| Non-coding RNAs and small 21-30 nt RNA molecules (sRNAs) derived from this DNA have been correlated with controlling chromatin states, particularly during initiation of a compact chromatin structure at constitutive heterochromatin, polycomb-repressed genes or transposable elements. However, the mechanisms by which these RNAs act are poorly understood. I have performed DNA methylation analysis in Chlamydomonas by methylated DNA immunoprecipitation (MeDIP), and analysed the immunoprecipitated DNA by Solexa sequencing. Combined with previous work on the analysis of the small RNA profile of Chlamydomonas reinhardtii (Molnar et al. (2007) Nature 447 1126-1129), this has identified many loci in the genome, including transposable elements, that are both methylated and have small RNAs directed to them. I am verifying methylation of these loci by bisulphite sequencing and methylation-specific PCR. Work is in progress to analyse histone modifications in a similar manner by chromatin immunoprecipitation followed by Solexa sequencing (ChIP-Seq) to analyse chromatin modifications on a global scale. In this way, I can correlate loci that are targeted by small RNAs, with the underlying DNA and chromatin modifications.
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