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The rate and mechanisms of evolution of transcription factor binding show striking differences across diverse metazoan phyla. This Review highlights insights gained from sequence-based comparisons of genomes and ChIP–seq studies analysing the evolution of transcription factor binding, as well as their conceptual contribution to models of regulatory evolution and gene expression control.
CCCTC-binding factor (CTCF) is a DNA-binding protein that has various, often seemingly contradictory, roles in gene regulation. This Review describes these disparate functions and how the context-dependent looping of DNA regions by CTCF is emerging as a potential unifying mechanism that underpins these diverse roles.
This Review discusses cryptic genetic variation and focuses particularly on empirical support for widespread cryptic genetic variation in natural populations, its potential role in human diseases and its contribution to evolution.
Increasing evidence suggests crucial functions for histone variants in diverse biological processes. This Review examines the roles of histone variants in mammalian germ cell and embryonic development, as well as the consequences of their aberrant regulation in human disease.
Enhancers are DNA elements that are key regulators of gene expression, but their complexities and context dependence makes their identification and characterization challenging. This Review discusses how an improved understanding of the varied properties of enhancers is being used in diverse approaches for the systematic prediction of enhancers genome wide.