Leaky RNA

Question

[Chris]

Hello all,

Would you please explain what leaky RNA means? Google didn't know this.

[ATpoint]

[Chris]

Oh. Sorry about that. I thought this concept can understand without context. It is from a course in scRNA-Seq using 10x technique (droplet-based, can have leaky RNA). Your comment is interesting and if the image is larger, it will be easier to read the keyword.

[ATpoint]

Never heard of it. Maybe ambient RNA contamination is what they mean.

[Chris]

Thank you! English is not the first language of the lecturer, so maybe the word choice is not clear. Would you please explain ambient RNA? I looked on the internet but still not clear. Where does ambient RNA come from?

[benformatics]

Droplets that don't end up with a cell inside of them could potentially acquire reads from extracellular RNA (e.g. from lysed/broken cells, etc...) is probably what they meant. It's essentially false positive signal.

[Medhat]

Some examples here:

In the absence of T7-polymerase, pT7-nef2 and pT7sh-nef confer a low level of inhibition on virus production probably due to leaky RNA expression from the plasmids (Figure 6b). With T7-polymerase, pT7-nef2 and pT7sh-nef confer up to 90% inhibition of HIV-1 production (Figure 6b).

Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA

In rich medium (YPGal), we obtained identical results for the T7hsp82TD strain expressing an integrated copy of the T7 RNA polymerase gene. However, in YPD medium theT7hsp82 strain exhibits slight splitting of one nucleosome in the absence of T7 RNA polymerase expression, which we attributed to leaky RNA polymerase II transcription based on Northern analyses. In the same strain such splitting is mildly enhanced in YPGal medium upon expression of the integrated copy of T7 RNA polymerase, which we attributed to increased leaky RNA polymerase II transcription triggered by a stress response.

RNA Polymerase-specific Nucleosome Disruption by Transcription in Vivo

The purpose of intron retention is not altogether clear - in fact, whether or not it is even a deliberate regulatory process, rather than leaky RNA metabolism, is itself a matter of debate. For this reason, studies providing additional data on how RBPs relate to intron retention are very welcome.

The RBPome: where the brains meet the brawn

[Chris]

Thank you so much!