Opinion

How did the complex regulatory networks that control eukaryotic gene expression evolve? This article explores evidence that transposable elements played an important part by providing thecis and transcomponents of these networks.

The ability to evolve — evolvability — is important in determining the course of evolution. But does evolvability itself evolve, and how should we even agree on a definition of evolvability?

Evo–devo is now a mature field encompassing a wide range of research areas. The author offers his assessment of its main theoretical implications and challenges for the immediate future.

Copy number variation constitutes a major source of inter-individual genetic variation that could explain variable disease penetrance and variation in the phenotypic expression of aneuploidies, and could be an important factor in the aetiology of complex traits. Therefore, systematic exploration of both single nucleotide and copy number variation will be key to identifying the genomic contributors to polygenic traits and diseases.

The prevailing view is that planar cell polarity is the outcome of one genetic pathway. On the basis of their observations in genetically mosaic adult flies, the authors challenge this assumption and discuss potentially far-reaching implications of their model.

Some structures, such as mammalian forelimbs and bird wings, are obviously homologous, but the basis of this is often elusive as the developmental genes involved are not homologous. The author argues that it is instead the gene regulatory networks that are homologous.

Evo–devo has inherited its model organisms from developmental biology. New models must now be chosen to study important phenomena that the original models do not represent. The authors discuss the best criteria for choosing new models.

Standardization and mass production have been invaluable in biological software, but what about accommodating the specific needs of different experiments? The authors propose a method for generating such customized software infrastructures from existing parts.

This article argues that recombination has a far more important role in the evolution of plant genomes than is currently appreciated, and that genome-wide patterns of recombination might explain some intriguing differences between plant and animal genomes.

Using cancer as an example of complex disease, the authors revisit the evidence for the hypothesis that human diseases result from interactions between genetic variants and the environment.

The ability to provide information about variants in genes is crucial to genome-wide association studies. This article argues that the currently available marker sets are unlikely to provide adequate coverage of genic variants, and suggests how this problem could be overcome.

Gene–environment interactions are key contributors to complex disease, but are hard to dissect in commonly used case–control designs. This article argues that large-scale prospective cohort studies, several of which are planned or under way, provide an essential alternative strategy.

Evolutionary theory denies the existence of competition between genetically identical cells. But cell–cell competition undeniably occurs at different levels in many organisms, suggesting that it is either itself advantageous or a relic of an advantageous process.

The ability to integrate data from different sources is crucial in many areas of biological research, particularly systems biology. This article argues that problems with life-science databases are holding back research, and proposes some practical solutions.

Many of the already characterized non-coding RNAs, including small interfering RNAs, microRNAs and small nucleolar RNAs, guide or target RNP complexes to specific nucleic-acid sequences. How did such chimeric RNA–protein enzymes evolve? And why are they common in some but not other organisms?

Multifactorial disorders have grabbed the limelight in recent years, at the expense of research on monogenic traits. This shift in emphasis might not be fully justified, given the insight that seemingly 'simple' disorders can bring to genome function and complex disease aetiology.

A growing body of evidence indicates that epigenetic states can be influenced by the environment. Considering that erasure of epigenetic marks between generations is not universal among multicellular organisms, what are the potential implications of inherited epigenetic variation for current theories of inheritance and evolutionary change?

Traditional QTL mapping approaches inadequately capture the complexity of gene networks. The authors show how functional mapping — a general statistical mapping framework — can provide a useful quantitative and testable framework for assessing the interplay between gene actions or interactions during development.

The patentability of genes is a controversial issue. As a partial remedy, many countries have exemptions from patent liability for non-commercial research. However, these exemptions are themselves problematic. The authors examine solutions to the problem and advocate the abolition of gene patents.

Patents for genetic inventions have increased in recent years, raising fears that this practice will restrict access to research and health care. Models for facilitating access to patented genetic inventions already exist, whereas others can be developed for use in genetics.