Distinct temporal changes in host cell lncRNA expression during the course of an adenovirus infection

Abstract

The deregulation of cellular long non-coding RNA (lncRNA) expression during a human adenovirus infection was studied by deep sequencing. Expression of lncRNAs increased substantially following the progression of the infection. Among 645 significantly expressed lncRNAs, the expression of 398 was changed more than 2-fold. More than 80% of them were up-regulated and 80% of them were detected during the late phase. Based on the genomic locations of the deregulated lncRNAs in relation to known mRNAs and miRNAs, they were predicted to be involved in growth, structure, apoptosis and wound healing in the early phase, cell proliferation in the intermediate phase and protein synthesis, modification and transport in the late phase. The most significant functions of cellular RNA-binding proteins, previously shown to interact with the deregulated lncRNAs identified here, are involved in RNA splicing, nuclear export and translation events. We hypothesize that adenoviruses exploit the lncRNA network to optimize their reproduction.

Porcine endemic diarrhea virus infection regulates long noncoding RNA expression

“…This effect may be due to the time and spatial-temporal expression of lncRNAs. The expression of lncRNAs can be affected by many factors, such as cell type, tissue type, development stage, culture time and stimulants (Cabili et al, 2011;Gaiti et al, 2015;Guo et al, 2016;Hart and Goff, 2016;Pauli et al, 2012;Peng et al, 2010;Zhao et al, 2016). The reasons for this effect can be explained as above.…”

Phosphorylation Time‐Course Study of the Response during Adenovirus Type 2 Infection

“…However, extensive studies of how specific phosphorylation sites are altered in a time series of infection have been scarcely reported, such as for herpes virus. [ 10 ] In the case of human adenovirus (HAds) infection, for which time series of ribonucleic acid (RNA) and proteome changes have been reported, [ 11–15 ] phosphorylation data is lacking.…”

“…Transcriptomic studies suggest that the infection cycle of human adenovirus type 2 (Ad2) in human primary lung fibroblasts (IMR‐90) can be divided into four periods, characterized by: i) the inhibition of cell growth; ii) the creation of an optimal environment for replication of the viral genome; iii) the replication of the viral genome; and iv) the alteration of genes involved in intra‐ and extracellular structure. [ 11–13 ] Complementary to these studies, time‐resolved mass spectrometry (MS)‐based proteomics studies have demonstrated that host protein regulation also fluctuates during Ad2 infection. [ 14,15 ] The overall correlation between the alterations at the protein and mRNA levels has been observed to be low, [ 15 ] but these discrepancies are not new and PTMs have been suggested to play essential roles.…”

“…In the present study, we have combined TiO 2 particle enrichment and SILAC MS to perform one of the most comprehensive quantitative time‐course study of the phosphoproteome changes during viral infection. The experimental times selected were the same as in our previous transcriptomics and proteomics studies, [ 13–15 ] but also included a very early time point of infection for improved monitoring of signaling pathway changes. Stringent cut‐off filters were applied to ascertain high‐quality data, and bioinformatics and statistical tools were used to extract information about the most relevant pathways and kinase–substrate relationships.…”

Protein-Coding Genes’ Retrocopies and Their Functions

“…Retrocopies may also be associated with the host response during pathogen infection in humans, as significant expression changes were observed after HIV-1 and human type 2 adenovirus infection [176,177]. For instance, expression pattern analysis after HIV-1 infection of human T-cells showed that the most upregulated pseudogene group was a group of retrocopies.…”