Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

Abstract

Messenger RNA molecules are tightly regulated, mostly through interactions with proteins and other RNAs, but the mechanisms that confer the specificity of such interactions are poorly understood. It is clear, however, that this specificity is determined by both the nucleotide sequence and secondary structure of the mRNA. Here, we develop RNApromo, an efficient computational tool for identifying structural elements within mRNAs that are involved in specifying posttranscriptional regulations. By analyzing experimental data on mRNA decay rates, we identify common structural elements in fastdecaying and slow-decaying mRNAs and link them with binding preferences of several RNA binding proteins. We also predict structural elements in sets of mRNAs with common subcellular localization in mouse neurons and fly embryos. Finally, by analyzing premicroRNA stem-loops, we identify structural differences between pre-microRNAs of animals and plants, which provide insights into the mechanism of microRNA biogenesis. Together, our results reveal unexplored layers of posttranscriptional regulations in groups of RNAs and are therefore an important step toward a better understanding of the regulatory information conveyed within RNA molecules. Our new RNA motif discovery tool is available online.bioinformatics ͉ motif prediction ͉ posttranscriptional regulation ͉ RNA secondary structure ͉ SCFGs R NA molecules undergo diverse posttranscriptional regulation of gene expression, including regulation of RNA transport and localization, mRNA translation, and RNA decay (1-3). In many cases, such posttranscriptional regulation occurs through elements on the mRNA molecule that interact with the hundreds of RNA binding proteins (RBPs) that exist in the cell (4). A well-known example is the iron-responsive element (IRE), a secondary structure RNA motif located on UTRs of members of the iron metabolism and transport pathway (5). The binding of the RBPs Irp1 and Irp2 to IRE elements affects the translation rate of the mRNA, and by that coordinates the response to changing levels of iron in the environment. Other examples include a 118-nucleotide stem-loop structure through which mRNAs are transported to the yeast bud tip by the RBP She2 (6) and the RBP Sbp2 that is involved in mediating UGA redefinition from a stop codon to selenocysteine by binding specific stem-loop structures, termed selenocystein insertion site (SECIS) elements, in the 3Ј UTR of selenoproteins (7). In other cases, elements on the mRNA molecule interact with other RNAs that direct the regulatory effect. For example, the recognition and binding affinity of a microRNA to its mRNA target is determined by both the sequence and structure of the target mRNA (8-11).The examples above suggest that the posttranscriptional regulation of mRNAs is determined not only by its linear nucleotide sequence but also by its secondary structure. Thus, a key goal is to understand the involvement of mRNA secondary structures in such regulation. One approach is to identify recurring patterns, termed m...

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

“…Many novel structural motifs were found to be associated with mRNA decay rates and localization. Notably, the results we obtained by analyzing structural motifs associated with mRNA decay are consistent with a previous study [32]. In addition, it is noteworthy that most of the mRNAs in our analysis are non-translating ones and do not represent the spectra of RBPs bound to mRNAs upon translation.…”

“…Additional predicted 3′ UTR structural motifs are consistent with previous results [32] (Figure S8 in Supporting Information). We also used MEME [52] to discover whether the same regions are enriched with any particular sequence motifs and found none.…”

“…We grouped the 5′ UTR and 3′ UTR sequences according to cellular localization and decay rates, respectively, and predicted the structural motifs in the UTRs' RBP binding regions using RNApromo [32]. We detected eight specific structural motifs regulating mRNAs' distinct cellular localizations ( Figure 5B; more examples in Figure S7 in Supporting Information).…”

“…The RBP binding to three RNA elements was profiled: (i) UTRs, (ii) structured canonical ncRNAs, and (iii) novel ncRNAs ( Figure 1B). (i) We detected various structural motifs affecting mRNA decay rates and localization in 3′ and 5′ UTR sequences, respectively, using RNApromo [32]. We also examined the secondary structural dynamics of RBP binding sites in 3′ UTRs upon glucose and nitrogen deprivation.…”

“…Some secondary structural motifs in UTRs involved in regulating mRNA decay rates and localization in yeast have been identified recently [32,50,51]. We grouped the 5′ UTR and 3′ UTR sequences according to cellular localization and decay rates, respectively, and predicted the structural motifs in the UTRs' RBP binding regions using RNApromo [32].…”