RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence

Badaoui, Bouabid; Rutigliano, Teresa; Anselmo, Anna; Vanhee, Merijn; Nauwynck, Hans; Giuffra, Elisabetta; Botti, Sara

doi:10.1371/journal.pone.0091918

Cited by 38 publications

(40 citation statements)

References 73 publications

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“…RNA-seq data analysis was performed as reported by Badaoui et al [30]. Briefly, sequence visualization and statistical analyses were performed with FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqch).…”

Section: Methodsmentioning

confidence: 99%

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae

Badaoui

Fougeroux

Petit³

et al. 2017

PLoS ONE

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Honeybees (Apis mellifera) are constantly subjected to many biotic stressors including parasites. This study examined honeybees infected with Nosema ceranae (N. ceranae). N. ceranae infection increases the bees energy requirements and may contribute to their decreased survival. RNA-seq was used to investigate gene expression at days 5, 10 and 15 Post Infection (P.I) with N. ceranae. The expression levels of genes, isoforms, alternative transcription start sites (TSS) and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation suggesting that bees use a range of tactics to cope with the stress of N. ceranae infection. N. ceranae infection may cause reduced immune function in the bees by: (i)disturbing the host amino acids metabolism (ii) down-regulating expression of antimicrobial peptides (iii) down-regulation of cuticle coatings and (iv) down-regulation of odorant binding proteins.

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Section: Methodsmentioning

confidence: 99%

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae

Badaoui

Fougeroux

Petit³

et al. 2017

PLoS ONE

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“…Studies have explored differentially expressed host mRNAs after PRRSV infection in pig lungs or PAM cells by transcriptome analyses (RNA-seq) 26, 27 . However, lncRNAs in the pig immune system have rarely been studied.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing

Zhang

Sun

Gan

et al. 2017

Sci Rep

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Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the global swine industry and causes tremendous economic losses. Its causative agent, porcine reproductive and respiratory syndrome virus (PRRSV), primarily infects immune cells, such as porcine alveolar macrophages and dendritic cells. PRRSV infection results in immune suppression, antibody-dependent enhancement, and persistent infection. Highly pathogenic strains in China cause high fever and severe inflammatory responses in the lungs. However, the pathogenesis of PRRSV is still not fully understood. In this study, we analysed the long noncoding RNA (lncRNA) and mRNA expression profiles of the HP-PRRSV GSWW15 and the North American strain FL-12 in infected porcine alveolar macrophages (PAMs) at 12 and 24 hours post-infection. We predicted 12,867 novel lncRNAs, 299 of which were differentially expressed after viral infection. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses of the genes adjacent to lncRNAs showed that they were enriched in pathways related to viral infection and immune response, indicating that lncRNAs might play regulatory roles in virus-host interactions. Our study provided information about lncRNAs in the porcine immune system and offers new insights into the pathogenic mechanism of PRRSV infection and novel antiviral therapy development.

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“…(5) Total RNA from macrophages infected with two PRRSV strains and a mock group was sequenced in 100-bp paired-end reads (SRP030003)43.…”

Section: Methodsmentioning

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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RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence

Cited by 38 publications

References 73 publications

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae

Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing

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

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