Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. To understand how MITF regulates transcription, we used tandem affinity purification and mass spectrometry to define a comprehensive MITF interactome identifying novel cofactors involved in transcription, DNA replication and repair, and chromatin organisation. We show that MITF interacts with a PBAF chromatin remodelling complex comprising BRG1 and CHD7. BRG1 is essential for melanoma cell proliferation in vitro and for normal melanocyte development in vivo. MITF and SOX10 actively recruit BRG1 to a set of MITF-associated regulatory elements (MAREs) at active enhancers. Combinations of MITF, SOX10, TFAP2A, and YY1 bind between two BRG1-occupied nucleosomes thus defining both a signature of transcription factors essential for the melanocyte lineage and a specific chromatin organisation of the regulatory elements they occupy. BRG1 also regulates the dynamics of MITF genomic occupancy. MITF-BRG1 interplay thus plays an essential role in transcription regulation in melanoma.
Melanocytes are pigment-producing cells found primarily in the skin. Many of the genes that help these cells to develop are also thought to affect the development of melanomas: an aggressive form of skin cancer that originates in these cells. One such gene encodes a protein called MITF. This protein binds to DNA and regulates genes that control the development, survival, and spread of melanocytes; it is also linked to the invasive properties of melanomas.
The MITF protein works together with partner proteins to control numerous genes, activating some while inhibiting others, by binding to nearby stretches of DNA that act as regulatory elements. Its interactions are therefore widespread and complex. Now, Laurette, Strub et al. have used techniques called tandem affinity purification and mass spectrometry to identify the proteins that interact with MITF. This investigation found many new protein partners for MITF, including proteins involved in DNA damage, repair, and replication. MITF also associates with two proteins—one of which is called BRG1—that are involved in modifying how tightly DNA is packaged inside cells. DNA wrapped around proteins is known as chromatin, and if chromatin is tightly packed, the genes in that stretch of DNA cannot be easily accessed or activated.
Removing BRG1 from melanocytes and melanoma cells caused the cells to die or stop growing. When BRG1 was removed from developing mouse embryos, melanocytes failed to form. Further investigation revealed that MITF, together with another protein, localize BRG1 to sites in the melanocyte's DNA to open up the chromatin and regulate nearby genes. Furthermore, Laurette, Strub et al. report that BRG1 binds to many such elements in a characteristic manner, in which two BRG1 proteins flank the stretch of DNA bound by MITF and several other key DNA-binding proteins that together regulate many aspects of melanocyte and melanoma cell physiology.
Laurette, Strub et al. have therefore revealed many details about the molecules that activate genes in melanomas and melanocyte cells, as well as the interactions between these molecules. The results could also help researchers to understand how the BRG1 protein organises chromatin packing in other cell types.