Review Articles in 2012

The adoption of electronic health records will provide a rich resource for biomedical researchers. This Review discusses the potential for their use in informed decision making in the clinic, for a finer understanding of genotype–phenotype relationships and for selection of research cohorts, along with the current challenges for their mining and use.

Owing to the important role of microRNAs in gene regulation, profiling repertoires of expressed microRNAs can be informative in basic research and clinical settings. This Review describes the methods that are available for microRNA profiling and considerations for choosing among analytical options.

Although genome sequencing is becoming routine, genome annotation is becoming increasingly challenging. The authors provide an overview of the steps and software tools that are available for annotating eukaryotic genomes, and describe the best practices for sharing, quality checking and updating the annotation.

This Review describes how genome-wide analyses have provided various insights into the most lethal malarial parasite,Plasmodium falciparum, including determinants of antimalarial drug resistance. The authors also propose how genetic tools can be refined to monitor future therapeutic interventions.

This Review provides a broad overview of the regulation of and by histone methylation. A balance between dynamism and stability is highlighted by links to disease and ageing, and current studies are exploring these histone marks in the context of inheritance.

Phylogenetic analysis is pervading every field of biological study. The authors review and assess the main methods of phylogenetic analysis — including parsimony, distance, likelihood and Bayesian methods — and provide guidance for selecting the most appropriate approach and software package.

A large array of viral sequences is being uncovered in eukaryotic genome sequences, revealing that almost any type of virus — not just retroviruses — can become part of host genomes. These discoveries provide new information about the origins and evolution of modern day viruses and host–virus relationships.

MicroRNAs are key regulators of gene expression. Emerging evidence points towards a reciprocal relationship between microRNAs and their targets and for roles of non-target RNAs and proteins in this crosstalk.

A growing understanding of the relationship between the microbiome and human health is made possible by advances in sequencing technologies and computational tools. These studies highlight how the composition and function of the microbiome varies across individuals and anatomical sites, over time, and also in disease.

The improving functional annotation of genomes through the analysis of genome-wide data sets is revealing important characteristics of promoters. Similar classes of promoters are now emerging across diverse metazoan species, and novel features that contribute to gene regulation are being identified.

mRNA decay is a post-transcriptional means by which to modulate protein expression. This Review summarizes the current understanding of the mechanisms and pathways involved in the regulation of the multiple mRNA decay processes that contribute to a responsive output of gene expression.

Transcription poses a risk to the genome through transcription-associated mutagenesis and recombination. This Review discusses recent findings about influences on this genomic instability, such as the rate and direction of transcription or nucleic acid structures, and how these phenomena may be considered across species.

The discovery of common and rare genetic variants underlying infectious disease susceptibility in humans highlights the involvement of shared host signalling pathways in diverse infectious diseases, and provides insights into the genetic control of immune signalling.

This article reviews our growing understanding of the varied roles of DM domain genes in metazoan sexual development: in the evolution of sexually dimorphic traits and new sex-determining mechanisms and, more recently, in maintaining cell fate in the gonad.

Some epigenetic information can be passed from parents to offspring, but it is difficult to identify the molecular basis of information transferred through the gametes. This Review evaluates the extent of our understanding in mammals.

Aneuploidy — an abnormal number of chromosomes — typically has a detrimental effect on viability. Somewhat paradoxically, it is a remarkably common feature of cancer. This Review discusses how aneuploidy occurs, the cellular responses to aneuploidy and how aneuploidy can provide particular selective advantages during tumorigenesis.

This Review presents arguments for and against each of two main models for the genetic basis of complex traits. It concludes that the infinitesimal model is essentially correct, but that rare, large-effect alleles also make an essential contribution to disease risk.

Many organisms have evolved dosage compensation mechanisms to normalize gene expression levels when copy numbers of sex chromosomes and autosomes are unequal. This Review discusses how multiple epigenetic processes fine-tune the twofold upregulation of gene expression across the entire male X chromosome ofDrosophila melanogaster.

Computer simulations can be valuable components of studies in many fields, including population genetics, evolutionary biology, genetic epidemiology and ecology. The recent increase in the available range of software packages is now making simulation an accessible option for researchers with limited bioinformatics experience.

There is considerable interest in exploring whether environmental factors, including chemicals and dietary components, can alter epigenomes. Environmentally induced changes in epigenetic marks are important in the development of several species, such as plants and insects; whether they influence human disease will be an area for future research.