Abstract
We address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance distribution and with clusters of overrepresented short distances. We speculate that patterns of overrepresentation of short distances between symmetric word pairs may allow the occurrence of non-standard DNA conformations, such as hairpin/cruciform structures. We focused on the human genome, and analysed both the complete genome as well as a version with known repetitive sequences masked out. We reported several well-defined features in the distributions of distances, which can be classified into three different profiles, showing enrichment in distinct distance ranges. We analysed in greater detail certain pairs of symmetric words of length seven, found by our procedure, characterised by the surprising fact that they occur at single distances more frequently than expected.
Highlights
The similarity between the frequency of complementary nucleotides in a single strand of DNA is known as Chargaff ’s second parity rule[1]
We suggest that patterns of overrepresentation of short distances between reversed complements may be related to the occurrence of cruciform structures, and we evaluate this hypothesis in the human genome
The study addressed in this paper shows yet another use of inter-word distances and distance distributions, which may lead to a deeper understanding of intra-strand symmetry and its connection with secondary DNA structures
Summary
The similarity between the frequency of complementary nucleotides in a single strand of DNA is known as Chargaff ’s second parity rule[1] An extension to this parity rule suggests that, for each DNA strand, the proportion of an oligonucleotide (a sequence of adjacent nucleotides, referred to as a genomic word) should be similar to that of its reversed complement, a property that has been studied both for prokaryotes and eukaryotes[2, 3]. Cruciforms are structures with four arms that can be formed at sites containing reversed complementary words They are relevant in biological processes, including those of replication and transcription, recombination and translocation[5]. The study addressed in this paper shows yet another use of inter-word distances and distance distributions, which may lead to a deeper understanding of intra-strand symmetry and its connection with secondary DNA structures
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