MicroRNAs: regulators of gene expression and cell differentiation

Abstract

The existence and roles of a class of abundant regulatory RNA molecules have recently come into sharp focus. Micro-RNAs (miRNAs) are small (approximately 22 bases), non-protein-coding RNAs that recognize target sequences of imperfect complementarity in cognate mRNAs and either destabilize them or inhibit protein translation. Although mechanisms of miRNA biogenesis have been elucidated in some detail, there is limited appreciation of their biological functions. Reported examples typically focus on miRNA regulation of a single tissue-restricted transcript, often one encoding a transcription factor, that controls a specific aspect of development, cell differentiation, or physiology. However, computational algorithms predict up to hundreds of putative targets for individual miRNAs, single transcripts may be regulated by multiple miRNAs, and miRNAs may either eliminate target gene expression or serve to finetune transcript and protein levels. Theoretical considerations and early experimental results hence suggest diverse roles for miRNAs as a class. One appealing possibility, that miRNAs eliminate low-level expression of unwanted genes and hence refine unilineage gene expression, may be especially amenable to evaluation in models of hematopoiesis. This review summarizes current understanding of miRNA mechanisms, outlines some of the important outstanding questions, and describes studies that attempt to define miRNA functions in hematopoiesis.

Figure 1.

miRNAs and siRNAs: differences in biogenesis and properties. siRNAs (left) derive from long endogenous dsRNA molecules that form either long hairpins or bimolecular duplexes. Processing of these dsRNA precursors can generate many different siRNAs from both strands. In contrast, processing of the shorter hairpin structures known as pre-miRNAs (right) produces a single miRNA molecule from one arm of the hairpin precursor. siRNAs recognize their target transcripts with perfect sequence complementarity (left), whereas miRNAs typically have a limited number of mismatches with their mRNA target sequences (right). Both classes of small regulatory RNA molecules cause posttranscriptional silencing of protein-coding genes.

Figure 2.

miRNA biogenesis and action. Most pri-mRNAs are the products of independent genes, transcribed by RNA polymerase II. The nuclear Microprocessor protein complex, which contains the RNase III Drosha and its partner DGCR8/Pasha, cleaves pri-miRNAs into 50- to 80-base pre-miRNA stem-loop moieties. The Ran-GTP–dependent factor exportin-5 actively transports pre-miRNAs into the cytoplasm, where the nuclease Dicer processes them further into duplexes that contain the 20- to 24-nucleotide mature miRNA; each pre-miRNA usually yields a single mature miRNA product. The functional strand is determined when one of the 2 strands of the duplex is loaded into the RISC, which contains Argonaute and related proteins and localizes in cytoplasmic P-bodies. Recognition of target mRNAs by partial sequence complementarity to the miRNA results in posttranscriptional gene repression by some combination of transcript degradation and translational inhibition.

Figure 3.

Models for the biological significance of miRNA functions. Three nonmutually exclusive models are presented, and the truth is likely to incorporate elements from each. Different modes may also operate in different cells or at different stages in development. Computational predictions form the basis for much of the current thinking and experimental evidence favoring each of the models remains limited.

Figure 4.

Working model for the regulatory circuit involving miR-223, C/EBPα, and NFI-A in neutrophil differentiation. Experimental results are consistent with the idea that NFI-A and C/EBPα compete for binding to partially overlapping DNA sequences in the miR-223 gene promoter, and as long as NFI-A is present, this miR gene is inactive. Cells committed to granulocytic differentiation express C/EBPα, which activates miR-223 expression, resulting in repression of its NFI-A mRNA target. Thus, miR-223 appears to participate in a simple regulatory circuit of TFs that control granulopoiesis and may help stabilize the neutrophil phenotype induced by C/EBPα. Reprinted from Fazi et al with permission.