Genetic variation in microRNA networks: the implications for cancer research

Abstract

Many studies have highlighted the role that microRNAs have in physiological processes and how their deregulation can lead to cancer. More recently, it has been proposed that the presence of single nucleotide polymorphisms in microRNA genes, their processing machinery and target binding sites affects cancer risk, treatment efficacy and patient prognosis. In reviewing this new field of cancer biology, we describe the methodological approaches of these studies and make recommendations for which strategies will be most informative in the future.

Figure 1. Illustrative overview of the miRNA network

RNA polymerase II (Pol II) produces a 500–3,000 nucleotide transcript, called the primary microRNA (miRNA), or pri-miRNA, that is then cropped to form a pre-miRNA hairpin by a multi-protein complex that includes DROSHA (~60–100 nucleotides) (a simplified view is shown here). This double-stranded hairpin structure is exported from the nucleus by RAN GTPase and exportin 5 (XPO5). Finally, the pre-miRNA is cleaved by DICER1 to produce two miRNA strands, a mature miRNA sequence, approximately 20 nucleotides in length, and its short-lived complementary sequence, which is denoted miR* and sometimes called the passenger strand or 3p strand. The thermodynamic stability of the miRNA duplex termini and the identity of the nucleotides in the 3′ overhang determines which of the strands is incorporated into the RNA-inducing silencing complex (RISC). In some cases, in which both the lead and passenger strands have a similar thermodynamic stability, both strands will be loaded. The single stranded miRNA is incorporated into RISC, which then targets it to the target 3′ untranslated region mRNA sequence to facilitate repression and cleavage. AA, poly A tail; m7G, 7-methylguanosine cap; ORF, open reading frame.

Figure 2. Diagrammatic representation of SNPs in pri-miRNA and pre-miRNA sequences

Single nucleotide polymorphisms (SNPs) can occur in the pri-miRNA and pre-miRNA strands and are likely to affect miRNA processing and subsequent mature miRNA levels. Such SNPs can lead to either an increase or decrease in processing.

Figure 3. Diagrammatic representation of SNPs in miRNA seed and regulatory regions

Single nucleotide polymorphisms (SNPs) in mature microRNAs (miRNAs) within the seed sequence can strengthen or reduce binding between the miRNA and its mRNA target. Moreover, such SNPs can create or destroy target binding sites, as is the case for mir-146a*. SNPs located within the 3′ untranslated region miRNA binding sites function analogously to seed region SNPs and modulate the miRNA–mRNA interaction. They can create or destroy miRNA binding sites and affect subsequent mRNA translation. AA, poly A tail; m7G, 7-methylguanosine cap; ORF, open reading frame.

Figure 4. Diagrammatic representation of SNP sin miRNA processing machinery

Single nucleotide polymorphisms (SNPs) can also occur within the processing machinery. Although still lacking biological validation, these SNPs are likely to affect the microRNAome (miRNAome) as a whole, possibly leading to the overall suppression of miRNA output. In addition, SNPs in cofactors of miRNA processing, such as p53, may indirectly affect miRNA maturation.