Global RNA modifications to the MALAT1 triple helix differentially affect thermostability and weaken binding to METTL16

Abstract

Therapeutic mRNAs are generated using modified nucleotides, namely N¹-methylpseudouridine (m¹Ψ) triphosphate, so that the mRNA evades detection by the immune system. RNA modifications, even at a single-nucleotide position, perturb RNA structure, although it is not well understood how structure and function is impacted by globally modified RNAs. Therefore, we examined the metastasis-associated lung adenocarcinoma transcript 1 triple helix, a highly structured stability element that includes single-, double-, and triple-stranded RNA, globally modified with N⁶-methyladenosine (m⁶A), pseudouridine (Ψ), or m¹Ψ. UV thermal denaturation assays showed that m⁶A destabilizes both the Hoogsteen and Watson-Crick faces of the RNA by ∼20 °C, Ψ stabilizes the Hoogsteen and Watson-Crick faces of the RNA by ∼12 °C, and m¹Ψ has minimal effect on the stability of the Hoogsteen face of the RNA but increases the stability of the Watson-Crick face by ∼9 °C. Native gel-shift assays revealed that binding of the methyltransferase-like protein 16 to the metastasis-associated lung adenocarcinoma transcript 1 triple helix was weakened by at least 8-, 99-, and 23-fold, respectively, when RNA is globally modified with m⁶A, Ψ, or m¹Ψ. These results demonstrate that a more thermostable RNA structure does not lead to tighter RNA-protein interactions, thereby highlighting the regulatory power of RNA modifications by multiple means.

Keywords: MALAT1; METTL16; RNA methylation; RNA methyltransferase; RNA modification; RNA structure; RNA triple helix; RNA–protein interaction; long noncoding RNA; mRNA.