Following the observation that a few lincRNAs act in cis 24,25, some recent papers have claimed that most lincRNAs act primarily in cis8,11,26. We found no evidence to support this latter notion: knockdown of only 2 lincRNAs showed effects on a neighbouring gene, only 13 showed effects within a window of ten genes on either side, and only 8 showed effects on genes within 300 kb; these proportions are no greater than observed for protein-coding genes (Supplemental Figure 3, Supplemental Table 6). In short, lincRNAs appear to affect expression largely in trans.
