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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

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Related Experiment Video

Updated: Jun 3, 2026

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis

Published on: April 25, 2022

MicroRNA programs in normal and aberrant stem and progenitor cells.

Christopher P Arnold¹, Ruoying Tan, Baiyu Zhou

¹Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.

Genome Research

|April 1, 2011

Summary

MicroRNAs (miRNAs) regulate gene expression in stem cells. This study identified specific miRNA signatures that control stem cell self-renewal and differentiation, impacting processes in normal and aberrant stem cells.

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A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

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Area of Science:

Molecular Biology
Genetics
Developmental Biology

Background:

MicroRNAs (miRNAs) are small regulatory RNAs controlling gene expression.
Stem and progenitor cells rely on precise genetic programs for self-renewal and differentiation.
Understanding miRNA roles is crucial for stem cell biology and disease.

Purpose of the Study:

To systematically examine miRNA expression profiles in adult stem cells and their differentiated progeny.
To identify common and unique miRNA signatures across different stem cell types (blood, muscle, neural).
To discover miRNA signatures associated with stem/progenitor cell transitions and their functional consequences.

Main Methods:

Systematic examination of miRNA expression profiles in adult tissue-specific stem cells and differentiated cells.
Analysis of miRNA signatures correlating with stem cell self-renewal, proliferation, and differentiation.
Identification and validation of a stem/progenitor transition miRNA (SPT-miRNA) signature.
Functional assessment of SPT-miRNAs in embryonic stem cells and hematopoietic stem cells (HSCs).

Main Results:

Distinct miRNA expression programs were identified in blood, muscle, and neural stem cells.
Specific miRNA signatures mark the transition from quiescent stem cells to proliferative progenitors.
A novel stem/progenitor transition miRNA (SPT-miRNA) signature was discovered, predicting effects of genetic perturbations.
Certain SPT-miRNAs were shown to control embryonic stem cell self-renewal and HSC reconstitution potential.
SPT-miRNAs were found to coordinately regulate key HSC self-renewal genes like Hoxb6 and Hoxa4.

Conclusions:

miRNA expression programs are integral to the regulation of normal and aberrant stem and progenitor cell functions.
The identified SPT-miRNA signature provides insights into post-transcriptional regulatory networks governing stem cell fate.
This work lays the foundation for dissecting miRNA-mediated control in stem cell biology and related diseases.