Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models.

ABSTRACT: A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry by an overlap of the nonpalindromic motif present on one of the half-sites of the sequences. Here, we show that the implementation of multicomponent mixture models allows for different interpretations consistent with the existence of both palindromic and nonpalindromic submotifs in the sets of integration site sequences. We further show that the weak palindromic motifs result from freely combined site-specific submotifs restricted to only a few positions proximal to the site of integration. The submotifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Usi

SUBMITTER: Miklik D 

PROVIDER: S-EPMC10547254 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature