Research Article: RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression

Date Published: June 17, 2019

Publisher: Public Library of Science

Author(s): Collin A. O’Leary, Ryan J. Andrews, Van S. Tompkins, Jonathan L. Chen, Jessica L. Childs-Disney, Matthew D. Disney, Walter N. Moss, Danny Barash.


The MYC gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting MYC expression, we analyzed secondary structures in the MYC mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished by calculating folding metrics across the MYC sequence using a sliding analysis window and generating unique consensus base pairing models weighted by their lower-than-random predicted folding energy. A series of 30 motifs were identified, primarily in the 5′ and 3′ untranslated regions, which show evidence of structural conservation and compensating mutations across vertebrate MYC homologs. This analysis was able to recapitulate known elements found within an internal ribosomal entry site, as well as discover a novel element in the 3′ UTR that is unusually stable and conserved. This novel motif was shown to affect MYC expression, potentially via the modulation of miRNA target accessibility or other trans-regulatory factors. In addition to providing basic insights into mechanisms that regulate MYC expression, this study provides numerous, potentially druggable RNA targets for the MYC gene, which is considered “undruggable” at the protein level.

Partial Text

The MYC proto-oncogene is an important transcription factor that is required for programmed cell death (apoptosis) and cell proliferation [1]. It is a key component of oncogenesis [2] and, indeed, MYC is dysregulated in >50% of all cancers [3]. Post-transcriptional control plays significant roles in the regulation of many genes including MYC. Within the 5′ untranslated region (UTR) of the MYC mRNA is a structured internal ribosomal entry site (IRES) that stimulates cap-independent translation under apoptotic conditions and other instances where cap-dependent translation is inhibited [4]. Consistent with many other IRESs [5] the MYC IRES secondary structure (deduced from in vitro chemical probing data [6]) contains pseudoknots, which are motifs comprised of “non-nested” base pairing between looped out regions of RNA [7]. In addition to the IRES, other post-transcriptional regulatory mechanisms affect MYC expression that may be affected by MYC RNA structure [8]: e.g. microRNAs (miRs) [9].

The analyses performed in this report provide insights into the functions of RNA secondary structure in expression of MYC. The ScanFold-Scan results map out local features of RNA structure across the MYC mRNA. Interesting trends are observed moving across the sequence, where RNA thermodynamic stability decreases going 5′ to 3′, with marked “jumps” in instability observed at the UTR/coding-region junctions (S1 Fig; S1–S3 Tables). Likewise shifts toward more positive ED and z-score values were observed in junction-spanning windows: which could be of particular functional interest at the 5′ junction, which includes both the CUG (non-canonical) and AUG (canonical) translation initiation sites. These results indicate a lack of stable structure here, reiterating previous observations that indicate inhibitory roles for thermodynamically stable RNA secondary structure at initiation sites [32]. We additionally find evidence that evolution may be specifically selecting for MYC initiation site sequences that are ordered to be less stable than that predicted for sequences of similar composition (thus the presence of several positive z-scores at these junctions; S1 File); as well, the junction sequence is expected to have a volatile conformational ensemble, where no particular structure dominates (high ED).




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