Instability: Mutation and DNA repair

• Mutations

• DNA repair

Instability: Mutation and DNA repair

• Substitution rates vary throughout the genome.

Instability: Mutation and DNA repair

• Different mutation rates in primates and rodents

Species Pair Sites Percent Divergence Substitution rate (x 109)

Human/Chimp 921 1.9 1.3 (7 myr)

Human/Old world monkey 998 11.0 2.2 (25 myr)

Mouse/rat 3886 23.7 7.9 (15 myr)

Instability: Mutation and DNA repair

• Higher mutation rates in males–Greater number of cell divisions

Instability: Mutation and DNA repair

• Sex-specific differences in mutation rates

Gene Mutation Ratio of male/female mutations

NF1 Point 4.5

VHL Point 1.3

RB Point 8.5

ZFX/ZFY Mutations in last intron 6

Instability: Mutation and DNA repair

• Mechanism of mutation–Simple sequence repeats and strand slippage

Instability: Mutation and DNA repair

• Mechanism of mutation–Homologous equal crossover yields fusion

genes.

Instability: Mutation and DNA repair

• Mechanism of mutation–Unequal crossover causes insertions and

deletions.

Instability: Mutation and DNA repair

• Mechanism of mutation–Unequal crossover in a tandem repeat array

can result in sequence homogenization.

Instability: Mutation and DNA repair

• Mechanism of mutation–Tandem gene duplication by unequal

crossover or sister chromatid exchange facilitated by short interspersed elements.

Instability: Mutation and DNA repair

• Mechanism of mutation–Gene conversion

Non reciprocal sequence exchange between allelic or nonallelic genes.

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Instability: Mutation and DNA repair

• Mechanism of mutation–Splicing mutations

• Intron retention• Exon skipping• Activation of cryptic splice sites

Instability: Mutation and DNA repair

• Mechanism of mutation–Short tandem repeats are deletion insertion

hotspots.

Instability: Mutation and DNA repair

• Mechanism of mutation–Spinocerebellar ataxia (SCA1) triplet repeat

expansion.

Instability: Mutation and DNA repair

• Mobile elements and mutations–Alu element–Insertion events–Recombination events

Pol III transcription

Reverse transcription and insertion

1. Usually a single ‘master’ copy

2. Pol III transcription to an RNA intermediate

3. Target primed reverse transcription (TPRT) – enzymatic machinery provided by LINEs

                                                                                          

What are SINEs?

1.1. Interspersed ElementsInterspersed Elements

2.2. 70 - 300 Bases in Length 70 - 300 Bases in Length

3.3. Very High Copy NumbersVery High Copy Numbers(>100,000 Copies/Genome)(>100,000 Copies/Genome)

Promoter

disrupts reading frame

disrupts splicing

no disruption

ALU INSERTIONS AND MUTATION

alters gene expression

ALU INSERTIONS AND DISEASE

LOCUS DISTRIBUTION SUBFAMILY DISEASE REFERENCE

BRCA2 de novo Y Breast cancer Miki et al, 1996Mlvi-2 de novo (somatic?) Ya5 Associated with

leukemiaEconomou-Pachnis andTsichlis, 1985

NF1 de novo Ya5 Neurofibromatosis Wallace et al, 1991APC Familial Yb8 Hereditary desmoid

diseaseHalling et al, 1997

PROGINS about 50% Ya5 Linked with ovariancarcinoma

Rowe et al, 1995

Btk Familial Y X-linkedagammaglobulinaemia

Lester et al, 1997

IL2RG Familial Ya5 XSCID Lester et al, 1997Cholinesterase one Japanese family Yb8 Cholinesterase

deficiencyMuratani et al, 1991

CaR familial Ya4 Hypocalciurichypercalcemia and

neonatal severehyperparathyroidism

Janicic et al, 1995

C1 inhibitor de novo Y Complement deficiency Stoppa Lyonnet et al, 1990ACE about 50% Ya5 Linked with protection

from heart diseaseCambien et al, 1992

Factor IX a grandparent Ya5 Hemophilia Vidaud et al, 19932 x FGFR2 De novo Ya5 Apert’s Syndrome Oldridge et al, 1997GK ? Sx Glycerol kinase

deficiencyMcCabe et al, (personalcomm.)

UNEQUAL Alu/Alu HOMOLOGOUS RECOMBINATION

ALU/ALU RECOMBINATION AND GERM-LINE DISEASE

LOCUS DISTRIBUTION DISEASE REFERENCE

8 x LDLR

Kindreds Hypercholesterolemia Lehrman et al, 1985, 1987 Yamakawa et al, 1989 Rudiger et al, 1991 Chae et al, 1997

5 x -globin Kindreds -thalassaemia Nicholls et al, 1987 Flint et al, 1996 Harteveld et al, 1997 Ko et al, 1997

5 x C1 inhibitor

Kindreds Angioneurotic adema Stoppa-Lyonnet et al, 1990 Ariga et al, 1990

C3 Kindred C3 deficiency Botto et al, 1992 HPRT Individual

Lesch-Nyhan

syndrome Marcus et al, 1993

DMD Kindred Duchenne’s muscular dystrophy

Hu et al, 1991

ADA Individual ADA deficiency-SCID Markert et al, 1988

Ins. Rec. Individual Insulin-independent diabetes

Shimada et al, 1990

Antithrombin Individual Thrombophilia Olds et al, 1993 XY Individual XX male Rouyer et al, 1987 Lysyl hydroxylase Kindreds Ehlers-Danlos

syndrome Pousi et al, 1994

ALU/ALU RECOMBINATION AND CANCER

LOCUS DISTRIBUTION MECHANISM DISEASE REFERENCE

10 xALL-1

Somatic Alu-Alu recombDup. intron 1-6

Acutemyelogenous

leukemia

Strout et al, 1998So et al, 1997;Schichman et al,1994

7 xBCR/Abl

Somatic X-Alu recomb. CML Jeffs et al, 1998Chen et al, 1989de Klein et al, 1986

All-1/AF9 Somatic Alu-Alutranslocation

Acutemyelogenous

leukemia

Super et al, 1997

2 xBRCA1

Somatic &A kindred

Alu-Alu recomb(del exon 17; del.

Promoter)

Breast cancer Puget et al, 1997Swensen et al,1997

2 xMLH1

2 kindreds Alu-Alu recomb.(del exon 16)(exons 13-16)

HNPCC Nystrom-Lahti etal, 1995Mauillon et al,1996

TRE Somatic InterchromosomalAlu-Alu recomb

Ewing's sarcoma Onno et al, 1992

RB Common Alu-Alu recomb.(799 bp del.)

Association withglioma

Rothberg et al,1997

EWS Subset of Africans Alu-Alu recomb.(del 2 kb)

Protective againstEwing Sarcoma?

Zucman-Rossi etal, 1997

Instability: Mutation and DNA repair

• DNA repair–Photodimer–DNA glycosylase /AP endonucleases–E-coli mismatch repair–Human mismatch repair

Instability: Mutation and DNA repair

• DNA repair–Photodimer

Instability: Mutation and DNA repair

• DNA repair–DNA glycosylase /AP endonucleases

Instability: Mutation and DNA repair

• DNA repair–E-coli mismatch repair–Human mismatch repair

Instability: Mutation and DNA repair

• DNA repair–Human mismatch repair