Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes
Mármol-Sánchez, Emilio (Centre de Recerca en Agrigenòmica)
Luigi Sierra, Maria Gracia (Centre de Recerca en Agrigenòmica)
Castelló Farré, Anna (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Guan, Dailu (Centre de Recerca en Agrigenòmica)
Quintanilla, Raquel (Institute for Research and Technology in Food and Agriculture. Animal Breeding and Genetics Program)
Tonda, Raul (Centre de Regulació Genòmica)
Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)

Fecha:	2021
Resumen:	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. 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. 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.
Ayudas:	Ministerio de Economía y Competitividad AGL2013-48742-C2-1-R Ministerio de Economía y Competitividad AGL2013-48742-C2-2-R Ministerio de Ciencia e Innovación CEX2019-000902-S Ministerio de Educación, Cultura y Deporte FPU15/01733 Ministerio de Economía y Competitividad BES-C-2017-0024
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Publicado en:	Genetics, selection, evolution, Vol. 53 (May 2021) , art. 43, ISSN 1297-9686

DOI: 10.1186/s12711-021-00632-3
PMID: 33947333

21 p, 2.2 MB

El registro aparece en las colecciones:
Documentos de investigación > Documentos de los grupos de investigación de la UAB > Centros y grupos de investigación (producción científica) > Ciencias > CRAG (Centro de Investigación en Agrigenómica)
Artículos > Artículos de investigación
Artículos > Artículos publicados