Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases

Abstract

CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to pathogenesis in addition to the well-known pathogenic effects of mutant proteins. We have analysed two crystal forms of RNA duplexes containing CAG repeats: (GGCAGCAGCC)2. One of the structures has been determined at atomic resolution (0.95 Å) and the other at 1.9 Å. The duplexes include non-canonical A–A pairs that fit remarkably well within a regular A-helix. All the adenosines are in the anti-conformation and the only interaction within each A–A pair is a single C2-H2···N1 hydrogen bond. Both adenosines in each A–A pair are shifted towards the major groove, although to different extents; the A which is the H-bond donor stands out more (the ‘thumbs-up’ conformation). The main effect on the helix conformation is a local unwinding. The CAG repeats and the previously examined CUG structures share a similar pattern of electrostatic charge distribution in the minor groove, which could explain their affinity for the pathogenesis-related MBNL1 protein.

Watson–Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation

“…A bending of the CCUG helix was also reported by Childs-Disney et al (2014). The bending/coiling effect was not observed in any of the tri-nucleotide repeats analyzed before (Kiliszek et al 2009(Kiliszek et al , 2010(Kiliszek et al , 2011(Kiliszek et al , 2012.…”

An innate twist between Crick’s wobble and Watson-Crick base pairs

“…Such large values of Δt and Δr are expected to significantly affect RNA conformations. These might be relevant for protein recognition interactions, as nWC pairs like U·U, U·C, C·C, A·A are involved in trinucleotide repeat expansion diseases (Gatchel and Zoghbi 2005) such as myotonic dystrophy (Kumar et al 2011), fragile X syndrome E (Kiliszek et al 2012), Huntington's disease, dentatorubral-palidoluysian atrophy, and spinocerebellar ataxias (Kiliszek et al 2010). Besides Δt, one might also expect Δr to play a significant role on the global conformation of RNA duplexes comprising purinepurine or pyrimidine-pyrimidine pairs.…”

Translation of HTT mRNA with expanded CAG repeats is regulated by the MID1–PP2A protein complex

“…CAG repeat RNAs fold into secondary hairpin structures [9][10][11][12] . To give an idea of how these hairpins could look like, we performed in silico RNA-structure predictions of CAG repeat stretches with different repeat sizes.…”

“…CAG sequences form double-stranded RNA structures, the stability of which increases with repeat-numbers [9][10][11] . For example the CAG repeat region of the HTT messenger RNA (mRNA) forms double-stranded hairpin structures 12 .…”