Chromosomal translocations and palindromic AT-rich repeats

Abstract

Repetitive DNA sequences constitute 30% of the human genome, and are often sites of genomic rearrangement. Recently, it has been found that several constitutional translocations, especially those that involve chromosome 22, take place utilizing palindromic sequences on 22q11 and on the partner chromosome. Analysis of translocation junction fragments shows that the breakpoints of such palindrome-mediated translocations are localized at the center of palindromic AT-rich repeats (PATRRs). The presence of PATRRs at the breakpoints indicates a palindrome-mediated mechanism involved in the generation of these constitutional translocations. Identification of these PATRR-mediated translocations suggests a universal pathway for gross chromosomal rearrangement in the human genome. De novo occurrences of PATRR-mediated translocations can be detected by PCR in normal sperm samples but not somatic cells. Polymorphisms of various PATRRs influence their propensity for adopting a secondary structure, which in turn affects de novo translocation frequency. We propose that the PATRRs form an unstable secondary structure, which leads to double-strand breaks at the center of the PATRR. The double-strand breaks appear to be followed by a non-homologous end-joining repair pathway, ultimately leading to the translocations. This review considers recent findings concerning the mechanism of meiosis-specific, PATRR-mediated translocations.

Figure 1. The region of 22q11 containing LCR-A–LCR-H is shown

A schematic diagram of proximal chromosome 22 indicating the position of the low copy repeats (LCRs) in 22q11.2. Boxes indicate the position of the LCRs. The bracket is indicates the recurrent 3Mb deletion of chromosome 22q11.2. The translocation breakpoint region on chromosome 22 is located within one of the remaining unclonable gap region from human genome project.

Figure 2. Characterization of PATRR sequences and their secondary structure

(A) PATRRs and their mediated translocations are listed. Deduced palindromic sequences of PATRR8, 4 and 1 are formed from translocation junction fragments. (B) Reconstructed translocation breakpoint regions for each translocation analyzed by M-fold to determine potential secondary structures [27] (http://mfold.rna.albany.edu/?q=mfold/DNA-Folding-Form). Breakpoint regions of all PATRRs are located around 600nt.

Figure 3. Possible involvement of DNA secondary structure

Palindromic sequence possesses the potential for forming an unusual secondary structure by intrastrand base pairing in single stranded DNA. (A) Palindromic DNA may form a hairpin structure during DNA replication. (B) Palindromic DNA can form a double-stranded cruciform structure. Palindromic regions are depicted blue arrows. The red arrows represent the complement of the sequence indicated by blue arrows.

Figure 4. Detection of de novo translocations by PCR of sperm DNA

(A) Diagram of the strategy used for estimation of translocation frequency by PCR. The green and orange arrowheads indicate the location of each individual PCR primer. White chromosomal regions indicate PATRR at the breakpoint; red chromosomal regions indicate the presence of a translocation. Combining the forward and reverse primers from different chromosomes allows the detection of the translocated product. Genomic DNA was isolated from sperm samples. Translocation-specific PCR was performed using multiple aliquots of template DNA. The translocation frequency was calculated using the equation, q = 1 - (1 - p)1/n; with n = number of haploid genomes per aliquot, p = the probability that an aliquot sustained a translocation [32]. The gel images show representative PCR results derived from sperm and lymphoblast DNA samples. The positive control is translocation carrier DNA. (B) PATRR polymorphisms affect the de novo t(11;22) translocation frequencies. In the histogram the vertical axis indicates the de novo translocation frequency for different alleles of PATRR11 (allele type L, SS, AS) and for different genotypes of PATRR22 (allele type A, B, C) in sperm. Also shown is frequency of the t(8;22), t(8;11) and t(17;22). Nucleotide size and accession number of PATRR11 and PATRR22 allele types are listed. Arrows indicate each arm of the palindromic sequences. Red and Blue arrows indicate complementary strands.