I’ve been giving some talks on Hedia’s work on non-coding RNA at some meetings where people talk about non-coding RNA, and I’ve realized that we can actually make some further claims that we didn’t think about at the time. Quick recap: we show (by RNA FISH, natch) that knocking down non-coding RNA (linc-Hoxa1) at the transcription site results in transcriptional upregulation of the nearby Hoxa1 gene. We also show that the RNA binds to the protein PurB in vitro and in vivo, and that knocking down PurB destroys the anti-correlation in expression between linc-Hoxa1 and Hoxa1–normally, they are strongly anti-correlated, which is what led us to think that linc-Hoxa1 negatively regulates Hoxa1 in the first place.
One question in the lincRNA field is whether the RNA itself is what regulates transcription, or if it's just the DNA sequence. For instance, if you knock out the DNA sequence including the RNA, can you be sure that it’s the RNA that causes the effect per se, or is it rather the DNA acting like a conventional enhancer (with the RNA itself being just an unimportant byproduct). Our results showing that knockdown at the site of transcription show that the RNA itself is important: the DNA sequence remains intact, but removal of the RNA causes the change in transcription.
The next question is whether it’s just the transcription of the lincRNA that affects transcription, or whether the sequence itself is important. The clearest way to show this would be to just replace the lincRNA sequence in the cell line with different ones and see what happens, but we didn’t do that. However, I think our PurB result argues that the sequence itself is important for transcriptional regulation. If it were merely the act of transcription, then knocking down a potential cofactor would not have any effect, since it’s the RNA that matters. PurB is a purine-binding protein, and seems to bind to a hundreds-of-bases-long sequence of Gs and As in the RNA, so it seems very likely that the specific sequence of the lincRNA is important to the regulation.
In summary, I think the important points are that, in the case of linc-Hoxa1, the RNA itself (and not the DNA) is responsible for the regulation, and that it’s not just the act of transcription but the presence of RNA with a specific sequence that is necessary for the regulation to occur. Whether this is the case in general is of course an area for further study.