Assessing a potential in cis regulatory function of the lncRNA Malat1 in CD4+ T cells

The long non-coding RNA (lncRNA) Metastasis Associated Lung Adenocarcinoma Transcript 1 (Malat1) has been indicated to have a variety of cellular functions, from cancer cell growth and survival to regulating pre-mRNA splicing. In several Malat1 knockout (KO) models, Malat1 neighbouring genes showed significant expression changes, but these effects were not consistent across all Malat1 KO mouse models. This implies potential and tissue specific in cis regulation of these genes by Malat1. Here, we assessed if Malat1 regulated its surrounding genes in cis in CD4+ T cells, as previous experiments on these cells showed significant downregulation of Malat1 upon T cell activation. This was achieved by analysing primary naïve mouse CD4+ cells in vitro under Th0, Th1 and Th2 differentiation conditions at two different time points. Our results showed significant expression changes in Neat1, Scyl1 and Map3k11 in Malat1 KO cells under specific activation conditions (e.g. naïve, 4 day Th0 and 6 day Th1 cultures). To assess the cell type specificity of these effect, mouse tail fibroblasts (MTFs) were isolated and analysed – only Scyl1 was differentially expressed in Malat1 KO MTFs. We also assessed potential in trans effects of Malat1. It has been shown that Malat1 binds the mRNA of several RNA binding proteins – amongst those, we found that Malat1 regulates U2af1 in specific CD4+ cell types. This data indicates that gene regulation in T helper cells by Malat1 does not occur uniformly across all subsets, but is dependent on the type and duration of activation. For the Malat1 neighbouring genes, this may be via transcription factors binding to the Malat1 locus and acting on nearby enhancer and promoter sequences.