We thank L. Giorgetti and L. Burger for suggestions and feedback, C. Wirbelauer for technical assistance, S. Smallwood for next-generation sequencing support and members of the Schübeler group for feedback on the project and manuscript. Brg1fl/fl embryonic stem cells were provided by G. Crabtree. Research in the laboratory of D.S. is supported by the Novartis Research Foundation, the European Research Council (ERC) under the European Union’s Horizon research and innovation program (grant agreement no. 667951) and the Swiss National Sciences Foundation. D.B. was funded by a Boehringer Ingelheim Fonds PhD fellowship. M.I. is funded by an EMBO long-term postdoctoral fellowship.

Reviewer information

Nature thanks David Clark, Jonathan Yuin-Han Loh and the other anonymous reviewer(s) for their contribution to the peer review of this work.