Mammalian microRNAs: a small world for fine-tuning gene expression

Abstract

The basis of eukaryotic complexity is an intricate genetic architecture where parallel systems are involved in tuning gene expression, via RNA-DNA, RNA-RNA, RNA-protein, and DNA-protein interactions. In higher organisms, about 97% of the transcriptional output is represented by noncoding RNA (ncRNA) encompassing not only rRNA, tRNA, introns, 5' and 3' untranslated regions, transposable elements, and intergenic regions, but also a large, rapidly emerging family named microRNAs. MicroRNAs are short 20-22-nucleotide RNA molecules that have been shown to regulate the expression of other genes in a variety of eukaryotic systems. MicroRNAs are formed from larger transcripts that fold to produce hairpin structures and serve as substrates for the cytoplasmic Dicer, a member of the RNase III enzyme family. A recent analysis of the genomic location of human microRNA genes suggested that 50% of microRNA genes are located in cancer-associated genomic regions or in fragile sites. This review focuses on the possible implications of microRNAs in post-transcriptional gene regulation in mammalian diseases, with particular focus on cancer. We argue that developing mouse models for deleted and/or overexpressed microRNAs will be of invaluable interest to decipher the regulatory networks where microRNAs are involved.

Fig. 1

Biogenesis of microRNAs and hypothetical mechanisms in regulation of gene expression. RNA polymerases II and III are believed responsible for microRNA transcription, although a recent publication indicates that polymerase II is the main RNA polymerase for microRNA transcription (Lee et al. 2004). (A) Exonic microRNAs in sense orientation as a part of annotated host genes are transcribed as parts of longer molecules that are processed in the nucleus into hairpin RNAs of 70–100 nt by the dsRNA-specific ribonuclease Drosha. The hairpin RNAs are transported to the cytoplasm where they are digested by a second, double-strand specific ribonuclease called Dicer. In animals, single-stranded miRNA binds specific mRNA through sequences that in most of cases are significantly, though not completely, complementary to the target mRNA. (B) The excision of intronic microRNAs out of the precursors is completed through the process of RNA splicing, followed by Dicer digestion. MicroRNAs are finally incorporated into an RNA-induced silencing complex (RISC) to induce translation suppression or degradation depending of the degree of complementary with the target mRNA. (C, D) Exonic and intronic microRNAs in antisense orientation as a part of annotated host genes can be trancribed as independent transcription units. The mature microRNA sequence, in our hypothetical mechanisms, can lead to translation or transcription suppression of the host gene of other target mRNAs. MicroRNA genes located in intergenic regions or gene deserts are transcribed as independent transcription units and their biogenesis can be described as in A.

Fig. 2

MicroRNAs as cancer players. MicroRNAs may act as tumor suppressors or oncogenes in cancer. Orange triangles represent mir promoters and blue ovals represent their corresponding mir genes. Orange rectangles represent promoters of protein-coding genes and blue rectangles represent the actual coding sequences of their corresponding genes. One mechanism for the downregulation of “suppressor-microRNAs” that has been identified is (A) Homozygous deletion of microRNA coding regions, as exemplified by deletion of the mir-15a/mir-16-1 cluster in B-CLL (Calin et al. 2002). Hypothetical mechanisms for downregulation of “suppressor-microRNAs” in cancer include (B) the combination of deletion plus promoter hypermethylation, and (C) deletion plus mutation. Mechanisms for the upregulation of “onco-microRNAs” that have been identified are (D) amplification and overexpression of pre-microRNAs, as exemplified by mir-155/BIC in children’s Burkitt’s lymphoma (Metzler et al. 2004), and (E) translocations of either protoconcogenes near the promoter of microRNAs or translocation of microRNAs near the promoters of oncogenes (modified after Calin et al. (©) 2004 PNAS, National Academy of Sciences, Washington, DC, USA).