YRNAs overexpression and potential implications in allergy

Abstract

Background: Small non-coding RNAs (snRNAs) develop important functions related to epigenetic regulation. YRNAs are snRNAs involved in the initiation of DNA replication and RNA stability that regulate gene expression. They have been related to autoimmune, cancer and inflammatory diseases but never before to allergy. In this work we described for the first time in allergic patients the differential expression profile of YRNAs, their regulatory mechanisms and their potential as new diagnostic and therapeutic targets.

Methods: From a previous whole RNAseq study in B cells of allergic patients, differential expression profiles of coding and non-coding transcripts were obtained. To select the most differentially expressed non coding transcripts, fold change and p-values were analyzed. A validation of the expression differences detected was developed in an independent cohort of 304 individuals, 208 allergic patients and 96 controls by using qPCR. Potential binding and retrotransponibility capacity were characterized by in silico structural analysis. Using a novel bioinformatics approach, RNA targets identification, functional enrichment and network analyses were performed.

Results: We found that almost 70% of overexpressed non-coding transcripts in allergic patients corresponded to YRNAs. From the three more differentially overexpressed candidates, increased expression was independently confirmed in the peripheral blood of allergic patients. Structural analysis suggested a protein binding capacity decrease and an increase in retrotransponibility. Studies of RNA targets allowed the identification of sequences related to the immune mechanisms underlying allergy.

Conclusions: Overexpression of YRNAs is observed for the first time in allergic patients. Structural and functional information points to their implication on regulatory mechanisms of the disease.

Keywords: Allergy; Epigenetics; Expression; Transcriptomics; YRNAs; ncRNA.

Fig. 1

Characteristics of Y_RNAs selected as best candidates. In the Clustal W2 Alignment the hYRNA3 more frequently mutated positions are marked in blue and the bases that vary with respect to hYRNA3 are marked in bold. 1: ENSG00000201555 (Y_RNA.269-201), 2: ENSG00000201228 (Y_RNA.231-201), 3: ENSG00000207499 (Y_RNA.575-201), and 4: ENSG00000202354 (hYRNA3 consensus sequence).

Fig. 2

qPCR validation study of YRNAs overexpression in allergic patients. Distribution of the fold change expression levels of Y_RNA.575-201 (ENSG00000207499), Y_RNA.231-201 (ENSG00000201228) and Y_RNA.269-201 (ENSG00000201555) in the population of controls (n ​= ​96), patients monosensitized to pollens (n ​= ​52) and patients monosensitized to mites (n ​= ​38). K–W test was performed, and significant differences were found between control individuals and those monosensitized to pollens and between individuals monosensitized to pollens and monosensitized to mites. (*p ​< ​0.05, **p ​< ​0.01).

Fig. 3

Y_RNA.269-201 In silico analyses.

Fig. 4

Functional relations of Y_RNA.269-201 (ENSG00000201555) potential targets. GeneMANIA algorithm prediction. Black circles represent gene targets. Grey circles represent associated genes to network inference. Grey rhombuses represent pathways. The green edges represent genetics relationship. Pink and blue edges represent to protein-protein interaction.