Reviews & Analysis

Spliceosomal introns are thought to have had a central role in shaping modern genomes. Recent studies have shed new light on the timing of intron evolution, mechanisms of intron loss and gain, and the forces that have driven these processes.

Microarray technology has led the way towards global and parallel analysis of cellular processes. The use of microarrays in transcription profiling and genotyping is now well established and the technology is being adapted to a wide range of applications, including genome-wide epigenetic analysis and on-chip synthesis.

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.

Crop genomes contain important information about mechanisms of domestication and the origins of the immense diversity of the angiosperms. This Review evaluates several approaches that can be taken to unlock this information, from full-genome sequencing to comparative genomics.

Global population growth and the increasing number of infertile couples are opposing health issues that can be addressed by investigating the molecular-genetic basis of mammalian preimplantation and implantation biology, thereby leading to novel contraceptives and more effective reproductive technologies.

Understanding the complex genetic basis of coronary artery disease — now the world's biggest killer — will provide a vital boost towards developing new prognostic and therapeutic strategies. Recent progress towards this goal has been made by using large-scale, systematic, genome-wide approaches.

New technologies have revealed widespread structural variation in the human genome, including copy-number variants, insertions, inversions and translocations. These variants are predicted to comprise millions of nucleotides of heterogeneity within every genome, with important implications for human diversity and disease.

Evolution experiments with digital organisms have allowed insights that are not possible in biological systems. This review discusses some of the advances in understanding the interaction between mutation rate and genomic architecture, and also the evolution of sex.

Genome annotation is rapidly moving beyond the one-dimensional view that sequence analysis provides. Growing information about component interactions allows two-dimensional annotations to be generated, while knowledge about the physical arrangement of chromosomes and the changes that occur during evolution add third and fourth dimensions.

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.

Contrary to the neutral theory, silent mutations can be under natural selection. This is often seen in organisms from large populations, but the authors present evidence that it also occurs in mammals, because synonymous mutations affect mRNA stability and splicing.

Recent advances in tools for extracting facts from the scientific literature will soon enable the automatic annotation and analysis of the growing number of system-wide experimental data sets. Mining the literature is also rapidly becoming useful for both hypothesis generation and biological discovery.

Studies on model organisms have led to crucial advances in understanding the molecular processes that are involved in repairing DNA double-strand breaks. These have been complemented and extended by the molecular dissection of human disorders in which double-strand break repair is compromised.

Even complicated networks such as those involved in eukaryotic development lead to reproducible outcomes, which indicates that there are molecular mechanisms that filter out noise. The authors describe the framework in which noise is studied and propose that Wnt signalling is a noise filter.

Recent years have seen a growing appreciation of the role that epigenetics has in tumorigenesis. The authors suggest that there might be a fundamentally common basis to cancer that lies in the polyclonal epigenetic disruption of stem/progenitor cells.

Traditional neuroscience and linguistic studies are being integrated with ever advancing developmental, genetic and genomic analyses, among others, and are converging on the view that human language, like many other traits, has evolved by descent with modification.

The wide range of methods for analysing microarray data can seem bewildering to researchers. This Review provides a guide to statistical analysis for the different stages of a microarray experiment, highlighting points of consensus and areas where more work is needed.