Question

In Pnueli et al., 2015, they knock down an enhancer RNA using RNAi, testing whether it is a mere byproduct or whether it has a key role in the enhancer's function. They find their system works: the siRNA knocks down the enhancer RNA that it's targeted to, enabling further study. Hooray!

... but I've read that RNAi and the RISC work outside the nucleus, and intra-nuclear effects are further downstream and indirect (example: Gosline et al. assume that effects on introns are indirect). I assume the paper's not wrong, so what's going on?

Conventional wisdom is wrong or incomplete: RNAi can work inside the nucleus too.
Pneuli et al.'s enhancer RNA gets exported to the cytoplasm and then re-imported to act on its target gene.
Something else?
Pnueli, L., Rudnizky, S., Yosefzon, Y., & Melamed, P. (2015). RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene. Proceedings of the National Academy of Sciences, 112(14), 4369-4374.

Gosline, S. J., Gurtan, A. M., JnBaptiste, C. K., Bosson, A., Milani, P., Dalin, S., ... & Fraenkel, E. (2016). Elucidating microRNA regulatory networks using transcriptional, post-transcriptional, and histone modification measurements. Cell reports, 14(2), 310-319.

Answer 1

The observation from Pnueli et al. that RNAi can knock down an enhancer RNA suggests that RNA interference may have nuclear roles in addition to its understood cytoplasmic activities, challenging the conventional wisdom of RNAi's functional exclusivity to the cytoplasm.

Step-by-step explanation:

The question revolves around whether RNA interference (RNAi) technology, which typically functions in the cytoplasm, can also exert effects within the nucleus. This inquiry is driven by results from Pnueli et al., 2015, where knocking down an enhancer RNA using RNAi seemed to affect the enhancer's function, suggesting intra-nuclear activity of RNAi. RNAi, involving small interfering RNAs (siRNAs) or microRNAs (miRNAs), usually works by degrading mRNA or inhibiting translation in the cytoplasm. However, recent findings suggest that RNAi components could have nuclear roles, such as modulating transcription or affecting RNA processing events within the nucleus. This broader understanding of RNAi may explain the observations in Pnueli et al., supporting the idea that the conventional wisdom regarding the exclusivity of cytoplasmic RNAi action is incomplete.