Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome

Background Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3′UTR binding sites can disrupt canonical conserved miRNA–mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. Results By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3′UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. Conclusions Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.

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“…4 c). These results are in agreement with data reported by Omariba et al [ 79 ] and Saunders et al [ 5 ].…”

Section: Discussionsupporting

confidence: 94%

Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

et al. 2021

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show abstract

“…4C ). These results were in agreement with data reported by Omariba et al (2020) [79] and Saunders et al (2007) [5].…”

Section: Discussionsupporting

confidence: 94%

Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

Mármol-Sánchez¹,

Guan

Quintanilla

et al. 2020

Preprint

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25 Background 26 Mature microRNAs (miRNAs) play an important role in repressing the expression of a 27 wide range of protein coding transcripts by promoting their degradation or inhibiting 28 their translation into functional proteins. The presence of segregating polymorphisms 29 inside miRNA loci and their corresponding 3'UTR binding sites might disrupt canonical 30 conserved miRNA-mRNA pairing, thus modifying gene expression patterns. 31 Results 32We aimed to investigate the variability of miRNA genes and their putative binding sites 33 by analyzing whole-genome sequences from 120 pigs and wild boars from Europe and 34 Asia. In total, 285 SNPs residing within miRNA loci were detected. From these, 221 35 were located in precursor regions, whereas 52 and 12 mapped to mature and seed 36 regions, respectively. Moreover, a total of 109,724 polymorphisms were identified in 37 predicted 7mer-m8 miRNA binding sites within porcine 3'UTRs. A principal 38 components analysis revealed a clear genetic divergence between Asian and European 39 samples, which was particularly strong for 3'UTR sequences. We also observed that 40 miRNA genes show reduced polymorphism compared with other non-miRNA regions. 41To assess the potential consequences of miRNA polymorphisms, we sequenced the 42 genomes of 5 Duroc pigs and, by doing so, we identified 15 miRNA SNPs that were 43 genotyped in the offspring (N = 345) of the five boars. Association analyses between 44 miRNA SNPs and hepatic and muscle microarray data allowed us to identify 4 45 polymorphisms displaying significant associations. Particularly interesting was the 46 rs319154814 polymorphism (G/A), located in the apical loop of the ssc-miR-326 47 3 precursor sequence. This polymorphism is predicted to cause a subtle hairpin 48 rearrangement that improves the accessibility to processing enzymatic factors. 49 Conclusions 50 Porcine miRNA genes show a reduced variability, particularly in the seed region which 51 plays a critical role in miRNA binding. Although it is generally assumed that SNPs 52 mapping to the seed region are the ones with the strongest consequences on mRNA 53 expression, we show that a SNP mapping to the apical region of ssc-miR-326 is 54 associated with the mRNA expression of several of its predicted targets. This result 55 suggests that porcine miRNA variability mapping within and outside the seed region 56 could have important regulatory effects on gene expression. 57 58 59 60 61 62 63 64 65 66 67 4 Background 68 Mature microRNA transcripts (miRNAs) are short (~22 nt) non-coding RNAs 69 which play an essential role in the regulation of gene expression [1]. During the 70 biogenesis of miRNAs, one strand of the miRNA duplex binds to the guide-strand 71 channel of an Argonaute protein forming an miRNA-induced silencing complex 72 (miRISC) with the ability of repressing mRNA expression through binding to specific 73 3'UTR target sites [2]. In postembryonic cells, this repressor mechanism mainly acts by 74 destabilizing the mRNA through decapping and poly(A)-tail...

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“…3 ). It corroborates the results published by Omariba and colleagues in the mouse genome 35 . In general, the proportion of single transitions in pre-miRNA and mature miRNA sequences was similar.…”

Section: Discussionsupporting

confidence: 93%

“…12 (16.5%) SNPs were called in mature miRNA sequences, beyond the seed region, while as many as 59 (80.8%) SNPs were mapped to pre-miRNA sequences beyond the mature sequence. This increasing accumulation of SNPs along with the distance from the seed region and mature sequences is in concordance with other studies and is believed to constitute the manifestation of the negative selection, because of the functional importance of the seed region in target gene recognition 30 , 34 , 35 .…”

Section: Discussionsupporting

confidence: 91%

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Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome

Pawlina-Tyszko

Semik-Gurgul

Gurgul

et al. 2021

Sci Rep

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MicroRNAs (miRNAs) are recognized as gene expression regulators, indirectly orchestrating a plethora of biological processes. Single nucleotide polymorphism (SNP), one of the most common genetic variations in the genome, is established to affect miRNA functioning and influence complex traits and diseases. SNPs in miRNAs have also been associated with important production traits in livestock. Thus, the aim of our study was to reveal the SNP variability of miRNA genes in the genome of the pig, which is a significant farm animal and large-mammal human model. To this end, we applied the targeted sequencing approach, enabling deep sequencing of specified genomic regions. As a result, 73 SNPs localized in 50 distinct pre-miRNAs were identified. In silico analysis revealed that many of the identified SNPs influenced the structure and energy of the hairpin precursors. Moreover, SNPs localized in the seed regions were shown to alter targeted genes and, as a result, enrich different biological pathways. The obtained results corroborate a significant impact of SNPs on the miRNA processing and broaden the state of knowledge in the field of animal genomics. We also report the targeted sequencing approach to be a promising alternative for the whole genome sequencing in miRNA genes focused studies.

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Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome

Cited by 13 publications

References 58 publications

Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome

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