The RNAi machinery can induce global changes in gene expression by regulating the formation of higher-order chromatin structures in Drosophila.
Small RNA pathways are skilled multi-taskers, regulating gene expression in various ways. A study of insulator activity has now uncovered a new role for the RNAi machinery: in organizing chromatin structure.
The gypsy transposable element of Drosophila melanogaster is widely used to study insulator function in assays because of its ability to shield genes from enhancers when it is inserted between them. gypsy recruits a protein complex that is thought to promote the formation of higher-order chromatin structures that prevent enhancers and promoters from meeting.
Lei and Corces identified a putative RNA helicase, Rm62, as a new component of the gypsy insulator complex that only interacts with the other components in the presence of an RNA molecule. Rm62 is essential for dsRNA-mediated silencing in flies, providing a potential link between the RNAi pathway and insulator function.
To check the functional significance of their finding, the authors tested the effects of mutating either Rm62 or other RNAi-pathway components on the insulating abilities of gypsy. Rm62 mutations increased insulator activity, indicating that the encoded helicase somehow inhibits gypsy function. By contrast, mutations in piwi and aubergine — which encode Argonaute proteins that are needed for RNAi-induced chromatin modifications — had the opposite effect. Epistasis analysis that used combinations of these mutations revealed that the two Argonaute proteins function upstream of Rm62 in a common pathway.
How might the RNAi machinery physically affect insulator function? Mutations in piwi, aubergine and Rm62 had no effect on the chromosomal localization of gypsy complex proteins, ruling out a role in recruitment. However, they did have an impact on the higher-order organization of insulator complexes, which usually form foci known as insulator bodies. Piwi and aubergine were found to be needed for these foci to form, whereas Rm62 seems to negatively regulate their accumulation.
This study adds the control of chromatin architecture to the growing list of skills of the RNAi machinery. Precisely how it does this — and how Rm62 carries out its counteracting role — awaits further investigation.
Lei, E. P. & Corces, V. G. RNAi machinery influences the nuclear organization of a chromatin insulator. Nature Genet. 2006 | Article |
Matzke, M. A. & Birchler, J. A. RNAi-mediated pathways in the nucleus. Nature Rev. Genet. 6, 24–35 (2005) | Article | PubMed |
this article was published in nature.