MicroRNA targeting in mammalian genomes: genes and mechanisms

Abstract

We briefly review the history of microRNA (miRNA) research and some of the lessons learnt. To provide some insights as to how and why miRNAs came into existence, we consider the evolution of the RNA interference machinery, miRNA genes, and their targets. We highlight the importance of systems biology approaches to integrate miRNAs as an essential subnetwork for modulating gene expression programs. Building accurate computational models that can simulate highly complex cell-specific gene expression patterns in mammals will lead to a better understanding of miRNAs and their targets in physiological and pathological situations. The impact of miRNAs on medicine, either as potential disease predisposing factors, biomarkers, or therapeutics, is highly anticipated and has started to reveal itself.

Figure 1. A schematic of lin-4 gene, pre-miRNA, and miRNA structure

The lin-4 miRNA was mapped to a 693 bp region (depicted by a bar) within the ninth intron of F59G1.4 (not drawn to scale) [59]. Processing of the primary lin-4 transcript (pri-miRNA) by Drosha-DGCR8 liberates the pre-miRNA. Dicer processes the pre-miRNA further into a 21 nt RNA duplex. The two miRNA strands are separated by an unknown mechanism, and typically one strand is loaded into Ago to form an active RISC, whereas the other strand (passenger strand) is excluded from RISC.

Figure 2. Sense-antisense binding of lin-4 miRNA to 3′ UTR of lin-14

Schematic depicts the seven putative lin-4 binding sites in the 3′ UTR of lin-14. Three out of the seven sites are complementary to the seed sequence of lin-4, and the predicted base-pairings are depicted for illustration [56, 61, 109]. The sense (top) strand represents the 3′ UTR sequence, and the anti-sense (bottom) strand represents the mature lin-4 sequence. The seed region is underlined by a bar in each case.

Figure 3. The miRNA silencing pathway

Transcription and pri-miRNA processing in the nucleus (large circle) are depicted, as well as miRISC assembly and silencing of target mRNAs in the cytoplasm. An interaction that results in activation is denoted by a positive symbol (+); whereas a negative symbol (−) denotes inhibition. Bottom, a legend of what the symbols represent are provided (inset box). A detailed description of the pathway can be found in the text.

Figure 4. evolution of RNA silencing machinery

The evolutionary scenario for proteins involved in RNA-dependent gene silencing mechanisms is superimposed on the major developments in terms of small RNAs. Details on the architectures of proteins involved in the process can be found in the text. This scenario is based on the current state of comparative genomics and may require revisions as new eukaryotic species are sequenced.