RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders

Wojciechowska, Marzena; Olejniczak, Marta; Galka-Marciniak, Paulina; Jazurek, Magdalena; Krzyzosiak, Wlodzimierz J.

Nucleic Acids Research, 2014, Vol. 42, No. 19 11855 Could any other features of transcripts undergoing RAN translation be considered to explain the process of noncanonical protein synthesis? Our in silico structure prediction of expanded repeats along with their flanking regions (Figure 1 ) revealed the presence of modifying factors that may potentially stimulate or inhibit RAN translation. The stimulatory factors may include additional hairpin stabilization by repeat flanking sequences (e.g. additional extension of (CGG)n hairpin by S-FMR1 flanking sequences (Figure 1b) ), AUG START codons and various AUG-like codons (CUG, GUG, UUG, AUA, ACG and AUU which differ from AUG by a single base only (61)). Whereas inhibitory factors may comprise STOP codons (UAG, UAA, UGA) in different reading frames. How significant is the presence of alternative START codons for RAN translation initiation, and do STOP codons that may abolish the influence of AUG-like codons in the same frame play a role? These sequences were found to occur with different frequencies in the analyzed transcripts, and their relation to RAN translation efficiency should be carefully examined. At first glance, in the sense C9 transcript, an alternative START codon upstream of the G 4 C 2 repeats that is not followed by STOP in the polyGlyAla frame ( Figure 1c) does not affect the abundance of RAN proteins in this frame (15) . Similarly, a STOP codon located directly before the G 4 C 2 repeats in the polyGlyPro frame does not seem to disturb protein expression in this frame. In the antisense C9 transcript, we found only one AUG-like codon in close proximity to the hexanucleotide repeats (Figure 1d ), but two additional start codons are present >100 nt upstream of the repeats (15) . Despite these differences in the frequency of potential stimulatory and inhibitory factors of RAN translation, both sense and antisense C9 transcripts undergo RAN translation; however, the intensity of this phenomenon is higher for the sense transcript (15, 17, 22) .