Thursday, 18 February 2010

Of moss and me

ResearchBlogging.orgI recently had a look through some new papers published on moss (Physcomitrella patens) and found one published in Cell titled ‘Transcriptional control of gene expression by microRNAs’ [1]. This didn’t seem to fit the same pattern of a lot of moss papers I have read (ie in less high impact journals). This paper shows how useful moss is for studying gene expression using reverse genetics (so hopefully my PhD wont be a failure).

I think it is important to study important biological problems, such as RNA silencing and epigenetics, in a diverse range of organisms. I take this title from a short review published in Nature Medicine recently (as well as the Steinberg book) by Sir David Baulcombe (who holds a prestigious chair at Cambridge). He wrote about what we have learnt by studying things in plants (eg discovery of transposons) and their importance as a model, using his own research into RNA silencing and epigenetics as the main example [2]. I think this new moss paper goes some way to support this, but also to show the importance of this particular organism. My choice to work with Physcomitrella was because I wanted to stay in the plant world but wanted to work with something where I could knock out specific genes by homologous recombination and was simple to grow. Physcomitrella can be grown on simple agar media plates and joins the few species where genes can be knocked out.

Khraiwesh et al (2010) looked at what happened when you knocked out two Dicer-like (DCL) proteins in moss [1]. Dicer proteins in animals and plants cut long dsRNA to make small RNAs loaded onto Argonaute proteins (producing the effector complex). This effector complex is what causes the target mRNA to be cut or repress its translation. When PpDCL1a was knocked out you see a lack of microRNAs (miRNAs) being produced and the plant is restricted to its first developmental stage only. Not surprising. Strangely, when you knocked out PpDCL1b get production of miRNAs but not cleavage of the targets. It has been shown in animals, but not other plants, Dicer proteins can sometimes be used to help a small RNA in the effector complex to cut the target, as well as in miRNA or siRNA biogenesis. Very interestingly they found these targets had a lower level of expression in the mutant plants. If cleavage is not reducing the mRNA levels then what? The answer to this as many other odd questions in biology is epigenetics. Well DNA methylation at least. siRNAs have been shown to cause gene silencing but not much evidence for miRNAs doing this before. The authors went onto show the ratio of miRNA to mRNA target is critical. If you only have a little miRNA compared to mRNA target you get cleavage. If you have lots of miRNA to target mRNA it causes DNA methylation and silencing. But the methylation was only seen in the knockout so why should we care?

Finally they end the paper by showing ratio of miRNA to target mRNA is important in an endogenous gene involved with a hormone response. The plant hormone ABA mediates drought response and abiotic stress. In moss, when ABA treated you get a decrease in a transcription factor response gene. This is a target of a natural miRNA. This down-regulation is due to an increase in miRNA expression, changing the effect from cleaving the transcription factor’s mRNA to targeting its promoter for methylation and silencing expression. This study shows that miRNAs have the potential to cause DNA methylation, which had not yet been show, as well as suggesting a mechanism for it. Future studies can now go on to show the relevance of this in other systems from yeast to flies to mammals.

I end by simply saying MOSS ROCKS.

Khraiwesh, B., Arif, M., Seumel, G., Ossowski, S., Weigel, D., Reski, R., & Frank, W. (2010). Transcriptional Control of Gene Expression by MicroRNAs Cell, 140 (1), 111-122 DOI: 10.1016/j.cell.2009.12.023

Baulcombe, D. (2008). Of maize and men, or peas and people: case histories to justify plants and other model systems Nature Medicine, 14 (10), 1046-1049 DOI: 10.1038/nm1008-1046


James Lloyd said...

And now its someone else's turn!

Menelaos Symeonides said...

James, would you say that we are getting closer to having some sort of general model of epigenetics or more specifically DNA methylation? I don't really follow the literature on it or anything but I am just surprised to find that we are still having to postulate as to how it even takes place at a basic level.

James Lloyd said...

Thanks for the comment.

I do not follow the field my self. from what i know it is established small RNAs can cause DNA methylation and silencing (definitely in plants) and people are developing plants where they target both the promoter with a small RNA (so not able to target an RNA only DNA) and another small RNA to the transcript so you can get down-regulation in two ways.

i think there is still a lot of work going on to figure the basics out. components of the pathway and mechanisms.

kent said...

epigenetics may have a neurological structure in the brain itself