Identification of differentially expressed lncRNAs in CD4+ T cell memory compartments

Abstract

Long non-coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that do not code for proteins, but have been shown to perform regulatory roles in various cellular processes and in disease conditions. They have also been shown to be involved in the regulation of cellular processes, disease conditions and lineage-specificity. Since the lncRNAs harbor immense regulatory potential at both transcriptional and post-transcriptional levels, identifying and molecular characterizing T cell memory subset-specific lncRNAs will add new dimensions to understanding T cell memory development and functioning. Hence, as part of my MS thesis, I analyzed the transcriptomic (RNA-Seq) and epigenomics (ATAC-Seq) data from six memory CD4+ T cell subsets, to identify memory subset-specific lncRNAs. Comparative analysis of differentially expressed genes identified 42 and 36 upregulated lncRNAs in long-term (TCM, TSCM) and short-term effector memory subsets (TEM, TEMRA-precursor and TEMRA-effector), respectively. Further to identify potential cis regulatory role of these lncRNAs, I identified differentially expressed protein-coding genes located upstream and downstream of these lncRNAs. This analysis has identified 16 such lncRNA-protein-coding genes pairs. Further functional characterization of these lncRNA-protein coding gene pairs for the co-regulation can yield interesting insights into the T cell memory development and commitment.