Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

Abstract

RNA binding proteins recognize RNA targets in a sequence specific manner. Apart from the sequence, the secondary structure context of the binding site also affects the binding affinity. Binding sites are often located in single-stranded RNA regions and it was shown that the sequestration of a binding motif in a double-strand abolishes protein binding. Thus, it is desirable to include knowledge about RNA secondary structures when searching for the binding motif of a protein. We present the approach MEMERIS for searching sequence motifs in a set of RNA sequences and simultaneously integrating information about secondary structures. To abstract from specific structural elements, we precompute position-specific values measuring the single-strandedness of all substrings of an RNA sequence. These values are used as prior knowledge about the motif starts to guide the motif search. Extensive tests with artificial and biological data demonstrate that MEMERIS is able to identify motifs in single-stranded regions even if a stronger motif located in double-strand parts exists. The discovered motif occurrences in biological datasets mostly coincide with known protein-binding sites. This algorithm can be used for finding the binding motif of single-stranded RNA-binding proteins in SELEX or other biological sequence data.

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

“…Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by rnajournal.cshlp.org Downloaded from (Hiller et al 2006), allowing partial pairing of putative RBP binding sites significantly reduces in vivo predictive accuracy for six RBPs. Five of these RBPs have previously been reported to require their entire binding site to be unpaired, strongly suggesting that the sixth, Khd1p, will have a similar requirement.…”

“…The method we employed, as proposed by Hackermuller and coworkers (Hackermuller et al 2005), requires the whole site to be unpaired for the protein to bind. However, other methods, including the EF option of MEMERIS (Hiller et al 2006), and some methods used to predict target site accessibility for miRNAs (Robins et al 2005;Ellis et al 2007;Kertesz et al 2007;Long et al 2007;Geis et al 2008;Tafer et al 2008), allow target sites to be partially paired. To determine which of these approaches most accurately predicts in vivo RBP binding, we compared transcripts scored by #ATS based on the accessibility of the whole target site and those scored by #ATS when target site accessibility was approximated by either the average or the minimum single-base accessibility of all bases in the target site.…”

“…A role for accessibility in RBP binding has long been supported by in vitro selection (Levine et al 1993;Gao et al 1994) and measurements of in vitro binding affinity (Hackermuller et al 2005). More recently, motiffinding algorithms have been developed that use measures of RNA single-strandedness to more accurately recover some RBP motifs from in vitro selection binding data (Hiller et al 2006). In all cases, computational models of RNA folding were used to predict RNA secondary structure.…”

Regulatory element identification in subsets of transcripts: Comparison and integration of current computational methods

“…Our goal was to try all methods that could be applicable on sets of coregulated nonaligned transcripts (for discussion of limitations, see the Introduction). We considered GPRM (Hu 2003), GeRNAMo (Michal et al 2007), CMfinder (Yao et al 2006), comRNA (Ji et al 2004), MEME (Bailey et al 2006), MEMERIS (Hiller et al 2006), and RNA Sampler (Xu et al 2007). Among these, our computational resources (Linux cluster allowing up to 90 GB of RAM) permitted us to use CMfinder, MEME, and MEMERIS (although we could not use MEMERIS on all possible element lengths due to computation time restrictions) (see Materials and Methods).…”

“…MEMERIS (MEME in RNAs including secondary structures) is an extension of MEME. MEMERIS computes the probabilities of unpaired bases and then uses this measure to guide element finding in single-stranded regions (Hiller et al 2006). As methods based only on sequence conservation could be used to search a set of coregulated transcripts, this raises the question of whether currently available TFBS detection methods could accurately and efficiently detect mRNA elements, which are often defined not only by sequence but also by combinations of sequence and structure.…”