Crossover and recombination hotspots massively spread across human genome

Abstract

Abstract The recombination landscape and subsequent natural selection have vast consequences in evolution and speciation. However, most of the recombination hotspots in the human genome are yet to be discovered. We previously reported colonies of CG-rich trinucleotide two-repeat units (CG-TTUs) across the human genome, several of which were shared, with extensive dynamicity, as phylogenetically distant as in mouse. Here we performed a whole-genome analysis of AT-rich trinucleotide two-repeat units (AT-TTUs) in human and found that the majority (96%) resided in approximately 1.4 million colonies, spread throughout the genome. In comparison to the CG-TTU colonies, the AT-TTU colonies were significantly more abundant and larger in size. Pure units and overlapping units of the pure units were readily detectable in the same colonies, signifying that the units are the sites of unequal crossover. Subsequently, we analyzed several of the AT-TTU colonies in several primates and mouse. We discovered dynamic sharedness of several of the colonies across the primate species, which mainly reached maximum complexity and size in human. In conclusion, we report massive crossover and recombination hotspots of the finest molecular resolution and evolutionary relevance in human. In respect of crossover and recombination, the human genome is far more dynamic than previously imagined.