Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle

Cardoso, Tainã Figueiredo; Coutinho, Luiz Lehmann; Bruscadin, Jennifer Jessica; Diniz, Wellison J. S.; Petrini, Juliana; Andrade, Bruno de Bezerril; Oliveira, P. S. N.; Poleti, Mirele Daiana; Silveira, Juliano Coelho da; Chiaratti, Marcos Roberto; Neto, A. Zerlotini; Mourão, Gerson Barreto; Regitano, L. C. de A.

doi:10.3390/genes12010067

Cited by 15 publications

(10 citation statements)

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“…In summary, a potential effect of the rs319154814 (G/A) SNP in the synthesis or degradation of myristic acid can be envisaged, but this hypothesis still needs to be confirmed at the functional level. Interestingly, Cardoso et al (2021) [99] explored the relationship between miRNA SNPs located in the seed and mature regions of bovine miRNA loci and fatty acid composition traits. By combining lipid-related phenotype data with mRNA and protein abundances in a multi-omics approach, they described three miRNA SNPs significantly associated with several unsaturated and polyunsaturated fatty acid traits, as well as with the expression levels of some of their predicted targets [99].…”

Section: Discussionmentioning

confidence: 99%

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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Section: Discussionmentioning

confidence: 99%

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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“…An Irish study has revealed polymorphisms in bovine miR-2419 modify its binding properties to target genes related to milk production (Braud, 2017). A recent multi-omics analysis shows that miR- 2419-3p is associated with muscle fatty acid traits of Nelore cattle, which may exhibit regulatory function at mRNA or protein level (Cardoso et al, 2021). In a previous study, miR-7861 was differentially expressed as a unique miRNA in Bovine serum compared to EX (Zhao et al, 2016).…”

Section: Plasma Ev and Ex Exhibit Unique Differentially Expressed Mirna Profilesmentioning

confidence: 95%

Differentially Expressed Extracellular Vesicle, Exosome and Non-Exosome miRNA Profile in High and Low Tick-Resistant Beef Cattle

Abeysinghe

Turner

Peiris

et al. 2021

Front. Cell. Infect. Microbiol.

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Heavy tick burden on beef cattle account for huge economic losses globally, with an estimated value of US$22-30 billion per annum. In Australia, ticks cost the northern beef industry approximately A$170-200 million. Methods to evaluate and predict tick resistance would therefore be of great value to the global cattle trade. Exosomes (EX) are small extracellular vesicles (EVs) of ~30-150nm diameter and have gained popularity for their diagnostic and prognostic potential. EX contain, among other biomolecules, various types of RNA including micro-RNA (miRNA) and long noncoding RNA (lncRNA). MiRNA specifically have been validated as therapeutic biomarkers as they perform regulatory functions at the post-transcriptional level and are differentially expressed between divergent groups. The objective of the present study was to evaluate the miRNA profiles of EV and fractionated exosomal samples of high and low tick-resistant beef cattle to highlight potential miRNA biomarkers of tick resistance. Cows (n = 3/group) were classified into high or low tick resistant groups according to a novel scoring system. EVs and EX were isolated and fractionated from the blood plasma of high and low tick resistant cattle using established isolation and enrichment protocols. The resultant EX and non-EX samples were processed for next generation miRNA sequencing. Offspring of the cows in each high and low tick resistant group underwent the same processing for blood plasma EX, non-EX and miRNA analysis to evaluate the heritability of miRNA associated with tick resistance. A total of 2631 miRNAs were identified in EX and non-EX fractionated samples from high and low tick-resistant beef cattle. MiR-449a was highly expressed in maternal high tick-resistant EX samples. Of these, 174 were novel miRNAs, and 10 were differentially expressed (DE) (FDR < 0.05). These 10 DE miRNAs were also present in EVs, and three miRNAs were highly expressed: miR-2419-3p, miR-7861-3p and miR-2372-5p. Although 196 novel miRNAs were identified in fractionated samples of offspring, no miRNA were differentially expressed in these animals.

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“…genome/transcriptome/proteome/ metabolome) to be integrated together in a multi-omics approach (Da Silva Diniz & Ward, 2021). Recent studies have taken such an approach to refining genomic regions and lists of potential candidate genes in pork (Welzenbach et al, 2016) and beef (Cardoso et al, 2021) and it is likely to grow in importance in future livestock studies. While SNP variation can be profiled with SNP chips and modern sequencing methods, other types of variation such as copy number variation and variation in low complexity repetitive regions are more challenging to routinely score in populations, and they potentially account for a substantial proportion of the so-called "missing heritability" observed in many livestock genomic traits, that is, heritability not accounted for by common SNP variants.…”

Section: Future Trends Of Genomics and Transcriptomics In The Field O...mentioning

confidence: 99%

Current research and emerging tools to improve fresh red meat quality

Gagaoua

Duffy

Álvarez

et al. 2022

Irish Journal of Agricultural and Food Research

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A consumer’s decision to purchase red meat is guided by a combination of many interacting factors including safety, nutrition, sustainability and perception of healthiness along with a variety of sensory characteristics such as colour, marbling, tenderness, juiciness and flavour. Red meat quality is complex and influenced by many intrinsic and extrinsic factors, spanning the chain from breed/genetics through to the final end product with key influences coming from on-farm management and post-mortem processing. As a result of various factors, including consumer demands, the importance of both red meat quality and safety has in recent times come to the fore for the meat industry, with steps to meet these requirements having a large bearing on profitability. Therefore, a critical review of steps which can help control these traits is very important. Accordingly, several processing strategies were proposed at the research and industry level aiming to improve fresh red meat quality traits. This review summarises the current methods applied to improve fresh red meat quality and safety, including the advances in management and prediction tools for carcass and technological and sensory quality traits. These methods are also relevant to the safety and microbiological status of carcasses and meat produced, along with the recent developments in sensory analysis, which aim to understand the sensory properties of red meat and consumers responses. The potential of foodomics approaches is discussed under the topics of genomics, proteomics and metabolomics, which help our understanding of the underlying biological mechanisms behind the variation of sensory and technological quality traits and their use for the discovery of putative biomarkers. We further considered the current and emerging sequencing-based methods used to understand microbial community composition of fresh red meat.

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Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle

Cited by 15 publications

References 94 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

Differentially Expressed Extracellular Vesicle, Exosome and Non-Exosome miRNA Profile in High and Low Tick-Resistant Beef Cattle

Current research and emerging tools to improve fresh red meat quality

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