Members of an array of zinc-finger proteins specify distinct Hox chromatin boundaries

Partitioning of repressive from actively transcribed chromatin in mammalian cells fosters cell-type-specific gene expression patterns. While this partitioning is reconstructed during differentiation, the chromatin occupancy of the key insulator, CCCTC-binding factor (CTCF), is unchanged at the developmentally important Hox clusters. Thus, dynamic changes in chromatin boundaries must entail other activities. Given its requirement for chromatin loop formation, we examined cohesin-based chromatin occupancy without known insulators, CTCF and Myc-associated zinc-finger protein (MAZ), and identified a family of zinc-finger proteins (ZNFs), some of which exhibit tissue-specific expression. Two such ZNFs foster chromatin boundaries at the Hox clusters that are distinct from each other and from MAZ. PATZ1 was critical to the thoracolumbar boundary in differentiating motor neurons and mouse skeleton, while ZNF263 contributed to cervicothoracic boundaries. We propose that these insulating activities act with cohesin, alone or combinatorially, with or without CTCF, to implement precise positional identity and cell fate during development. [Display omitted] •ZNFs function at chromatin boundaries to determine cellular identities•PATZ1 and ZNF263 regulate distinct Hox gene borders in motor neurons•Loss of PATZ1 results in reduction of looping interactions•PATZ1 loss in mice leads to homeotic transformations in skeletal patterning How insulation regulates genome organization and cellular fate remains unresolved. Ortabozkoyun et al. identify a family of zinc-finger proteins (ZNFs), including PATZ1 and ZNF263, which regulate Hox gene borders in motor neurons. Importantly, loss of PATZ1 impacts genome organization in cells and skeletal patterning in mice, highlighting insulation activities.