LincRNAs do not need to be polyadenylated to be functional [30]. Because of this, we included in our analysis many RNA-seq libraries that were not polyA+ selected. In fact, earlier tiling array studies revealed that intergenic transcripts tend to be bimorphic; that is, they appear in both polyA+ and polyA− fractions, as opposed to protein coding transcripts that are primarily polyA+ [3]. The recently published ENCODE results corroborate this finding [14], [19]. In agreement with these studies, we found that the polyadenylation status of lincRNAs in our catalog is reproducibly bimorphic across multiple cell types while protein coding transcripts are strongly enriched in the polyA+ sample. The reproducibility of this lincRNA bimorphic state suggests that lincRNA polyadenylation is regulated and that many lincRNAs exist at least partially as nonpolyadenylated transcripts (Figure 3B and Figure S5). This finding indicates that future studies of lincRNAs should not ignore the nonpolyadenylated RNA fraction.
