Marcinkowska et al. BMC Genomics 2011, 12:183 http://www.biomedcentral.com/1471-2164/12/183 Page 6 of 9 Figure 2 Potential mechanism of CNV-mediated variation of miRNA dosage. Schematic representation of an miRNA gene and its primary transcript (solid or dotted arrow-lines). The position of the pre-miRNA sequence is indicated as a hairpin-loop structure in the miRNA primary transcript. Dotted lines represent transcripts unlikely to be produced due to the lack of promoter and transcriptional start sequences. Orange boxes represent CNV regions (deletions, duplications and dispersed duplications). The following panels show a CNV spanning different parts of the miRNA gene: (A) whole gene, (B) 5’-portion, (C) 3’-portion and (D) intragenic region of the gene. +, - and 0 indicate potential increase, decrease and no change of miRNA dosage, respectively. that control transcription or splicing), the most obvious mechanism is in the variability of dosage (number of functional copies). All of these mechanisms can affect both protein-coding and miRNA genes. However, mechanisms of dosage variation may be different for protein-coding and miRNA genes. In Figure 2, potential consequences of different CNV types overlapping differ- ent parts of miRNA genes are proposed. Not only whole gene amplification but also certain partial gene duplica- tions (multiple duplications) can increase the dosage of miRNAs. Conversely, partial gene deletions may not always result in decreased miRNA dosage. This con- trasts with the situation observed for protein-coding genes, in which only duplication of the entire gene (including the promoter and regulatory sequences) can lead to an increased number of functional copies, and almost every (even partial) gene deletion is deleterious. Analysis of 11 miRNAs located in CNVs with well defined breakpoints (Table 1) showed that (i) 3 of these miRNAs are located in the protein coding genes which are entirely positioned within CNVs, (ii) 4 of the miR- NAs are located in intergenic regions and are flanked by at least 20 kb of CNV sequences, (iii) 3 miRNAs are located in intergenic regions flanked by short CNV sequences (< 5 kb) and (iv) 1 miRNA is located in a gene of which the 3’end extends beyond CNV (Addi- tional file 4). Taking into account the average size of a human gene (~30 kb) one can expect that miRNAs located in large CNVs (groups (i) and (ii)) will be expressed from genes entirely embedded within the CNV regions. According to the model presented in Fig- ure 2A the expression of such miRNAs very likely will correlate with expression (number of copies) of genes from which these miRNAs are generated (no matter whether generated from protein-coding or non-coding transcripts). MiRNA located in short CNVs (group (iii)) most likely will form the tandem copies transcribed from one promoter. A number of such copies may mod- ulate the number of miRNA precursors (pre-miRNAs) present in one primary transcript (pri-miRNA) and thus may modulate expression of miRNA (Figure 2D). Expression of miRNA whose gene only partially is embedded in CNV (iii) may be modified according to the model shown in Figure 2B and will depend on expression and stability of the transcript truncated at the 3’end. Moreover, it should be noted that some pre- miRNA sequences occur in the genome in multiple copies. Although the functionality of such copies is still mostly unknown, the duplicated copies of miRNA genes may mask the effect of copy number variations that usually affect only one copy. Finally, not only common CNVs, but also CNVs implicated in specific diseases can affect miRNA loci and thus can play important role in pathogenesis. We