RNAi in the Nucleus ~ It’s no longer limited to the cytoplasm
Posted by Linda, on 18 January 2011
Hot off the press from the holidays is an article from PNAS that’s worth a gander if you’re into RNAi. We know RNAi associated with epigenetics is possible in the nucleus (Somehow, siRNAs could trigger the methylation and silencing of genes in the nucleus.) However, one soy bean group was able to provide evidence for mRNA slicing in the nucleus.
RNAi is becoming relevant in soy oil production. If certain genes are down regulated, they can reduce the poly-unsaturated fatty acids content levels by 65% (a higher level of saturated fat instead of unsaturated could increase the heat capacity of oil, making it better for deep fries). However, many genes are involved in fatty acid production. Some are from the same family and are highly similar in sequence. To focus on one family member, Hoffer et al. produced an siRNA directed against unique sequences in the intron (perhaps expecting some epigenetic silencing).
Typically, all data pointed to the main mechanisms of RNAi taking place in the cytoplasm, where all the action of mRNA takes place. siRNAs and other small fry had to be shuttled from the nucleus to the cytoplasm. There they would regulate the mRNAs either by slicing them or blocking protein synthesis.
So, it came as a surprise when Hoffer et al. found accumulation of siRNAs against the intron sequence in their targeted mRNA. They were also able to detect sliced up target pre-mRNA. It’s unusual since generally intronic sequences are spliced out of mRNA before transport to the cytoplasm. It could mean that siRNAs can be directed against immature mRNAs in the nucleus. Potentially, this would be another way of attaining further specificity of RNAi. However, levels of the fatty acids were reduced to 20%, so it may not be efficient as cytoplasmic silencing.
Not a whole lot of research has been done on RNAi in the nucleus. So we don’t particularly know much about the active siRNAs that accumulate there. Were they produced in the nucleus and then active at RNAi straightaway? Or were they transported back from the cytoplasm? A worm study isolated an Argonaute protein that transports siRNAs from the cytoplasm into the nucleus. One in mammalian cells has shown that some miRNAs have sequences that can direct them to the nucleus.
Evidently, RNAi in nucleus could have potential in increasing its specificity for a single target. Many genes, especially those from the same family, have high homology (sequence similarity). If even intronic sequences of an mRNA can be targeted, it’s more to choose from.
It’s also a bit like finding out that penguins aren’t just indigenous to the Arctic/Antarctic. You can find native species in South Australia & New Zealand. I had no idea that there are wild penguins in Australia, but there they are. (Flikr CC, M Kuhn)
*In their analyses, the authors fractionated cells into nuclear and cytoplasmic samples and looked at the accumulation of siRNAs and target mRNA transcripts. They were able to detect an accumulation of siRNAs specificity to intron and exon spanning regions. As well, they found a lower level of mRNA transcript in the nucleus than in the cytoplasm. Normally you would expect the reverse, as mRNAs are usually sliced up in the cytoplasm. Via blotting, they were also able to show an accumulation of sliced up mRNA transcripts in nuclear fractions.
Using reporter genes, they then looked for RNAi proteins responsible for producing siRNAs in the nucleus. They could see nuclear localization for the two proteins analyzed: RDR6 (reverse transcribes RNAs) & Dicer Like proteins (excises dsRNA into siRNAs). What would be more interesting, however, is if they looked at the effector proteins of mRNA slicing, the Argonautes.
Hoffer, P., Ivashuta, S., Pontes, O., Vitins, A., Pikaard, C., Mroczka, A., Wagner, N., & Voelker, T. (2010). Posttranscriptional gene silencing in nuclei Proceedings of the National Academy of Sciences, 108 (1), 409-414 DOI: 10.1073/pnas.1009805108
Guang, S., Bochner, A., Pavelec, D., Burkhart, K., Harding, S., Lachowiec, J., & Kennedy, S. (2008). An Argonaute Transports siRNAs from the Cytoplasm to the Nucleus Science, 321 (5888), 537-541 DOI: 10.1126/science.1157647
Heinrichs, A. (2008). Gene expression: Argonaute on the move Nature Reviews Molecular Cell Biology, 9 (9), 666-666 DOI: 10.1038/nrm2473
Hwang, H., Wentzel, E., & Mendell, J. (2007). A Hexanucleotide Element Directs MicroRNA Nuclear Import Science, 315 (5808), 97-100 DOI: 10.1126/science.1136235
(1 votes)
Loading...
I think I read the same 2007/2008 papers when I was writing up my thesis, because the returning to the nucleus story sounds very familiar. Interesting story to catch up on!