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Significance The protein CTCF plays a major role in large-scale organization of the genome. Binding sites for the protein MAZ are found adjacent to many CTCF sites. We show that, at such double sites, MAZ stabilizes CTCF binding. MAZ, like CTCF, acts independently as an “insulator” element to block the effects of a distal enhancer on a promoter, and, like CTCF, it can block the advance of a transcribing RNA polymerase II, leading to alternative RNA splicing patterns. Depletion of MAZ causes loss of short-range interactions within the nucleus and disruption of some longer-range interactions. Thus, MAZ plays a complementary role to CTCF in the nucleus, enhancing the organizational properties of CTCF and displaying many functions related to genome organization.

The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization