Chromosomal illegitimate recombination in mammalian cells is associated with intrinsically bent DNA elements.

Abstract

Illegitimate recombination is the most frequent mechanism for chromosomal rearrangements in mammalian cells, yet little is known about this process. Most of the studies to date have looked at the sequences present at illegitimate junctions. These revealed the presence of recurrent DNA motifs, none of which was consistently found. We have undertaken to determine if intrinsic DNA structures such as bent DNA elements could be a major determinant in chromosomal illegitimate recombination. Using a two dimensional electrophoretic assay we found that eight out of eight junctions, resulting from various types of chromosomal rearrangements, had migration behaviour characteristic of DNA containing intrinsically bent DNA elements. In all cases, these occurred within one kilobase of the junctions, and in most cases could be found in both participating DNA segments. We also found that these bent DNA elements were present before the recombination event. When we analysed the frequency of intrinsically bent DNA elements in random chromosomal fragments, we found it to be about one per 11 kilobases. Thus these results suggest that bent DNA is associated with chromosomal illegitimate recombination.

Illegitimate DNA integration in mammalian cells

“…It should be noted, however, that the integrated DNA studied is often of viral or bacterial origin, and that this DNA is not necessarily 'neutral' in terms of stability. Bacterial and viral origins of replication, as well as plasmid sequences, often contain structures such as bent DNA that have been implicated in illegitimate rearrangements, 76 and that seem to play a role in integration. 77 Moreover, some foreign DNA sequences can by themselves induce instability: integration of a vector containing pericentromeric alphoid DNA can promote increases in chromosome number, changes in chromosome structure, higher frequencies of sister chromatid exchange, and the appearance of dicentric or ring chromosomes.…”

“…43,44,59,94,95 It has been demonstrated that integration of a circular bent DNA-containing vector preferentially occurs at the bent site, while bent DNA structures are often found at illegitimate recombination junctions and rearrangement breakpoints. 76 This suggests that such bent DNA sites in the genome (which are numerous) might be involved in integration. 77 As mentioned earlier, fragile sites are also frequently involved in illegitimate integration events when cells are treated with the appropriate inducing chemicals.…”

A Tandem of SH3-like Domains Participates in RNA Binding in KIN17, a Human Protein Activated in Response to Genotoxics

“…7 KIN17 is part of high molecular mass complexes that mediate different types of nucleic acid transactions. 8,9 The mammalian KIN17 protein binds to curved DNA found at hot-spots of illegitimate recombination in eukaryotic chromosomes, [10][11][12] and partially complements the bacterial transcriptional regulator in Escherichia coli called H-NS. 13 Moreover, proteomic analysis detected protein KIN17 in several complexes of the human spliceosome, a large RNAprotein assembly consisting of small ribonucleoprotein particles (snRNP) and associated non-small ribo-nucleoproteins.…”

Sequence-Directed DNA Curvature in Replication Origins Segments

“…Figure 2A shows an example of this application for a hypothetical segment of 800 bp, using a 120-bp window width and a 10-bp step. Values greater than or equal to 1.10 is indicative of the presence of intrinsically bent DNA sites (Milot et al, 1992). The twist angle corresponds to a rotation around the local twist axis that runs vertically through, or near, the centers of any two neighboring base pairs.…”