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• W1566705283 abstract "In recent years, new classes and members of known classes of small regulatory RNAs have been discovered. Examples include small nucleolar RNAs (snoRNAs) that act in ribonucleoprotein complexes, where they guide the modification or splicing of target transcripts, and microRNAs (miRNAs) that modulate the turnover rate and protein output of mRNAs. Although small RNAs recognize their targets through RNA–RNA hybridization, this interaction is constrained by protein factors in the ribonucleoprotein complexes, which makes target prediction challenging. Genomic regions that are functionally important for the organism, such as protein-coding genes, noncoding RNA genes or regulatory sites, are conserved over longer evolutionary distances compared to regions that do not carry functional elements. As whole-genome sequencing became available, comparisons of genomic sequences of different species have become instrumental in predicting and identifying functional elements. In this chapter, the comparative genomics approaches used to discover the binding sites of small regulatory RNAs are described. A model is first defined describing the interaction between the regulatory RNA and its target, after which the putative binding sites of the regulatory RNA genome- or transcriptome-wide are identified in species of interest. Orthologous genomic regions from other species are examined to determine whether the site is conserved. In parallel, this procedure is applied to randomized variants of the regulatory RNAs with similar properties (e.g., nucleotide composition). Based on the extent to which the number of putative sites conserved across species is larger for a real regulatory RNA compared to its randomized variants, it can be inferred that: (i) the RNA–RNA interaction model defined is appropriate for describing productive interactions of the small RNA of interest; and (ii) a distinction can be made between functional, meaningful targets of the small RNAs from similar sequences in the reference genome." @default.
• W1566705283 created "2016-06-24" @default.
• W1566705283 creator A5018588101 @default.
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• W1566705283 date "2012-01-11" @default.
• W1566705283 modified "2023-10-01" @default.
• W1566705283 title "Comparative Genomics Methods for the Prediction of Small RNA‐Binding Sites" @default.
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• W1566705283 doi "https://doi.org/10.1002/9783527636778.ch55" @default.
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