RiboMeth-seq Reveals Selective rRNA 2′-O-Methylation Changes in the Dorsolateral Prefrontal Cortex of Major Depressive Disorder Subjects

Background Major depressive disorder (MDD) is associated with widespread molecular abnormalities in the brain, yet the contribution of ribosome-centered regulatory mechanisms remains poorly understood. Ribosomal RNA (rRNA) 2′-O-methylation (Nm) is the most abundant and evolutionarily conserved RNA modification and has emerged as a determinant of ribosome heterogeneity and translational control. However, the rRNA Nm landscape has not been examined in psychiatric illness. Here, we used RiboMeth-seq to map site-specific rRNA Nm in the MDD brain. Methods RiboMeth-seq was performed in the dorsolateral prefrontal cortex (dlPFC) from MDD (N=17) and matched non-psychiatric controls (N=20) using Illumina NextSeq200 in 50 bp single-end mode. Specific RiboMeth-seq scores (RMS) were calculated in +/-2 nt intervals for all RNA positions and extracted for positions of known Nm residues in target RNA. Results The overall distribution of ribose methylation scores was highly similar between groups, indicating preservation of the global rRNA Nm landscape in MDD. At the same time, we identified eight significantly altered Nm sites, including four in 28S rRNA (Am2802, Cm2848, Cm3866, and Gm4593) and four in 18S rRNA (Um172, Am576, Am1031, and Gm1490). These selective changes occurred in the absence of widespread remodeling, supporting a model in which MDD is associated with targeted modification of functionally relevant ribosomal positions rather than generalized disruption of ribosome integrity. Conclusions Our findings identify rRNA Nm as a previously unrecognized layer of molecular alteration in MDD and suggest that site-specific variation in ribosome composition may contribute to aberrant translational regulation in the depressed brain.