Nonhomologous recombination in the human genome: Deletions in the human factor VIII gene

doi:10.1016/0888-7543(91)90489-2

Genomics

Volume 10, Issue 1, May 1991, Pages 94-101

https://doi.org/10.1016/0888-7543(91)90489-2 Get rights and content

Abstract

Four deletions in the human factor VIII gene have been characterized at the sequence level in patients with hemophilia A. Deletion JH 1 extends 57 kb from IVS 10 to IVS 18. Intron 13 and exon 14 are partially deleted in patients JH 7 and JH 37, with a loss of 3.2 and 2.4 kb of DNA, respectively. The 3′ deletion breakpoint of the JH 21 event resides in intron 3 and extends 5′ into intron 1, resulting in the loss of exons 2 and 3. Seven of the eight breakpoints sequenced (5′ and 3′ for each of the four deletions) occur in nonrepetitive sequence, while the 3′ breakpoint of the JH 1 resides in an Alu repetitive element. All of the deletions are the result of nonhomologous recombination. The 5′ and 3′ breakpoints of JH 1, JH 7, and JH 37 share 2- to 3-bp homologies at the deletion junctions. In contrast, two nucleotides have been inserted at the JH 21 deletion junction. Short sequence homologies may facilitate end-joining reactions in nonhomologous recombination events.

References (53)

A.M. Albertini et al.
On formation of spontaneous deletion: The importance of short sequence homologies in the generation of large deletions
Cell
(1982)
R. Anand et al.
Molecular characterization of a β⁰ thalassemia resulting from a 1.4 kilobase deletion
Blood
(1988)
S.E. Antonarakis et al.
The molecular basis of hemophilia A in man
Trends Genet
(1988)
D. Brunier et al.
Copy choice illegitimate DNA recombination
Cell
(1988)
P.L. Deininger et al.
Base sequence studies of 300 nucleotide renatured repeated human DNA clones
J. Mol. Biol
(1981)
A. Efstratiadis et al.
The structure and evolution of the human β-globin gene family
Cell
(1980)
P.J. Farabaugh et al.
Genetic studies of the lac repressor VII: On the molecular nature of spontaneous hotspots in the lac I gene of Escherichia coli
J. Mol. Biol
(1978)
A.P. Feinberg et al.
A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity
Anal. Biochem
(1983)
B.D. Halligan et al.
Intra- and intermolecular strand transfer by HeLa DNA topoisomerase I
J. Biol. Chem
(1982)
P.S. Henthorn et al.
Molecular analysis of deletions in the human β-globin gene cluster: Deletion junctions and locations of breakpoints
Genomics
(1990)

M. Higuchi et al.

Molecular defects in hemophilia A: Identification and characterization of mutations in the factor VIII gene and family analysis

Blood

(1989)

H.H. Hobbs et al.

Deletion of exon encoding cysteine rich repeat of LDL receptor alters its binding specificity in a subject with familial hypercholesterolemia

J. Biol. Chem

(1986)

R. Kornreich et al.

Alpha-galactosidase A gene rearrangements causing Fabry disease: Identification of short direct repeats at breakpoints in Alu-rich gene

J. Biol. Chem

(1990)

M.A. Lehrman et al.

Duplication of seven exons in LDL receptor gene caused by Alu-Alu recombination in a subject with familial hypercholesterolemia

Cell

(1987)

M.A. Lehrman et al.

Alu-Alu recombination deletes splice acceptor sites and produces secreted LDL receptor in a subject with familial hypercholesterolemia

J. Biol. Chem

(1987)

S. Murru et al.

Illegitimate recombination produced a duplication within the FVIII gene in a patient with mild hemophilia A

Genomics

(1990)

R. Myerowitz et al.

A deletion involving Alu sequences in the β-hexosaminidase α-chain gene of French Canadians with Tay-Sachs disease

J. Biol. Chem

(1987)

R.D. Nicholls et al.

Recombination at the human alpha globin gene cluster: Sequence features and topological constraints

Cell

(1987)

E.F. Vanin et al.

Unexpected relationships between four large deletions in the human β-globin gene cluster

Cell

(1983)

G.C. White et al.

Factor VIII gene and hemophilia A

Blood

(1989)

S.E. Antonarakis et al.

Hemophilia A: Molecular defects and carrier detection by DNA analysis

N. Engl. J. Med

(1985)

M.D. Been et al.

DNA breakage and closure by rat liver type 1 topoisomerase: Separation of the half reactions by using a single-stranded DNA substrate

M.D. Been et al.

Nucleotide sequence preference at rat liver and wheat germ type 1 DNA topoisomerase breakage sites in duplex SV40 DNA

Nucleic Acids Res

(1984)

F.R. Blattner et al.

Cloning human fetal β-globin and mouse β-type globin DNA: Preparation and screening of shotgun collections

Science

(1978)

P. Bullock et al.

Association of crossover points with topoisomerase I cleavage sites, a model for nonhomologous recombination

Science

(1985)

S. Canning et al.

Short direct repeats at the breakpoints of deletions of the retinoblastoma gene

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Nonhomologous recombination in the human genome: Deletions in the human factor VIII gene

Abstract

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DNA breakage and closure by rat liver type 1 topoisomerase: Separation of the half reactions by using a single-stranded DNA substrate

Nucleotide sequence preference at rat liver and wheat germ type 1 DNA topoisomerase breakage sites in duplex SV40 DNA

Nucleic Acids Res

Cloning human fetal β-globin and mouse β-type globin DNA: Preparation and screening of shotgun collections

Science

Association of crossover points with topoisomerase I cleavage sites, a model for nonhomologous recombination

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