The Myc‐Associated Zinc Finger Protein (MAZ) Controls Cohesin Positioning and Genome Organization Independently OR In Concert With CTCF

The Myc-associated zinc finger protein (MAZ) is a transcription factor that has been shown to regulate transcriptional initiation and termination. However, the underlying mechanisms of MAZ function in the context of chromatin is not fully understood. By applying biochemistry and genetics approaches, we show that MAZ binds to many genomic sites adjacent to the CCCTC-binding factor (CTCF), a protein that is best known for its insulation function in three-dimensional organization of eukaryotic genomes. We demonstrate that, similar to CTCF, MAZ physically interacts with the cohesin subunit Rad21. In addition, we find that MAZ shares with CTCF the ability to independently pause the elongating form of RNA polymerase II, and subsequently affects RNA alternative splicing. Our ChIP-seq analysis of the genome wide distribution of cohesins and CTCF reveals that depletion of CTCF results in preferential loss of CTCF from sites not occupied by MAZ, showing that the binding of both CTCF and cohesin is more stable at the CTCF/MAZ double sites than at the sites occupied by CTCF alone. In an insulation assay like that used for CTCF, we find that binding of MAZ to sites between an enhancer and promoter results in downregulation of reporter gene expression, supporting a role for MAZ as a novel insulator protein. Hi-C analysis indicates that depletion of MAZ in cells not only disrupts local interactions within Topologically associating domains (TADs) but also reduces contacts that establish the boundaries of individual TADs. Taken together, our results suggest that MAZ shares properties with CTCF that allow it to act independently or synergistically in organizing higher order genome architectures, thereby controlling gene expression.