Reviews & Analysis

The use of phylogenetics in cancer genomics is increasing owing to a growing appreciation of the importance of evolutionary theory to cancer progression. The authors provide guidance on the design and analysis of tumour phylogeny studies by surveying the range of phylogenetic methods and tools available to the cancer researcher and discussing their key applications and the unsolved problems in the field.

Here, the authors review the complex gene regulatory mechanisms that underlie limb development and that determine forelimb versus hindlimb identity. They explain how the modification of these regulatory elements leads to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.

During the cell cycle, the centromeres of chromosomes have important roles and face key challenges, such as mediating successful chromosome segregation during mitosis and faithfully propagating their chromatin state to daughter chromosomes during S phase. This Review describes cell cycle-related features of centromeres, focusing on the nature and dynamics of centromeric chromatin, how it is intricately regulated and the potential implications for disease when these processes are disrupted.

Lineage analyses of multicellular organisms provide key insights into developmental mechanisms and how these developmental trajectories go awry in diverse diseases. This Review discusses the features, technical challenges and latest opportunities of an evolving range of sophisticated genetic techniques for tracking cell lineages in organisms. These strategies include methods for prospective tracking using engineered genetic constructs, as well as retrospective tracking based on naturally occurring somatic mutations.

In this article, the authors review the mechanisms by which the pluripotency gene regulatory network governs the acquisition, maintenance and dissolution of the pluripotent state, including the interaction of these networks with chromatin-mediated and RNA-mediated regulatory mechanisms. They discuss recent evidence for alternative pluripotency states and the factors that affect transitions between these states.