Sub-compartment specific small non-coding RNA expression deregulation and altered nucleoli in mesial temporal lobe epilepsy

Large scale changes in coding and non-coding RNA expression is a common feature of the resected hippocampal tissue from pharmacoresistant mesial temporal lobe epilepsy (mTLE) patients. However, there is very less insight on the expression and localization changes of the key regulatory RNAs at a sub-compartment level contributing to pathological mechanisms in mTLE. In the present study we set out to understand the global sub-compartment specific changes in miRNA expression and localization and the alterations in the nucleus that possibly drive these changes and the consequences towards mTLE pathogenesis. We compared the nuclear and cytoplasmic distribution of miRNAs by small RNA-seq in subcellular fractionations of hippocampal tissue from mTLE patients and controls. Several miRNAs were found to be specifically enriched in the nucleus of hippocampal cells from patients compared to the controls, where miR-92b-3p (a miRNA-enriched in neurons) was the most de-regulated nuclear miRNA. By performing miR-92b co-immunoprecipitation (co-IP) assay on N2A nuclei and RNA-seq we identified enrichment of mTLE relevant pathways involving mitochondrial and ribosomal processes. Overall design: To understand the nuclear targets of miR-92b, we performed pulldown assays for biotin-tagged miR-92b in nuclear and whole cell compartments from mouse neuroblastoma N2A cells. Biotin immunoprecipitation was performed after overexpression of miR-92b or a Scramble mimic tagged with biotin. Cellular fractionations were performed and RNA collected from nuclear and whole cell fractions was subjected to total RNA sequencing.