Reviews & Analysis

A wealth of microarray gene expression data and a growing volume of RNA sequencing data are now available in public databases. The authors look at how these data are being used and discuss considerations for how such data should be analysed and deposited and how data reuse could be improved.

Transposable elements are important sources of genetic and epigenetic variation in plant genomes. The author discusses the evidence that this variation has been important for plant evolution and how new genomic resources should allow a systematic assessment of this issue.

A potential role for chromatin in the maintenance of genome integrity has recently emerged. The potential roles for chromatin regulators in coordinating signalling from chromatin during the replication and repair processes, in addition to evidence for a role for chromatin remodellers in accurate segregation, are presented.

Despite their complexity and dynamics, proteomes are starting to be comprehensively characterized; this has been made possible particularly by various technical advances in mass spectrometry. This Review highlights how proteomic studies are contributing to our understanding of various cellular processes in health and disease.

In addition to somatic mutations in tumours, inherited genetic variants can influence how a patient with cancer responds to drug treatment. This Review considers best practice in design and analysis for pharmacogenomic studies to identify such variants, potentially leading to personalized oncology.

This Review discusses the roles of mitochondrial DNA (mtDNA) mutations in human disease. In addition to many primary mitochondrial diseases, there is emerging — and sometimes controversial — evidence that mutations in mtDNA are involved in complex traits such as neurodegeneration, ageing and cancer.

The theoretical principles of adaptive evolution are being put to the test in a growing range of species and populations, particularly with new sequencing technologies and high-throughput experimental methods making headway in this area.

The growing availability of primate genome sequences has allowed an evaluation of the genetic and genomic changes that may have contributed to human-specific traits. This article focuses on these unique changes and the potential mechanisms by which they may have occurred.

Text mining — retrieving information from papers and databases — is increasingly used in data-rich fields such as genomics, systems biology and biomedical research. This Review discusses recent tools that can aid researchers and sets out the potential of enhancing integrative research using text mining.

This Review introduces the applications of single-molecule approaches to the study of genomic processes such as transcription and translation. The authors explain the basic principles of key techniques and provide examples of recent insights fromin vitro and in vivostudies.

This Review discusses recent improvements to ChIP–seq and a range of complementary techniques, such as DNaseI hypersensitivity mapping, for studying protein–DNA interactions. Functional characterization of protein binding can be improved by methods analysing chromatin conformation or allele-specific binding.

We asked five experts their opinions on issues that arise from new clinical tests that are based on next-generation sequencing. Crucial gaps in infrastructure need to be addressed for the results of these tests to be optimally handled.

The advance of DNA-sequencing technologies is allowing the investigation of cancer genome evolution at an unprecedented resolution. This article presents recent insights into cancer genome heterogeneity and adaptation gained from the application of novel strategies.

Genome-wide association studies (GWASs) of mice provide an alternative means of identifying genes and genetic variants that are important for human physiology and disease. This Review describes the various resources and strategies for GWASs of mice, emphasizing their advantages and pitfalls relative to human studies.

Recent advances in genetic technologies have progressed the understanding of the biological pathways mediating the control of germ cell development. In this Review the genes and strategies involved inDrosophila melanogaster, Caenorhabditis elegansand mouse germline development are compared and contrasted.

Revealing genetic influences on metabolic phenotypes is important in further understanding the aetiology of many complex diseases. Here, the authors introduce study design considerations and applications for genome-wide association studies with metabolic traits.

Growing evidence is implicating non‑B-form DNA structures in processes related to DNA stability and function, including replication and transcription. In particular, genomic studies are suggesting that sequences that could form G-quadruplex structures are widespread, so there is a need to improve our understanding of these structures.

The analysis and interpretation of genome-wide DNA methylation data poses unique bioinformatics challenges. In this article, the tools that are available for processing, visualizing and interpreting these epigenetic data sets are discussed, and the relative advantages of various methods are considered.

Emerging evidence points towards RNA polymerase II promoter-proximal pausing as a widespread regulatory mechanism in higher eukaryotes. Here, the authors discuss the evidence for this from genome-wide studies and present potential functions of this regulatory mechanism.

Human pluripotent stem cells hold promise for disease modelling and for cell-based regenerative medicine. This Review summarizes our growing understanding of the genetic and epigenetic abnormalities that can occur in these cells, including their phenotypic consequences and the safety implications for therapies.