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      Single nucleotide polymorphisms affect miRNA target prediction in bovine

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          Abstract

          Single nucleotide polymorphisms (SNPs) can have significant effects on phenotypic characteristics in cattle. MicroRNAs (miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators by binding them to target mRNAs. In the present study, we scanned ~56 million SNPs against 1,064 bovine miRNA sequences and analyzed, in silico, their possible effects on target binding prediction, primary miRNA formation, association with QTL regions and the evolutionary conservation for each SNP locus. Following target prediction, we show that 71.6% of miRNA predicted targets were altered as a consequence of SNPs located within the seed region of the mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE), which represents the capacity to alter molecule stability and, consequently, miRNA maturation. A total of 48.6% of the sequences analyzed showed values within those previously reported as sufficient to alter miRNA maturation. We have also found 131 SNPs in 46 miRNAs, with altered target prediction, occurring in QTL regions. Lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to affect bovine phenotypes and could be of great value for genetic improvement studies, as well as production.

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          Most cited references75

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              MicroRNAs: genomics, biogenesis, mechanism, and function.

              MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: SoftwareRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: MethodologyRole: SoftwareRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: MethodologyRole: SoftwareRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                21 April 2021
                2021
                : 16
                : 4
                : e0249406
                Affiliations
                [1 ] Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
                [2 ] School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
                University of Tennessee Health Science Center, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                ‡ These authors also contributed equally to this work.

                Author information
                https://orcid.org/0000-0001-8856-7164
                https://orcid.org/0000-0002-4773-9473
                https://orcid.org/0000-0002-7254-1960
                https://orcid.org/0000-0002-3173-3712
                Article
                PONE-D-20-28956
                10.1371/journal.pone.0249406
                8059806
                33882076
                9521750c-049b-450e-8c90-15fbc7db3871
                © 2021 Sousa et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 14 September 2020
                : 17 March 2021
                Page count
                Figures: 4, Tables: 1, Pages: 17
                Funding
                Funded by: National Council for Scientific and Technological Development (CNPq)
                Award Recipient :
                Funded by: Coordination for the Improvement of Higher Level Education (CAPES)
                Award Recipient :
                FLL is a PQ-2 Scholar of the National Council for Scientific and Technological Development (CNPq). Studentship to FRFA was financed by the Coordination for the Improvement of Higher Level Education (CAPES). Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                Non-coding RNA
                Natural antisense transcripts
                MicroRNAs
                Biology and life sciences
                Genetics
                Gene expression
                Gene regulation
                MicroRNAs
                Biology and Life Sciences
                Genetics
                Single Nucleotide Polymorphisms
                Biology and Life Sciences
                Nutrition
                Diet
                Beverages
                Milk
                Medicine and Health Sciences
                Nutrition
                Diet
                Beverages
                Milk
                Biology and Life Sciences
                Anatomy
                Body Fluids
                Milk
                Medicine and Health Sciences
                Anatomy
                Body Fluids
                Milk
                Biology and Life Sciences
                Physiology
                Body Fluids
                Milk
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bovines
                Cattle
                Biology and Life Sciences
                Zoology
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bovines
                Cattle
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Ruminants
                Cattle
                Biology and Life Sciences
                Zoology
                Animals
                Vertebrates
                Amniotes
                Mammals
                Ruminants
                Cattle
                Physical Sciences
                Chemistry
                Chemical Compounds
                Acids
                Lactic Acid
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Quantitative Trait Loci
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Gene Prediction
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Gene Prediction
                Biology and Life Sciences
                Genetics
                Genomics
                Animal Genomics
                Mammalian Genomics
                Custom metadata
                All relevant data are within the paper and its Supporting information files.

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