Gardening the genome: DNA methylation in Arabidopsis thaliana.

DNA methylation has two essential roles in plants and animals - defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight has been the discovery that DNA methylation can be guided by small RNAs produced through RNA-interference pathways. Plants and mammals use a similar suite of DNA methyltransferases to propagate DNA methylation, but plants have also developed a glycosylase-based mechanism for removing DNA methylation, and there are hints that similar processes function in other organisms.

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Enticing general engineering undergrads into signal processing with Photo-Editing and image search

The University of Cambridge is unusual in that its Department of Engineering is a single department which covers virtually all branches of engineering under one roof. In their first two years of study, our undergrads study the full breadth of engineering topics and then have to choose a specialization area for the final two years of study. Here we describe part of a course, given towards the end of their second year, which is designed to entice these students to specialize in signal processing and information engineering topics for years 3 and 4. The course is based around a photo editor and an image search application, and it requires no prior knowledge of the z-transform or of 2-dimensional signal processing. It does assume some knowledge of 1-D convolution and basic Fourier methods and some prior exposure to Matlab. The subject of this paper, the photo editor, is written in standard Matlab m-files which are fully visible to the students and help them to see how specific algorithms are implemented in detail. © 2011 IEEE.