analysis

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Repetitive elements

• Main classes based on origin
• Tandem repeats
• Interspersed repeats
• Segmental duplications

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1) Tandem repeats

• Blocks of tandem repeats at
• subtelomeres
• pericentromeres
• Short arms of acrocentric chromosomes
• Ribosomal gene clusters

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Tandem / clustered repeats
Broadly divided into 4 types based on size
class Size of repeat Repeat block Major chromosomal location
Satellite 5-171 bp gt 100kb centromeric heterochromatin
minisatellite 9-64 bp 0.120kb Telomeres
microsatellites 1-13 bp lt 150 bp Dispersed
HMG3 by Strachan and Read pp 265-268
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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
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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
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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
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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

• .

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strand slippage during replication
How are tandem repeats generated in the genome?
Fig 11.5 HMG3 by Strachan and Read pp 330
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strand slippage during replication
Fig 11.5 HMG3 by Strachan and Read pp 330
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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

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Interspersed repeats (transposon-derived)
major types
class family 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
DNA transposon mariner 0.25kb 1-2x104 2.8
Updated from HGP publications
HMG3 by Strachan Read pp268-272
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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

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LINEs (long interspersed elements)
Nature (2001) pp879-880
HMG3 by Strachan Read pp268-272
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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
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Alu repeats evolved from processed copies of the
7SL RNA gene
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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.

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• 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

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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.

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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
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DNA transposons (lateral transfer?)

• DNA transposons
• Inverted repeats on both sides of element
• e.g. ATGCNNNNNNNNNNNCGTA

Nature (2001) pp879-880
From GenesVII by Levin
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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

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Segmental duplications

• Interchromosomal segments
• duplicated among non homologous chromosomes
• Prone to deletions/ duplications

Intrachromosomal duplications occur within a
chromosome / arm Prone to translocations
Nature Reviews Genetics 2, 791-800 (2001)
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Segmental duplications
Segmental duplications in chromosome 22
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Segmental duplications - chromosome 7.
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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
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Unstable deletions of STRs?

• STRs tend to be deletion hotspots

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Interspersed repeats are susceptible to
deletions/duplications
E.g. Kearns-Sayre syndrome- encephalomyopathy

• External opthalmoplegia
• Ptosis
• Ataxia
• Cataract

• Common 4977bp deletion in mt DNA

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Pathogenic potential of segmental duplications
Nature Reviews Genetics 2, 791-800 (2001)
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References

• Chapter 9 pp 265-268
• HMG 3 by Strachan and Read
• Chapter 10 pp 339-348
• Genetics from genes to genomes by Hartwell et al
  (2/e)
• Nature (2001) 409 pp 879-891