Molecular cloning of a translocation breakpoint hotspot in 22q11.
It has been well documented that 22q11 contains one of the most rearrangement-prone sites in the human genome, where the breakpoints of a number of constitutional translocations cluster. This breakage-sensitive region is located within one of the remaining unclonable gaps from the human genome project, suggestive of a specific sequence recalcitrant to cloning. In this study, we cloned a part of this gap and identified a novel 595-bp palindromic AT-rich repeat (PATRR). To date we have identified three translocation-associated PATRRs. They have common characteristics: (1) they are AT-rich nearly perfect palindromes, which are several hundred base pairs in length; (2) they possess non-AT-rich regions at both ends of the PATRR; (3) they display another nearby AT-rich region on one side of the PATRR. All of these features imply a potential for DNA secondary structure. Sequence analysis of unrelated individuals indicates no major size polymorphism, but shows minor nucleotide polymorphisms among individuals and cis-morphisms between the proximal and distal arms. Breakpoint analysis of various translocations indicates that double-strand-breakage (DSB) occurs at the center of the palindrome, often accompanied by a small symmetric deletion at the center. The breakpoints share only a small number of identical nucleotides between partner chromosomes. Taken together, these features imply that the DSBs are repaired through nonhomologous end joining or single-strand annealing rather than a homologous recombination pathway. All of these results support a previously proposed paradigm that unusual DNA secondary structure plays a role in the mechanism by which palindrome-mediated translocations occur.
Kurahashi
Hiroki
H
Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan. kura@fujita-hu.ac.jp
Inagaki
Hidehito
H
Hosoba
Eriko
E
Kato
Takema
T
Ohye
Tamae
T
Kogo
Hiroshi
H
Emanuel
Beverly S
BS
D020856:AT Rich Sequence; D000818:Animals; D001483:Base Sequence; D019457:Chromosome Breakage; D002880:Chromosomes, Human, Pair 11; D002886:Chromosomes, Human, Pair 17; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D003001:Cloning, Molecular; D006224:Cricetinae; D004247:DNA / Q000737:chemistry / Q000235:genetics; D006801:Humans; D006822:Hybrid Cells; D051379:Mice; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D014178:Translocation, Genetic
D004247:DNA