Identification of putative pathogenic SNPs implied in schizophrenia-associated miRNAs

Abstract

Background: Schizophrenia is a severe brain disorder, and SNPs (Single nucleotide polymorphism) in schizophrenia-associated miRNAs are believed to be one of the important reasons for dysregulation which might contribute to the altered expression of genes and ultimately result in the disease. Identification of causal SNPs in associated miRNAs may have certain significance in understanding the mechanism of schizophrenia.

Results: For the above purposes, a method based on detection of free energy change is proposed for identification of causal SNPs in schizophrenia-associated miRNAs. A miRNA is firstly segmented, and free energy change is computed after adding an SNP into a segment. The method discovers successfully 6 out of 32 known SNPs and some artificial SNPs could cause significant change in free energy, and among which, 6 known SNPs are supposed to be responsible for most cases of schizophrenia in population.

Conclusions: The proposed method is not only a convenient way to discover causal SNPs in schizophrenia-associated miRNAs without any biochemical assay or sample comparison between cases and controls, but it also has high resolution for causal SNPs even if the SNPs are not reported for their very rare cases in the population. Moreover, the method can be applied to discover the causal SNPs in miRNAs associated with other diseases.

Figure 1

miRNA biogenesis. MiRNAs are processed from hairpin-containing primary transcripts (pri-miRNAs). Pri-miRNA is cleaved firstly by Drosha to produce precursor miRNA (pre-miRNA), and then by Dicer to yield an imperfect miRNA:miRNA* duplex (mature miRNA duplex) about 22 nucleotides in length [20]. Although either strand of the duplex may potentially act as a functional miRNA, only the one strand which is incorporated into the RNA-induced silencing complex (RISC) is termed as mature miRNA.

Figure 2

Flowchart of the method. (A) Basis of segmentation, (B) Flowchart to search causal SNPs. Based on the requirements of miRNA maturation and miRNA/mRNA interaction in A, a miRNA is divided into three segments: terminal loop, mature miRNA duplex and extension duplex in B. B presents the procedure to discover causal SNPs in detail.

Figure 3

Segmentation of hsa-miR-29c. (A) Sequence of hsa-miR-29c, (B) Secondary structure of hsa-miR-29c. The sequences in green and in yellow in A are mature miRNA-5p and mature miRNA-3p which compose mature miRNA duplex in B. The extension sequence-5p and extension sequence-3p in A compose extension duplex in B.

Figure 4

Segments of hsa-miR-198. Mature miRNAs annotated artificially are shown in box and overlapping bases are shown in larger font size and italic.

Figure 5

Secondary structure of terminal loop of hsa-miR-29b-2. (A) Secondary structure of original terminal loop of hsa-miR-29b-2, (B) Secondary structure of terminal loop of hsa-miR-29b-2 with the sixteenth base varied from U to G. Both the two secondary structures are predicted by RNAfold (software to predict the secondary structures of single stranded RNA or DNA sequences).