Next-generation sequencing revealed that the majority of the human genome is transcribed but has no coding function. It is estimated that >30000 long noncoding RNAs (lncRNAs) are expressed in humans, but their functions are largely unknown (Suckau et al., 2009; Rinn and Chang, 2012; Poller et al., 2013). Consideration of noncoding genomic elements in pathogenetic studies is warranted and enabled by technological advances allowing comprehensive transcriptome mapping of protein-coding genes as well as small and long ncRNAs. We searched for lncRNAs influencing antiviral capacity in patients with Coxsackievirus B3 (CVB3) cardiomyopathy (Kuhl et al., 2012) and assign here immunoregulatory functions to the lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and its enzymatic processing product MALAT1-associated small cytoplasmic RNA (mascRNA). Some lncRNAs undergo complex posttranscriptional processing (Wilusz et al., 2008; Kuhn et al., 2015). The MALAT1-mascRNA system is particularly interesting in this regard, since the ∼7-kb primary transcript localizes to the nucleus (Tripathi et al., 2010), whereas the small MALAT1-derived mascRNA is found exclusively in the cytoplasm.
