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Coupling next-generation sequencing to chromatin immunoprecipitation has transformed the resolution and genomic coverage of DNA-binding protein and nucleosome mapping studies. However, successful ChIP–seq requires careful consideration of the experimental and analytical approaches; this Review evaluates the current strategies and challenges.
Bayesian analyses are increasingly being used in genetics, particularly in the context of genome-wide association studies. This article provides a guide to using Bayesian analyses for assessing single-SNP associations and highlights the advantages of these methods compared with standard frequentist analyses.
The ability of mobile genetic elements to move and multiply means that they have a unique influence on genome sequences. Developments in comparative genomics have shown how important non-long terminal repeat retrotransposons have been in shaping the human genome.
Alterations in microRNA function contribute to the pathogenesis of many cancers. Recent studies have shown that such changes can result not only from mutations but also from epigenetic silencing or the dysregulation of transcription factors that target specific microRNAs.
Disparate fields have provided advances in our understanding of the impact of protein-synthesis errors on cellular fitness, disease and evolution. Although organisms show adaptations to minimize the deleterious effects of such errors, erroneous protein synthesis can also be exploited for the organism's benefit.
The authors argue that ancient whole-genome duplications might be linked to major ecological upheavals and extinction. When established, polyploidy might lead to increased vigour, species diversity and phenotypic novelties, and could therefore contribute to the evolutionary success of a lineage.
