Abstract Despite the nuclear localization of m 6 A machinery, genomes multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively A-modified. However, these findings mostly based on A-Seq, an antibody-dependent technique with a high rate false positives. Here, we address presence in CHIKV DENV RNAs. For this, combine A-Seq antibody-independent SELECT nanopore direct sequencing techniques functional, molecular, mutagenesis...

Abstract Background A major determinant of influenza infection is the presence virus receptors on susceptible host cells to which viral haemagglutinin able bind. Avian viruses preferentially bind sialic acid α2,3-galactose (SAα2,3-Gal) linked receptors, whereas human strains α2,6-galactose (SAα2,6-Gal) receptors. To date, there has been no detailed account published distribution SA in pig, a model that avian and subtypes, thus with potential for reassortment. We examined relative expression...

One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an internal reference gene that invariant regardless treatment, such as virus infection. Several studies have found variability in expression commonly used housekeeping genes, beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), under different experimental settings. However, ACTB GAPDH remain widely host response infections, including influenza viruses. To date no detailed...

N6-methyladenosine (m6A) is the most abundant internal RNA modification of cellular mRNAs. m6A recognised by YTH domain-containing proteins, which selectively bind to m6A-decorated RNAs regulating their turnover and translation. Using an m6A-modified hairpin present in Kaposi’s sarcoma associated herpesvirus (KSHV) ORF50 RNA, we identified seven members from ‘Royal family’ as putative readers, including SND1. RIP-seq eCLIP analysis characterised SND1 binding profile transcriptome-wide,...

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic associated with various AIDS-related malignancies. Like other herpesviruses, multiple processes required for KSHV lytic replication, including viral transcription, DNA synthesis and capsid assembly occur in virus-induced intranuclear structures, termed replication transcription compartments (RTCs). Here we utilised a novel methodology, combining subcellular fractionation quantitative proteomics, to identify cellular proteins...

Current methods of isolation muscle satellite cells from different animal species are highly variable making inter-species comparisons problematic. This variation mainly stems the use proteolytic enzymes to release tissue (sometimes a single enzyme is used but often combination preferred) and extracellular matrix proteins coat culture ware. In addition, frequently laborious sometimes may require pre-plating cell preparation on uncoated flasks or Percoll centrifugation remove contaminating...

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of sarcoma (KS) and primary effusion lymphoma (PEL), which are aggressive malignancies associated with immunocompromised patients. For many non-viral malignancies, therapeutically targeting ubiquitin proteasome system (UPS) has been successful. Likewise, laboratory studies have demonstrated that inhibition UPS might provide a promising avenue for treatment KSHV-associated diseases. The largest class E3 ligases cullin-RING...

Recent methods for transcriptome-wide N 6 -methyladenosine (m A) profiling have facilitated investigations into the RNA methylome and established m A as a dynamic modification that has critical regulatory roles in gene expression may play role human disease. However, bioinformatics resources available analysis of sequencing data are still limited. Here, we describe m6aViewer—a cross-platform application visualization peaks from data. m6aViewer implements novel peak-calling algorithm...

The epitranscriptomic modification N6-methyladenosine (m6A) is a ubiquitous feature of the mammalian transcriptome. It modulates mRNA fate and dynamics to exert regulatory control over numerous cellular processes disease pathways, including viral infection. Kaposi’s sarcoma-associated herpesvirus (KSHV) reactivation from latent phase leads redistribution m6A topology upon both mRNAs within infected cells. Here we investigate role in transcripts upregulated during KSHV lytic replication. Our...

Respiratory epithelial cells and macrophages are the key innate immune that play an important role in pathogenesis of influenza A virus infection. We found these two cell types from both human pig showed comparable susceptibilities to initial infection with a highly pathogenic avian (HPAI) H5N1 (A/turkey/Turkey/1/05) moderately H1N1 (A/USSR/77), but there were contrasting differences host responses. Human mounted vigorous cytokine (tumor necrosis factor alpha [TNF-α] interleukin-6 [IL-6])...

The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected a wide range modifications. In this study, we focused on the chikungunya virus (CHIKV) as model ssRNA study landscape viral modification in infected human cells. Among 32 distinct modifications analysed by mass spectrometry, inosine was found enriched genomic CHIKV RNA. However, orthogonal validation Illumina RNA-seq analyses did not identify any along genome. Moreover, infection alter...

Skeletal muscle, at 30 to 40% of body mass, is the most abundant soft tissue in body. Besides its primary function movement and posture, skeletal muscle a significant innate immune organ with capacity produce cytokines chemokines respond proinflammatory cytokines. Little known about role during systemic influenza A virus infection any host particularly avian species. Here we used chicken duck multinucleated myotubes examine their susceptibility response infections. Both expressed human...

The coupling of mRNA processing steps is essential for precise and efficient gene expression. human transcription/export (hTREX) complex a highly conserved multi-protein responsible eukaryotic stability nuclear export. We have previously shown that the Kaposi's sarcoma-associated open reading frame 57 (ORF57) protein orchestrates recruitment hTREX onto viral intronless mRNA, forming stable export-competent ribonucleoprotein particle (vRNP). Recently, additional cellular proteins, namely...

The γ‑herpesviruses Epstein-Barr virus and Kaposi's sarcoma‑associated herpesvirus are successful pathogens, each infecting a large proportion of the human population. These viruses persist for life host may contribute to number malignancies, which there currently no cures. Large‑scale proteomic-based approaches provide an excellent means increasing collective understanding proteomes these complex elucidating their numerous interactions within infected cell. large‑scale studies important...

The epidemic form of Bovine Spongiform Encephalopathy (BSE) is generally considered to have been caused by a single prion strain but at least two variants cattle disorders recently recognized. An additional neurodegenerative condition, idiopathic brainstem neuronal chromatolysis and hippocampal sclerosis (IBNC), rare neurological disease adult cattle, was also recognised in sub-set submitted under the BSE Orders which lesions were absent. Between years 1988 1991 IBNC occurred Scotland with...

Abstract The epitranscriptomic modification N 6 -methyladenosine (m A) is a ubiquitous feature of the mammalian transcriptome. It modulates mRNA fate and dynamics to exert regulatory control over numerous cellular processes disease pathways, including viral infection. Kaposi’s sarcoma-associated herpesvirus (KSHV) reactivation from latent phase leads redistribution m A topology upon both mRNAs within infected cells. Here we investigate role in transcripts upregulated during KSHV lytic...

Abstract Despite the nuclear localization of m 6 A machinery, genomes multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively A-modified. However, these findings mostly based on A-seq, an antibody-dependent technique with a high rate false positives. Here, we addressed presence in CHIKV DENV RNAs. For this, combined A-seq antibody-independent SELECT nanopore direct sequencing techniques functional, molecular, mutagenesis...