Fragile site orthologs FHIT/FRA3B and Fhit/Fra14A2: evolutionarily conserved but highly recombinogenic

Abstract

Common fragile sites are regions that show elevated susceptibility to DNA damage, leading to alterations that can contribute to cancer development. FRA3B, located at chromosome region 3p14.2, is the most frequently expressed human common fragile site, and allelic losses at FRA3B have been observed in many types of cancer. The FHIT gene, encompassing the FRA3B region, is a tumor-suppressor gene. To identify the features of FHIT/FRA3B that might contribute to fragility, sequences of the human FHIT and the flanking PTPRG gene were compared with those of murine Fhit and Ptprg. Human and mouse orthologous genes, FHIT and Fhit, are more highly conserved through evolution than PTPRG/Ptprg and yet contain more sequence elements that are exquisitely sensitive to genomic rearrangements, such as high-flexibility regions and long interspersed nuclear element 1s, suggesting that common fragile sites serve a function. The conserved AT-rich high-flexibility regions are the most characteristic of common fragile sites.

Fig. 1.

The distribution of repetitive elements. The percentage of the repetitive elements and GC content in every 50-kbp sequence are diagrammed in the bar charts. The numbering of the horizontal axes indicates nucleotide positions of sequences in human FHIT and mouse Fhit. The positions of exons are shown by arrowheads with numbers.

Fig. 2.

Comparison of human and murine orthologous sequences. The dotplot views of the alignments were produced by the advanced pipmaker program. (A) The dotplot comparison of FHIT vs. Fhit. (B) The dotplot comparison of PTPRG vs. Ptprg. In A and B, the horizontal and vertical axes represent the nucleotide number of human and mouse sequences, respectively, and the bottom rows show aligned regions in green and strongly aligned regions (at least 100 bp without a gap and with at least 70% nucleotide identity) in red. The locations of exons in human and mouse Fhit are also shown by arrowheads in A.

Fig. 3.

The transition of flexibility in sequences of FHIT and Fhit. Whole sequences of human FHIT and mouse Fhit were analyzed by flexstab. The flexstab program calculates helix flexibility. The peaks scoring >14 were considered HFRs. The horizontal axes indicate the nucleotide positions of sequences in human FHIT and mouse Fhit. The positions and the numbers of exons are shown by arrowheads.

Fig. 4.

The difference in position of conserved sequences and the distribution of elements. x and left y axes indicate the nucleotide number of mouse Fhit and human FHIT sequences, respectively, and the gray line represents the alignment of these two orthologs. The differences in positions of conserved regions, the green line, were calculated on the assumption that the difference is 0 at the first nucleotide of exon 1 in human and mouse Fhit sequences. The difference in position is scaled on the right y axis. The elements that are prone to be affected by rearrangement, MARs and HFRs, are highlighted by red and blue arrows, respectively. The positions of exons in mouse Fhit are provided.