Alcohol withdrawal is associated with altered PCBP1 RNA binding in the hippocampus

Withdrawal from chronic alcohol exposure disrupts brain gene expression and RNA splicing programs. The multifunctional RNA-binding protein PCBP1 has been previously implicated in RNA alternative splicing in the hippocampus during withdrawal from chronic alcohol (ethanol) exposure. However, the transcriptome-wide RNA targets associated with PCBP1 during ethanol withdrawal are not known. Here, we generated a map of PCBP1 RNA binding in the hippocampus of male and female rats following a 24-h withdrawal from chronic ethanol exposure using RNA immunoprecipitation and sequencing (RIP-Seq) with an antibody to PCBP1. No individual PCBP1-associated RNA peak reached significance after correction for multiple testing; therefore, peaks meeting an unadjusted p < 0.01 threshold were considered nominally significant and are referred to here as differentially associated peaks based on this threshold. These peaks showed sex-dependent patterns, with reduced PCBP1 RNA association predominating in males and increased association predominating in females. PCBP1 differentially associated sites on RNA were primarily intronic and mapped to genes involved in synaptic organization, neuronal connectivity, cell adhesion, glutamatergic signaling, and myelination-related pathways. Motif analysis identified heterogeneous sequence features, whereas positional analysis showed enrichment of PCBP1-bound regions near exon–intron boundaries, supporting a link with RNA splicing regulation. Integration of RIP-Seq with hippocampal RNA splicing data further identified candidate PCBP1-associated transcripts that also exhibited differential splicing in males, with enrichment of transcripts in synaptic vesicle cycling, neurotransmitter release and adhesion-related pathways. These findings identify ethanol withdrawal-associated changes in hippocampal PCBP1 RNA binding and highlight PCBP1-associated RNA networks as a potential component of post-transcriptional neuroadaptation during alcohol withdrawal. More broadly, our results implicate PCBP1-associated RNA regulation in synaptic and myelination-related pathways that may contribute to the molecular adaptations occurring during alcohol withdrawal.