The effects of structure on pre-mRNA processing and stability

Abstract

Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and various algorithms that use minimum free energy, maximum expected accuracy and comparative evolutionary based methods have been developed to predict secondary structures. However, these tools are not perfect, and this remains an active area of research. The secondary structure of pre-mRNA molecules can have an enhancing or inhibitory effect on pre-mRNA splicing. An example of enhancing structure can be found in a novel class of introns in zebrafish. About 10% of zebrafish genes contain a structured intron that forms a bridging hairpin that enforces correct splice site pairing. Negative examples of splicing include local structures around splice sites that decrease splicing efficiency and potentially cause mis-splicing leading to disease. Splicing mutations are a frequent cause of hereditary disease. The transcripts of disease genes are significantly more structured around the splice sites, and point mutations that increase the local structure often cause splicing disruptions. Post-splicing, RNA secondary structure can also affect the stability of the spliced intron and regulatory RNA interference pathway intermediates, such as pre-microRNAs. Additionally, RNA secondary structure has important roles in the innate immune defense against viruses. Finally, tertiary structure can also play a large role in pre-mRNA splicing. One example is the G-quadruplex structure, which, similar to secondary structure, can either enhance or inhibit splicing through mechanisms such as creating or obscuring RNA binding protein sites.

Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing

“…Finally, as observed with exonic secondary structure, the intronic secondary structure may also have a regulatory role in splicing. For example, certain types of intronic hybridization have been proposed to be involved in the promotion of splicing (60). Our preliminary observations of intronic hybridization (IH) mutants of β-globin showing distinct enhancement in splicing and the IH mutant of AdML exhibiting a small defect in splicing suggest that intronic secondary structure could have contributed to splicing regulation.…”

Future directions for high‐throughput splicing assays in precision medicine

“…In addition to variant interpretation, MPRAs can identify the effects of drugs on splicing. Many drugs, such as amiloride, demonstrate widespread, but tolerable effects on splicing (Chang et al, 2011;Soemedi et al, 2017a). These drugs can be screened against a library of variants to determine their personalized effects on patients with rare diseases (Soemedi, Vega, Belmont, Ramachandran, & Fairbrother, 2014).…”

Global spatial analysis of Arabidopsis natural variants implicates 5′UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature

“…There is now clear evidence that pre‐mRNA secondary structure can influence the outcome of the splicing process (Buratti & Baralle, ; Ding et al, ; Gueroussov et al, ; Li et al, ; Soemedi et al, ; Vandivier, Anderson, Foley, & Gregory, ). Pre‐mRNA processing is simultaneous, and mechanistically coupled, to transcription with splicing factors (SFs) recruited either constitutively or on an “as needed” basis to intron‐containing genes (Bentley, ).…”

“…There is now clear evidence that pre-mRNA secondary structure can influence the outcome of the splicing process (Buratti & Baralle, 2004;Ding et al, 2014;Gueroussov et al, 2017;Li et al, 2012;Soemedi et al, 2017;Vandivier, Anderson, Foley, & Gregory, 2016).…”