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The Majority of Recent Short DNA Insertions in the Human Genome Are Tandem Duplications

Summary: The Majority of Recent Short DNA Insertions in the Human Genome Are
Tandem Duplications
Philipp W. Messer and Peter F. Arndt
Max-Planck-Institute for Molecular Genetics, Berlin, Germany
Nucleotide substitutions, insertions, and deletions constitute the principal molecular mechanisms generating genetic var-
iation on small length scales. In contrast to substitutions, the nature of short DNA insertions and deletions (indels) is far less
understood. With the recent availability of whole-genome multiple alignments between human and other primates, detailed
investigations on indel characteristics and origin have come within reach. Here, we show that the majority of short (1­100
bp) DNA insertions in the human lineage are tandem duplications of directly adjacent sequence segments with conserved
polarity. Indels in microsatellites comprise only a small fraction. The underlying molecular processes generating indels do
not necessarily rely on the presence of preexisting duplicates, as would be expected for unequal crossing over, as well as
replication slippage. Instead, our findings point toward a mechanism that preferentially occurs in the male germline and is
not recombination-mediated. Surprisingly, nonframeshifting tandem duplications and deletions in coding regions still oc-
cur at approximately 50% of their genomic background rates. As is already well established in the context of gene and
segmental duplications, our results demonstrate that duplications are also likely to constitute the predominant process for
rapid generation of new genetic material and function on smaller scales.
The identification and precise characterization of the
fundamental molecular processes that induce genomic var-
iation will shed light on evolution's key mechanisms under-


Source: Arndt, Peter - Max-Planck-Institut für molekulare Genetik
Spang, Rainer - Computational Molecular Biology Group, Max-Planck-Institut für molekulare Genetik


Collections: Biology and Medicine; Biotechnology; Computer Technologies and Information Sciences; Physics