Progress

Until recently, large-scale transcriptome studies in bacteria and archaea were limited by technical challenges, and there was a perception that microbial transcription was relatively simple compared with eukaryotic transcription. Now, prokaryotic transcriptomics is revealing unexpected aspects of transcriptional control, genome organization and non-coding RNAs.

Recent studies have identified common genetic variants that contribute to colorectal cancer aetiology, providing new insight into the genetic architecture of the disease. Associations identified so far suggest an overlap with familial cases in terms of biological mechanisms, and also provide new avenues for exploration.

Recent studies have shown that viral oncoproteins induce specific epigenetic changes to stimulate the replication of normally quiescent cells. These findings have implications for understanding the roles of epigenetics in cancer, and in normal biological processes such as differentiation.

Recent advances in genotyping technology have identified or confirmed more than 20 loci that are associated with susceptibility to systemic lupus erythematosus (SLE). These findings add detail to our current understanding of the molecular basis of this complex disease and provide new avenues for investigation.

Genome-wide linkage and association studies have reliably implicated a growing number of genes in susceptibility to addiction. An emerging theme is the substantial overlap in loci that are associated with addiction to multiple substances.

The recent discovery that most of the eukaryotic genome is transcribed has focused interest on the importance of non-coding transcripts. Long non-coding RNAs are emerging as a class with wide-ranging functions in gene regulation.

Recent genome-wide association and expression array studies have provided new insights into prostate cancer genetics. The germline and somatic variants identified in these studies have been proposed to predict prostate cancer risk and aggressiveness. These results are discussed in the context of their implications for the screening and treatment of prostate cancer.

Mitochondrial DNA reproduces asexually and is therefore susceptible to the accumulation of deleterious mutations. Recent results suggest that there is purifying selection against such mutations within the female germ line, which has important consequences for studies of evolution and human disease.

It is now feasible to dissect the influence of the environment on gene function in many species — a desirable goal from a biomedical, agricultural and evolutionary perspective. This article describes the progress made so far, and the analytical challenges to be overcome.

Some DNA viruses express abundant non-coding RNAs, but their function has been mostly unknown. Several recent reports show how viruses can use non-coding RNAs to tackle host defences and control their gene expression levels.

Studies of Crohn disease have benefited spectacularly from genome-wide association scans. Newly identified susceptibility loci support previously suspected underlying pathways, but also reveal hitherto unexpected putative mechanisms of this disease.

Functions of histone lysine demethylases in a range of developmental and physiological processes are rapidly being uncovered, as are the roles of these enzymes in disease. Histone demethylases also provide a promising new route towards the therapeutic targeting of epigenetic regulators.

Type 2 diabetes has been described as a geneticist's nightmare. Following a recent spate of impressive results from genome-wide association studies, the author looks at how they have advanced our understanding of this disease and informed future use of this approach towards identifying genetic variants in general.