Insight into noncanonical small noncoding RNAs in Influenza A virus infection

Abstract

Influenza A virus (IAV) induces acute respiratory infections in birds and various mammals, including humans, and presents a significant global public health concern, with considerable economic consequences. Recently, researchers have shown keen interest in noncanonical small noncoding RNAs (sncRNAs) as carriers of epigenetic information, including tRNA-derived small RNAs (tsRNAs), rRNA-derived small RNA (rsRNAs), and Y RNA-derived small RNAs (ysRNAs). Particularly, tsRNAs and rsRNAs are detected in diverse species and demonstrate evolutionary conservation. We analyzed sncRNAs sequencing data in the pulmonary tissue of two genetically distinct mouse strains, C57BL/6J and DBA/2J, to explore strain-specific variations of sncRNAs in response to IAV infection. We systematically compiled information on noncanonical sncRNAs in these two strains and investigated the tsRNAs/rsRNAs/ysRNAs profiles influenced by IAV infection. Specifically, four noncanonical sncRNA families, including rsRNA-12S, GtsRNA-Arg-CCT, GtsRNA-Arg-TCT, and GtsRNA-Lys-TTT, exhibited upregulation upon IAV infection. Notably, DBA/2J mice showed earlier systemic differential expression of noncanonical sncRNAs after IAV infection compared to C57BL/6J mice. Additionally, our study revealed a strain-specific biogenesis of MtsRNAs in response to IAV infection. Also, distinct co-expression patterns of MtsRNAs were observed between C57BL/6J and DBA/2J mice, with DBA/2J mice showing broader positive co-expression of MtsRNAs with various sncRNA families compared to C57BL/6J mice. Our study provides a novel insight into noncanonical sncRNAs and their implications in IAV pathology and mouse strain specificity.

Keywords: Influenza A virus; Small noncoding RNAs; rsRNAs; tsRNAs; ysRNAs.

Fig. 1

Comparison in noncanonical sncRNA profiles between the two mouse stains. (A) Principal component analysis on the expression of noncanonical sncRNA families. PC1: the first principal component; PC2: the second principal component. (B) Comparison in tsRNA/rsRNA/ysRNA length distribution between the two mouse strains. (C) Expression heatmap of the differentially expressed tsRNA/rsRNA/ysRNA families between the two mouse strains. Red means relatively higher expression while blue denotes lower expression.

Fig. 2

The common differential expressed noncanonical sncRNA families between the two strains. (A) Comparison in the relationship between the expression of noncanonical sncRNA families and IAV post infection hours. Spearman’s rank correlation test was used to measure the relationship between the expression of tsRNA/rsRNA/ysRNA families and the infection hours for the C57BL/6J and DBA/2J strains, respectively. Four sncRNA families were identified to be commonly upregulated with the infection hours, which were highlighted in red. (B) Boxplots showing the expression of the sncRNA families highlighted in panel A in response to IAV infection. (C) Comparison in the relationship between the expression of noncanonical sncRNA families and hours of post mock treatment. Spearman’s rank correlation test was used to measure the relationship for the C57BL/6J and DBA/2J strains, respectively. No sncRNA family was identified to be commonly upregulated with the mock treatment.

Fig. 3

Volcano plots of the differentially expressed sncRNA species between the mock and infection treatments at the individual time points. Each dot represents one sncRNA species. Pink dots indicate the upregulated sncRNA species, while light blue dots indicate the downregulated sncRNA species. The sncRNA species with false discovery rate < 5 % and fold change in expression > 2 were defined as differentially expressed.

Fig. 4

Correlation in log₂-transformed fold changes between the C57BL/6J and DBA/2J strains. The log₂FC values were computed between the mock and infection treatments at 120 h. The correlation in log₂FC between the two mouse strains was calculated by Spearman’s rank correlation test. MtsRNA species show the least accordance in differential expression patterns between the two strains. DE: differentially expressed in both strains.

Fig. 5

Comparison in co-expression pattern between the two mouse strains. (A) Correlation in total abundance between GtsRNA and rsRNA and between GtsRNA and MtsRNA. Spearman’s rank correlation test was used to measure the relationship between the individual sncRNA categories. (B) Co-expression heatmap of the noncanonical sncRNA families in the C57BL/6J strain. Spearman’s rank correlation test was used to measure the pairwise relationship in expression between the individual noncanonical sncRNA families. Red means positively co-expressed (positive correlation) while blue means negatively co-expressed (negative correlation).