Evolutionary divergence of Firre localization and expression

Long non-coding RNAs (lncRNAs) are rapidly evolving and thus typically poorly conserved in their sequences. The extent to which these sequence differences affect the characteristics and potential functions of lncRNAs with shared synteny remains unclear. Here we show that the syntenically conserved lncRNA Firre displays distinct expression and localization patterns in human and mouse. Single molecule RNA FISH reveals that in a range of cell lines, mouse Firre (mFirre) is predominantly nuclear, while human FIRRE (hFIRRE) is distributed between the cytoplasm and nucleus. This localization pattern is maintained in human/mouse hybrid cells expressing both human and mouse Firre, implying that the localization of the lncRNA is species autonomous. We find that the majority of hFIRRE transcripts in the cytoplasm are comprised of isoforms that are enriched in RRD repeats. We furthermore determine that in various tissues, mFirre is more highly expressed than its human counterpart. Our data illustrate that the rapid evolution of syntenic lncRNAs can lead to variations in lncRNA localization and abundance, which in turn may result in disparate lncRNA functions even in closely related species. To assess whether abundance and localization differences between human and mouse Firre are sequence intrinsic, RNA-seq was performed on the wild type mouse/human hybrid cell line AHA 11a (Coriell, GM10324) which retains the human X chromosome. Three biological replicates for rRNA-depleted (total) and poly-A selected RNA were sequenced using 75-bp paired-end sequencing and mapped to mm39 with human chrX from hg38 appended. Reads were aligned and quantified with nf-core/rnaseq v1.4.2 using the Salmon v0.14.1 pseudo-aligner.