Palindrome-mediated chromosomal translocations in humans

Abstract

Recently, it has emerged that palindrome-mediated genomic instability contributes to a diverse group of genomic rearrangements including translocations, deletions, and amplifications. One of the best studied examples is the recurrent t(11;22) constitutional translocation in humans that has been well documented to be mediated by palindromic AT-rich repeats (PATRRs) on chromosomes 11q23 and 22q11. De novo examples of the translocation are detected at a high frequency in sperm samples from normal healthy males, but not in lymphoblasts or fibroblasts. Cloned breakpoint sequences preferentially form a cruciform configuration in vitro. Analysis of the junction fragments implicates frequent double-strand-breaks (DSBs) at the center of both palindromic regions, followed by repair through the non-homologous end joining (NHEJ) pathway. We propose that the PATRR adopts a cruciform structure in male meiotic cells, creating genomic instability that leads to the recurrent translocation.

Fig. 1

Palindrome-mediated translocation in humans. (a) Schematic representation of the t(11;22)(q23;q11). The PATRR11 and the PATRR22 are located at the breakpoints on 11q23 and 22q11, respectively. (b) Palindromic sequence possesses the potential for forming a cruciform configuration. Short palindromic sequences have the potential to form such double-stranded cruciform structures by intra-strand base pairing in the single-stranded DNA. DNA sequences indicated by blue arrows are the complement for those depicted by red arrows.

Fig. 2

Palindrome-mediated deletion. Upper panel shows replication-dependent pathway of the deletion. A hairpin structure is formed in the template strand because of intra-strand base pairing of the palindrome. Replication machinery may stall just before the palindrome, or may enter the palindrome and stall after progressing some distance. Since the deletion often utilizes short direct repeats within or flanking the palindrome, the palindromic region is partially or completely deleted. Lower panel depicts an alternative pathway, cruciform-mediated resection of the palindromic DNA. Red lines indicate palindromic regions.

Fig. 3

High frequency of de novo t(11;22) in sperm from normal males. (a) Translocation-specific PCR. Hatched boxes indicate chromosome 11, whereas dotted boxes depict chromosome 22. Centromeres are depicted as circles, while the PATRRs are indicated as filled boxes. The four PCR primers used for translocation-specific PCR (arrows) can be distinguished by the different colors. (b) Strategy for estimation of translocation frequency by PCR. Genomic DNA was extracted from sperm samples. Translocation-specific PCR was performed using multiple batches of template DNA. The translocation frequency was calculated using the equation, q = 1 − (1 − p)^1/n; n = number of haploid genomes per aliquot, p = the probability that an aliquot contains a translocation product, and q = the probability that one randomly selected haploid genome in a given aliquot sustained a translocation. (c) The results of PCR. Upper panel shows the results from sperm DNA, whereas the lower panel indicates those from lymphoblast DNA. Lane M, size marker; lane N, negative control; lane P, genomic DNA from a t(11;22) carrier serving as a positive control.

Fig. 4

Model for the mechanism of PATRR-mediated translocation. (a) The PATRR might be cleaved at the tip of the hairpin structure, which corresponds to the center of the palindrome (“center-break mechanism”). (b) Alternatively, the PATRR might be cleaved diagonally at the base of the cruciform (“kesa-giri” refers to the way a Japanese samurai kills an enemy with his sword). Two PATRRs, located on different chromosomes, are indicated by red and blue lines, respectively.