Strategies to distinguish between the function of a lncRNA product and its transcription. Both DNA strands are shown as separate boxes to indicate a lncRNA transcribed from the top reverse strand, overlapping a pc gene transcribed from the bottom forward strand in antisense orientation. A silencing function of the lncRNA can be predicted by an anti-correlating expression pattern. (a) Left: the lncRNA silencing effect is mediated by tethering of the lncRNA product at the site of transcription, sequence-specific binding of an EM to the lncRNA and guidance of the EM to the pc gene promoter. Right: silencing is mediated by a transcription process independent of the lncRNA product. (b) Posttranscriptional knockdown removes the lncRNA product, thus reversing a lncRNA product-mediated effect (left) but not the transcription-mediated effect (right). (c) lncRNA promoter deletion removes both lncRNA product- (left) and transcription-mediated (right) effects. (d) Truncation experiments inserting transcriptional stop signals at different positions within the lncRNA gene identify the functional region of the lncRNA gene (RNAPII is not shown). Left: lncRNA is only functional when the region corresponding to EM binding site is present. Right: lncRNA is only functional when it crosses the promoter of the overlapped pc gene. For details see Figure 1g, Figure 2e, Figure 3c, Figure 4d and text.
Kornienko et al. BMC Biology 2013 11:59 doi:10.1186/1741-7007-11-59