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Algorithms for path-constrained sequence alignment - supplementary materials

miRNAs play a central role in gene regulation, by interacting with other RNAs. Understanding miRNA-mRNA interaction (hybridization) is an ongoing effort in recent years, resulting in improved target prediction methods [1]. Typically, such a hybridization contains a seed, that is, 6 or more consecutive Watson-Crick base-pairs starting at position 2 at the 5’ end of the miRNA (see Fig. 3(a)). Position 1 of the miRNA is usually unpaired and often the mRNA contains an A base in the corresponding position (in which case it may be paired with base U in the miRNA sequence). In some cases, position 2 in the miRNA is unpaired as well. Rarely (about 1% of preferentially conserved sites in mammals [1]), the hybridization has an imperfect seed with a single-nucleotide bulge or mismatch, followed by a 1-5 nucleotide long bulge and at least 4-5 Watson-Crick base-pairs long compensatory seed at positions 13-16 (see Fig. 3(b)). Recently, Clip-Seq (also known as HITS-CLIP) experiments, yielding genomewide identification of functional protein-RNA interaction sites in living tissue [2, 3], contribute to the study of miRNA-mRNA interaction. Chi et. al [4] used Clip-Seq produced data, consisting of Argonaute (Ago) bound miRNA and Ago bound mRNA segments (tags), to create a canonical seed based mapping of miRNA-mRNA interactions in mouse brain. Analysis of Ago-bound Clip-Seq tags narrow the search for functional binding sites to both the subset of Agobound miRNA and to Ago-bound ∼100 nucleotide long mRNA tags. While 27% of these Ago-bound mRNA (clustered) tags were unmapped (’orphan’ clusters) with respect to the canonical seed based mapping, analysis of orphan clusters supports the existance of alternative hybridization modes with imperfect seeds, such as single-nucleotide G-bulges in the mRNA at the pivot position 5-6 [5, 6]. Chi et al. [5] report that bulged sites comprise more than 15% of all Ago-miRNA interactions in mouse brain.