The long non-coding RNA MALAT1 contributes to the pathogenesis of multiple sclerosis through alternative splicing and backsplicing regulation

Since we found an upregulation of the long non coding RNA MALAT1 in Multiple Sclerosis (MS) patients, we decided to explore the global effect of MALAT1 modulation on transcriptome. We hence performed high-coverage RNA-seq experiments of MALAT1 knockdown in Jurkat E6-1 T cells to analyze gene expression, alternative splicing (AS), and backsplicing profiles. We found 107 differentially expressed genes, 1114 dysregulated AS events, and 49 circular RNAs that were modulated by MALAT1. These results highlighted the role of MALAT1 in splicing and backsplicing regulation. Jurkat E6-1 cells were incubated with 500 nM GapmeR targeting MALAT1 (kd) or 500 nM GapmeR negative control (mock)