primiReference: a reference for analysis of primary-microRNA expression in single-nucleus sequencing data

Area of Science:

• Molecular Biology
• Neuroscience
• Genomics

Background:

• Single-nucleus RNA sequencing (snRNA-seq) offers insights into cell-type-specific gene expression.
• Understanding microRNA (miRNA) regulation is limited in snRNA-seq due to short miRNA length and incomplete nuclear transcript references.
• Primary miRNA (pri-miRNA) transcripts are crucial precursors for mature miRNAs.

Purpose of the Study:

• To develop a method for analyzing pri-miRNAs in single-nucleus RNA sequencing data.
• To investigate the role of pri-miRNAs in neural stem cell (NSC) differentiation during aging.
• To explore pri-miRNA expression in the context of Alzheimer's disease (AD) pathology.

Main Methods:

• Construction of a custom reference database for aligning and counting pri-miRNA sequences.
• Application of the custom reference to analyze snRNA-seq data from young and aged mouse subventricular zone (SVZ) nuclei.
• Analysis of snRNA-seq data from wild-type and 5XFAD mouse model cortex nuclei.

Main Results:

• Differential expression of pri-miRNAs targeting NSC differentiation genes in the aged SVZ.
• Identification of cell-type-specific pri-miRNA expression patterns in the cortex of an AD mouse model.
• Demonstration that pri-miRNAs are likely involved in NSC dysregulation associated with aging and AD.

Conclusions:

• The developed custom reference, primiReference, enables comprehensive analysis of pri-miRNAs in snRNA-seq data.
• Pri-miRNAs play a significant role in age-related neural stem cell dysfunction and Alzheimer's disease pathogenesis.
• This approach provides critical insights into cell-type-specific regulatory mechanisms and opens avenues for studying miRNA-mediated gene regulation in disease and aging.