Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells

Abstract

In mammalian cells, little is known about the nature of recombination-prone regions of the genome. Previously, we reported that the immunoglobulin heavy chain (IgH) mu locus behaved as a hotspot for mitotic, intrachromosomal gene conversion (GC) between repeated mu constant (Cmu) regions in mouse hybridoma cells. To investigate whether elements within the mu gene regulatory region were required for hotspot activity, gene targeting was used to delete a 9.1 kb segment encompassing the mu gene promoter (Pmu), enhancer (Emu) and switch region (Smu) from the locus. In these cell lines, GC between the Cmu repeats was significantly reduced, indicating that this 'recombination-enhancing sequence' (RES) is necessary for GC hotspot activity at the IgH locus. Importantly, the RES fragment stimulated GC when appended to the same Cmu repeats integrated at ectopic genomic sites. We also show that deletion of Emu and flanking matrix attachment regions (MARs) from the RES abolishes GC hotspot activity at the IgH locus. However, no stimulation of ectopic GC was observed with the Emu/MARs fragment alone. Finally, we provide evidence that no correlation exists between the level of transcription and GC promoted by the RES. We suggest a model whereby Emu/MARS enhances mitotic GC at the endogenous IgH mu locus by effecting chromatin modifications in adjacent DNA.

Gene conversion and deletion frequencies during double-strand break repair in human cells are controlled by the distance between direct repeats

“…It is possible that differences in chromatin structure at different loci influence the rate of strand excision, which in turn would influence the frequencies of conversion and SSA. Differences in chromatin appear to influence spontaneous gene-conversion rates (44). Nonetheless, at any particular locus, conversion frequencies are likely to increase with distance between repeats, as observed in the present study.…”

Effects of Replication and Transcription on DNA Structure-Related Genetic Instability

“…Maintaining the accuracy and integrity of DNA is crucial for cell survival and, thus, cells have developed highly sophisticated DNA damage-monitoring and repair systems to avoid mutation to maintain genome integrity. Interestingly, the distribution of mutations in human genomes is not random, and many mutational “hotspots” that have been identified in disease etiology are often located in specific repetitive, non-B DNA-forming sequences [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ].…”