RNA silencing

A link between mRNA turnover and RNA interference in Arabidopsis. Gazzani, S. et al. Science 306, 1046–1048 (2004)

MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Bao, N. et al. Dev. Cell 7, 653–662 (2004)

These papers provide new insights into RNA-mediated silencing. RNA-dependent RNA polymerase (RdRP) promotes RNA interference in several species, but its substrate is unknown. Gazzani et al. showed that mutation of the Arabidopsis thaliana XRN4 exonuclease gene promotes RdRP-dependent silencing of a transgene. Plants that lack both RdRP and XRN4 accumulate decapped transgene mRNA, implicating uncapped transcripts as RdRP substrates. Bao et al. investigated the regulation of the A. thaliana PHB and PHV leaf-patterning genes. Both genes are heavily methylated in wild-type plants, but this is reduced by mutation of microRNA binding sites that are present in PHB and PHV mRNAs, but not in the corresponding genomic sequences. MicroRNAs therefore seem to regulate expression of these genes by interacting with their transcripts to produce epigenetic changes at the genomic level.

Epigenetics

DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. Rakyan, V. K. et al. PLoS Biol. 2, e405 (2004)

DNA methylation has a crucial function in vertebrate development, gene regulation and disease. The Human Epigenome Project (http://www.epigenome.org) aims to identify and catalogue the pattern of cytosine methylation across the human genome. As a prelude to this large-scale project, Rakyan and colleagues have analysed the DNA-methylation profile of the human major histocompatibility complex. The project, which involved the development of high-throughput analysis methods, revealed that most regions of the 90 genes studied were either hypo- or hypermethylated.

Technology

A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Slade, A. J. et al. Nature Biotechnol. 5 December 2004 (doi:10.1038/nbt1043)

Modifying the wheat genome is an attractive goal for agriculture and industry, but the size of this large, polyploid genome makes the application of transgenic methods particularly challenging. Ann Slade and colleagues have now applied a reverse genetic, non-transgenic method called TILLING to isolate 246 alleles of a gene (GBSSI) that is involved in starch biosynthesis, showing that this method can be used effectively for crop improvement. Plants with null alleles of GBSSI produce highly branched starches that have unique and commercially valuable properties.