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

Animals Computational Biology Feasibility Studies Genome Livestock / genetics MicroRNAs / genetics Models, Animal Nucleic Acid Conformation Polymorphism, Single Nucleotide RNA Precursors / chemistry RNA Processing, Post-Transcriptional / genetics RNA, Small Interfering / chemistry Sequence Analysis, DNA / methods Sus scrofa / genetics

Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
10 05 2021
Historique:
received: 06 10 2020
accepted: 21 04 2021
entrez: 11 5 2021
pubmed: 12 5 2021
medline: 26 10 2021
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41598-021-89363-5 PMID: 33972633 PMC: PMC8110958
pubmed: 33972633
doi: 10.1038/s41598-021-89363-5
pii: 10.1038/s41598-021-89363-5
pmc: PMC8110958
doi:

Substances chimiques

MicroRNAs 0
RNA Precursors 0
RNA, Small Interfering 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

9848

Références

Carcinogenesis. 2008 Oct;29(10):1963-6
pubmed: 18660546
Proc Natl Acad Sci U S A. 2008 May 20;105(20):7269-74
pubmed: 18474871
Anim Genet. 2013 Feb;44(1):101-6
pubmed: 22583385
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
EMBO J. 2004 Oct 13;23(20):4051-60
pubmed: 15372072
Nature. 2003 Sep 25;425(6956):415-9
pubmed: 14508493
Vet Q. 1998;20 Suppl 3:S42-5
pubmed: 9689724
Gene. 2012 Nov 10;509(2):267-72
pubmed: 22922391
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Bioinformatics. 2018 Jun 1;34(11):1937-1938
pubmed: 29360956
Cell Mol Neurobiol. 2014 Jan;34(1):17-30
pubmed: 24213247
Nature. 2000 Mar 16;404(6775):293-6
pubmed: 10749213
Am J Med Genet A. 2010 Apr;152A(4):856-62
pubmed: 20358594
Trends Genet. 2008 Oct;24(10):489-97
pubmed: 18778868
Algorithms Mol Biol. 2011 Nov 24;6:26
pubmed: 22115189
Gene. 2012 Sep 10;506(1):211-6
pubmed: 22750317
Clin Cancer Res. 2010 Mar 1;16(5):1577-86
pubmed: 20179230
PLoS One. 2017 May 24;12(5):e0178045
pubmed: 28542522
Nucleic Acids Res. 2015 Jul 1;43(W1):W467-73
pubmed: 26019179
Nucleic Acids Res. 2019 Jan 8;47(D1):D701-D710
pubmed: 30407520
Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2257-61
pubmed: 16461460
Ann Ist Super Sanita. 2004;40(2):241-4
pubmed: 15536277
BMC Genomics. 2014 Feb 05;15:100
pubmed: 24499489
Mutat Res. 2005 Jun 3;573(1-2):41-53
pubmed: 15829236
Pathobiology. 2000;68(6):283-90
pubmed: 11493762
J Virol. 2006 Jun;80(11):5321-6
pubmed: 16699012
J Genomics. 2015 Feb 15;3:51-6
pubmed: 25874014
Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
pubmed: 17991681
Clin Chim Acta. 2010 Sep 6;411(17-18):1287-90
pubmed: 20488170
Nucleic Acids Res. 1981 Jan 10;9(1):133-48
pubmed: 6163133
Biology (Basel). 2012 Dec 14;1(3):895-905
pubmed: 24832523
Nucleic Acids Res. 2019 Jul 2;47(W1):W530-W535
pubmed: 31114926
Curr Opin Gastroenterol. 2005 Jan;21(1):44-50
pubmed: 15687884
J Stroke. 2017 May;19(2):166-187
pubmed: 28480877
Mol Biol Rep. 2011 Mar;38(3):1609-15
pubmed: 20842445
Nucleic Acids Res. 2016 Jan 4;44(D1):D827-33
pubmed: 26602686
Nat Rev Genet. 2004 Jul;5(7):522-31
pubmed: 15211354
Bioinformatics. 2020 Apr 15;36(8):2628-2629
pubmed: 31882993
Science. 2007 Dec 21;318(5858):1931-4
pubmed: 18048652
J Clin Invest. 2008 Jul;118(7):2600-8
pubmed: 18521189
Sci Rep. 2020 Apr 1;10(1):5789
pubmed: 32238847
Hum Mol Genet. 2007 May 1;16(9):1124-31
pubmed: 17400653
PLoS One. 2012;7(1):e30737
pubmed: 22303453
Hum Mutat. 2012 Jan;33(1):254-63
pubmed: 22045659
Genome. 2015 Feb;58(2):81-90
pubmed: 26053224
Biochem Biophys Res Commun. 2010 Aug 20;399(2):117-22
pubmed: 20621067
Biosci Biotechnol Biochem. 2018 Jul;82(7):1081-1089
pubmed: 29658390
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
pubmed: 16381832
Nucleic Acids Res. 2007 Jan;35(Database issue):D51-4
pubmed: 17099235
Nature. 2004 Sep 16;431(7006):343-9
pubmed: 15372041
Cancer. 2010 Oct 15;116(20):4753-60
pubmed: 20549817

Auteurs

Klaudia Pawlina-Tyszko (K)

Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland. klaudia.pawlina@iz.edu.pl.

Ewelina Semik-Gurgul (E)

Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland.

Artur Gurgul (A)

Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland.
Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland.

Maria Oczkowicz (M)

Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland.

Tomasz Szmatoła (T)

Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland.
Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland.

Monika Bugno-Poniewierska (M)

Department of Animal Reproduction, Anatomy and Genomics, The University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059, Kraków, Poland.

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

Assessing the feasibility and acceptability of a hands-on surgical robotics workshop for medical students and early-career doctors.

Nyi Tun San, Khandakar Rezwanur Rahman, Joseph Ryan Wong Sik Hee et al.
1.00
Humans Students, Medical Robotic Surgical Procedures Feasibility Studies Female

Evaluating the efficacy of telesurgery with dual console SSI Mantra Surgical Robotic System: experiment on animal model and clinical trials.

Sudhir Prem Srivastava, Vishwajyoti Pascual Srivastava, Avinesh Singh et al.
1.00
Robotic Surgical Procedures Animals Humans Telemedicine Models, Animal

Odour generalisation and detection dog training.

Lyn Caldicott, Thomas W Pike, Helen E Zulch et al.
1.00
Animals Odorants Dogs Generalization, Psychological Smell

Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Application of the targeted sequencing...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › Application of the targeted sequencing...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Caractéristiques des études épidémiologiques › Études de faisabilité › Application of the targeted sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Application of the targeted sequencing...
questionsmedicales.fr › Eucaryotes › Animaux › Groupes animaux › Animaux domestiques › Bétail › Application of the targeted sequencing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › Application of the targeted sequencing...
questionsmedicales.fr › Techniques d'investigation › Modèles animaux › Application of the targeted sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Application of the targeted sequencing...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Application of the targeted sequencing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Précurseurs des ARN › Application of the targeted sequencing...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Maturation post-transcriptionnelle des ARN › Application of the targeted sequencing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › Petit ARN interférent › Application of the targeted sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Application of the targeted sequencing...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Artiodactyla › Suidae › Sus scrofa › Application of the targeted sequencing...