A curated human cellular microRNAome based on 196 primary cell types

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• MicroRNA (miRNA) expression patterns across human cell types remain incompletely understood, hindering the study of their regulatory roles.
• Advancements in small RNA sequencing offer a significant opportunity to comprehensively map miRNA distribution at the cellular level.

Purpose of the Study:

• To create the most complete reference of miRNA expression patterns in human primary cells.
• To analyze the distribution and abundance of miRNAs across diverse human cell types.

Main Methods:

• Processed 4,184 human primary cell small RNA sequencing datasets from the NCBI Sequence Read Archive using miRge3.0.
• Curated data to 2,077 samples from 196 unique cell types across 175 studies based on shared miRNA expression.
• Utilized miRBase (v22.1) to identify and quantify detected miRNAs.

Main Results:

• Detected 2,452 out of 2,731 putative miRNAs (89.8%) across the analyzed cell types.
• Identified distinct expression categories: 108 cell-specific/near-specific, 59 infrequent, 52 frequent, 54 near-ubiquitous, and 50 ubiquitous miRNAs.
• Demonstrated that cellular miRNA expression complexity mirrors tissue-level patterns and influences plasma miRNA composition.

Conclusions:

• This work establishes the most extensive reference for miRNA expression profiles in human primary cells to date.
• The comprehensive dataset is accessible via the UCSC Genome Browser and an R/Bioconductor package for further research.
• The findings provide crucial insights into miRNA regulation and function across human cellular landscapes.