Abstract
Duplication plays an important role in creating drastic changes in genome evolution. In addition to well-known tandem duplication, duplication can occur such that a duplicated DNA fragment is inserted at another location in the genome. Here, we report several genomic regions in the human genome that could be best explained by two types of insertion-based duplication mechanisms, where a duplicated DNA fragment was modified structurally and then inserted into the genome. In one process, the DNA fragment is turned into an extrachromosomal circular DNA, cut somewhere in the circle, and reintegrated into another location in the genome. And in the other, the DNA fragment forms a “lariat structure” with a “knot”, the strand is swapped at the knot, and is then reintegrated into the genome. Our results suggest that insertion-based duplication may not be a simple process; it may involve a complicated procedures such as structural modification before reintegration. However, the molecular mechanism has yet to be fully understood.
Highlights
Duplication plays an important role in creating drastic changes in genome evolution
We searched for extrachromosomal circular DNA (eccDNA)- and eltDNA-mediated duplications in the human genome
We found 3 and 20 cases with fairly strong evidence for eccDNA- and eltDNA-mediated duplications, respectively
Summary
Duplication plays an important role in creating drastic changes in genome evolution. In addition to wellknown tandem duplication, duplication can occur such that a duplicated DNA fragment is inserted at another location in the genome. We report several genomic regions in the human genome that could be best explained by two types of insertion-based duplication mechanisms, where a duplicated DNA fragment was modified structurally and inserted into the genome. Duplication can occur non-tandemly, that is, a duplicated region arises elsewhere in the genome For this type of duplication, one may imagine that a duplicated fragment is inserted into an independent location some distance away from the corresponding segment, the molecular mechanism not fully understood (see[6,7,8]). We could observe a duplicated region in the syntenic order efghijabcd in the recipient region, which can be distinguished from the standard direct duplication that can be recognized as abcdefghij in the recipient region (Fig. 1A) We report another type of duplication that may involve structural modification before reintegration. We found a number of regions with strong evidence for eltDNA-mediated duplications in the human genome
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