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Background   Toxoplasma gondii  is an obligate intracellular protozoan parasite that can infect mammalian cells and thereby regulate host gene expression. The long non-coding RNAs (lncRNAs) have been demonstrated to be an important class of RNA molecules that regulate many biological processes, including host-pathogen interactions. However, the role of host lncRNAs in the response to  T. gondii  infection remains largely unknown.    Methods  We applied a microarray approach to determine the differential expression profiles of both lncRNAs and mRNAs in the human foreskin fibroblast (HFF) cells after  T. gondii  infection. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to reveal the potential functions of  T. gondii -induced genes. Based on the co-expression networks of lncRNAs and immune-related genes, the role of NONSHAT022487 on the regulation of UNC93B1 related immune signaling was investigated by the knockdown and over-expression of lncRNA in human macrophage derived from the PMA-induced promonocytic cell line THP-1.    Results  Our data showed that 996 lncRNAs and 109 mRNAs in HFF cells were significantly and differentially expressed following  T. gondii  infection (fold change ≥ 5,  P  < 0.05). The results from the GO and KEGG pathway analyses indicated that the mRNAs with differential expression were mainly involved in the host immune response. Remarkably, we identified a novel lncRNA, NONSHAT022487, which suppresses the expression of the immune-related molecule UNC93B1. After  T. gondii  infection, NONSHAT022487 impaired the secretion of the cytokines IL-12, TNF-α, IL-1β and IFN-γ by downregulating UNC93B1 expression in human macrophage cells.    Conclusions  Our study identified infection-induced lncRNA expression as a novel mechanism by which the  Toxoplasma  parasite regulates host immune signaling, which advances our understanding of the interaction of  T. gondii  parasites and host cells.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2697-8) contains supplementary material, which is available to authorized users.

Microarray analysis of long non-coding RNA expression profiles uncovers a Toxoplasma-induced negative regulation of host immune signaling