Stabilizing mammalian RNA thermometer confers neuroprotection in subarachnoid hemorrhage
Authors: Zhang Min , Zhang Bin , Liu Chengli , Preußner Marco , Ayachit Megha , Li Weiming , Huang Yafei , Liu Deyi , He Quanwei , Emmerichs Ann-Kathrin , Meinke Stefan , Chen Shu , Wang Lin , Zheng Liduan , Li Qiubo , Huang Qin , Haltenhof Tom , Gao Ruoxi , Qin Xianan , Cheng Aifang , Wei Tianzi , Yu Li , Schubert Mario , Gao Xin , Li Mingchang , Heyd Florian 
Published: May 2024

Mammals tightly regulate their core body temperature, yet how cells sense and respond to small temperature changes at the molecular level remains incompletely understood. Here, we discover a significant enrichment of RNA G-quadruplex (rG4) motifs around splice sites of cold-repressed exons. These thermosensing RNA structures, when stabilized, mask splice sites, reducing exon inclusion. Focusing on cold-induced neuroprotective RBM3, we demonstrate that rG4s near splice sites of a cold-repressed poison exon are stabilized at low temperatures, leading to exon exclusion. This enables evasion of nonsense-mediated decay, increasing RBM3 expression at cold. Additionally, increasing intracellular potassium concentration stabilizes rG4s and enhances RBM3 expression, leading to RBM3-dependent neuroprotection in a mouse model of subarachnoid hemorrhage. Our findings unveil a mechanism how mammalian RNAs directly sense temperature and potassium perturbations, integrating them into gene expression programs. This opens new avenues for treating diseases arising from splicing defects and disorders benefiting from therapeutic hypothermia.

Highlights

rG4s are enriched near splice sites of cassette exons repressed upon cold shock

rG4s act as RNA thermometers in mammals by controlling accessibility of splice sites

rG4 stability mediates temperature-dependent RBM3 expressionex vivoandin vivo

Stabilizing rG4s in RBM3 exon 3a reduces brain damage in subarachnoid hemorrhage

Graphical abstract

Here is a refined model of RNA G-quadruplexes acting as evolutionarily conserved thermo- and potassium sensors, modulating alternative splicing in mammals. RNA G-quadruplexes (rG4s) function as reversible temperature sensors, impacting alternative splicing dynamics. In low temperatures or high potassium conditions, rG4s can mask surrounding splice sites, rendering these sites inaccessible, thereby promoting exon skipping. Conversely, at high temperatures or under low potassium conditions, rG4s become destabilized, allowing splice sites to be exposed, and facilitating efficient exon inclusion. RBM3, a well-known cold-induced protein with neuroprotective functions, harbors a poison exon with rG4s around splice sites, that, upon inclusion, triggers NMD (non-sense mediated decay) of the RBM3 mRNA. Under low temperatures or high potassium conditions, rG4s shield the splice sites, leading to poison exon skipping and increased RBM3 expression. Stabilization of these rG4s through increased K+promotes poison exon skipping, enabling escape from NMD, and ultimately elevating RBM3 expression. Notably, 4-AP, a clinically used pan voltage-gated potassium channel blocker, protects against neuronal damage in a subarachnoid hemorrhage mouse model in an RBM-dependent manner. (ISS: intronic splicing silencer, ESE: exon splicing enhancer, ACA: anterior cerebral artery, MCA: middle cerebral artery, PPA: pterygopalatine artery, ICA: internal carotid artery, ECA: external carotid artery, CCA: common carotid artery)