RNA structural switches play crucial roles in regulating gene expression, particularly in bacteria, but their study in more complex organisms like humans has been limited. Recently, researchers at UCSF introduced SwitchSeeker, a novel approach combining computational analysis with experimental validation to identify functional RNA structural switches within the human transcriptome.
SwitchFinder identifies candidate RNA switches in the human genome
a, Example of SwitchFinder locating the RNA switch in the VEGFA mRNA sequence. b, Receiver operating characteristic (ROC) curves of SwitchFinder predictions of RNA switches from the common Rfam families. SwitchFinder was applied to a mix of real sequences and their shuffled counterparts (with preserved dinucleotide content). ROC curves measure its ability to correctly select the real sequences. AUC, area under the ROC curve; riboswitch families, c-di-GMP-I (Cyclic di-GMP); FMN, flavin mononucleotide; NiCo, nickel or cobalt ions; SAM, S-adenosyl-l-methionine; THF, tetrahydrofolate; TPP, thiamine pyrophosphate. c, AUCs of RNA switch predictions across the Rfam families for two models: SwitchFinder and SwiSpot. Each dot represents one Rfam family. The lines show the change in accuracy between the two models. The families that have higher AUCs for SwitchFinder are shown with blue lines; the ones that have higher AUCs for SwiSpot are shown in red. P value calculated with the paired two-sided t-test (P = 0.00056). d, AUCs of RNA switch predictions across various groups of natural and synthetic riboswitches, calculated as in b.
Applying SwitchSeeker to the vast human RNA landscape, the researchers uncovered 245 potential RNA switches. To validate their findings, they focused on a specific RNA switch located in the 3ʹ untranslated region of the RORC gene. Using advanced techniques like in vivo dimethyl sulfate mutational profiling (DMS-MaPseq) and cryogenic electron microscopy, they confirmed that this RNA region can adopt two distinct structural conformations.
Moreover, genome-scale CRISPR screens highlighted that nonsense-mediated mRNA decay machinery interacts with this RNA switch in a conformation-specific manner, influencing gene expression outcomes. This discovery underscores the intricate regulatory mechanisms that RNA structural switches contribute to eukaryotic gene expression.
SwitchSeeker represents a significant advancement, offering a systematic and unbiased approach to uncovering RNA structural switches in complex organisms. By revealing these regulatory elements, researchers gain deeper insights into how RNA molecules dynamically control gene expression, paving the way for future studies and potential therapeutic applications targeting these mechanisms.
Availability – SwitchFinder source code is available at https://github.com/goodarzilab/SwitchFinder.
Khoroshkin M, Asarnow D, Zhou S. et al. (2024) A systematic search for RNA structural switches across the human transcriptome. Nat Methods [Epub ahead of print]. [article]