Functionally prioritized identification of T cell lncRNAs in Mammals

Abstract

Long non-coding RNA (lncRNA) is a transcript longer than 200 nt that has no protein-coding potential. lncRNAs have been known to play important functions in the development and differentiation of T cells. Although many lncRNAs have been annotated with the development of high-throughput sequencing, it is difficult to find functionally important lncRNAs and therefore functional prioritization is prerequired. lncRNAs can be prioritized with expression specificity, with correlation to T cell-specific transcription factors (TFs), and with evolutionary conservation. In this paper, I used RNA-seq data from mouse T cell subtypes to annotate lncRNAs from mouse T cells and identified 3,840 novel lncRNAs. Differentially expressed genes (DEGs) were classified and their functions annotated by Gene Ontology enrichment analysis, and then evolutionarily conserved lncRNAs in human and mouse were identified. RNA-seq data from bystander-activated memory-like CD4+ T cells were used to identify lncRNAs associated with characteristics of bystander activation. Seven evolutionarily conserved lncRNAs were identified as potential functional lncRNAs in bystander activation. This study upgraded the mouse lncRNA catalog in terms of specific expression, TF-associated expression, and evolutionary conservation, identifying functionally prioritized lncRNAs that are specifically expressed in each T cell subtype, providing new insights into the function of lncRNAs in T cells.