Expression profiling of the <i><scp>GBP</scp>1</i> gene as a candidate gene for porcine reproductive and respiratory syndrome resistance

Gol, S.; Estany, J.; Fraile, Lorenzo; Pena, Ramona N.

doi:10.1111/age.12347

Cited by 18 publications

(14 citation statements)

References 30 publications

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“…Since the role of posttranscriptional modification has gradually gained attention, more and more studies have also focused on the polyadenylation of single gene in pig [46][47][48]. Many methods based on NGS technology currently emerged as the times require, including poly(A) site sequencing…”

Section: Discussionmentioning

confidence: 99%

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Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles

Deng

Zou

et al. 2020

BioMed Research International

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Many increasing documents have proved that alternative polyadenylation (APA) events with different polyadenylation sites (PAS) contribute to posttranscriptional regulation. However, little is known about the detailed molecular features of PASs and its role in porcine fast and slow skeletal muscles through microRNAs (miRNAs) and RNA binding proteins (RBPs). In this study, we combined single-molecule real-time sequencing and Illumina RNA-seq datasets to comprehensively analyze polyadenylation in pigs. We identified a total of 10,334 PASs, of which 8734 were characterized by reference genome annotation. 32.86% of PASassociated genes were determined to have more than one PAS. Further analysis demonstrated that tissue-specific PASs between fast and slow muscles were enriched in skeletal muscle development pathways. In addition, we obtained 1407 target genes regulated by APA events through potential binding 69 miRNAs and 28 RBPs in variable 3′ UTR regions and some are involved in myofiber transformation. Furthermore, the de novo motif search confirmed that the most common usage of canonical motif AAUAAA and three types of PASs may be related to the strength of motifs. In summary, our results provide a useful annotation of PASs for pig transcriptome and suggest that APA may serve as a role in fast and slow muscle development under the regulation of miRNAs and RBPs.

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Section: Discussionmentioning

confidence: 99%

“…Finally, we took the simultaneous existence of genes that are associated with tissue-specific PASs above and the predicted differential target genes of miRNA and RBPs. Some shared genes were discovered to be involved in muscle fiber transformation, such as HDAC (47)(48)(49), TRIB3 (50), and GYS1 [45].…”

Section: Annotation Of Mirnas and Rbps To Detect Possiblementioning

confidence: 99%

Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles

Deng

Zou

et al. 2020

BioMed Research International

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“…) and the association of GBP1 with respiratory and reproductive syndrome resistance (Gol et al . ). Previous research has also shown that the myosin, heavy chain 4, skeletal muscle gene ( MYH4 ) in Landrace pigs may be a potential molecular marker related to meat quality traits (Cho et al .…”

Section: Introductionmentioning

confidence: 97%

Detection of selection signatures of population‐specific genomic regions selected during domestication process in Jinhua pigs

Chen

Wang

et al. 2016

Animal Genetics

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Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome-wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross-population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population-specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds.

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“…The porcine GBP1 gene is a negative regulator of the T-cell response, the gene expression of which might be associated with viremia levels and lower weight gain following porcine reproduction and respiratory syndrome virus (PRRSV)22. Recently, Gol et al .…”

mentioning

confidence: 99%

“…Interestingly, different alleles of the mutation affected the usage of two PASs in 3′UTR of GBP1 gene. The distal PAS is more commonly used in all test samples, and the short transcript is generated by the proximal PAS when the A allele is present22. The study suggested that the APA participates in the formation of different lengths of transcripts and results in various expressions for GBP1 .…”

mentioning

confidence: 99%

Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data

Wang

Zhou

et al. 2016

Sci Rep

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Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.

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Expression profiling of the GBP1 gene as a candidate gene for porcine reproductive and respiratory syndrome resistance

Cited by 18 publications

References 30 publications

Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles

Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles

Detection of selection signatures of population‐specific genomic regions selected during domestication process in Jinhua pigs

Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data

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