biostudies-literatureZhang YNational Natural Science Foundation of China (National Science Foundation of China)9890https://www.ebi.ac.uk/biostudies/studies/S-EPMC11564809biostudies-literatureUnknown15(1)RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structural remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in 3'UTR regions. DHX36 binding increases structural accessibility at 3'UTRs which is correlated with decreased post-transcriptional mRNA abundance.Nature communicationsDHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m<sup>6</sup>A reader YTHDF1.PMC11564809821724363230070332270587Guo XWang HYang FZhao YKwok CKQiao YDing YLyu KZhang YChen XKang JSun HZhao JfalseDHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m<sup>6</sup>A reader YTHDF1.RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structural remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in 3'UTR regions. DHX36 binding increases structural accessibility at 3'UTRs which is correlated with decreased post-transcriptional mRNA abundance.2024-01-01T00:00:00Z2024 Nov2026-07-15T01:44:19.721Z2025-04-07T04:30:32.24ZS-EPMC115648093954309710.1038/s41467-024-54000-y