A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer

Abstract

HMG-box proteins, including Sox/SRY (Sox) and TCF/LEF1 (TCF) family members, bind DNA via their HMG-box. This binding, however, is relatively weak and both Sox and TCF factors employ distinct mechanisms for enhancing their affinity and specificity for DNA. Here we report that Capicua (CIC), an HMG-box transcriptional repressor involved in Ras/MAPK signaling and cancer progression, employs an additional distinct mode of DNA binding that enables selective recognition of its targets. We find that, contrary to previous assumptions, the HMG-box of CIC does not bind DNA alone but instead requires a distant motif (referred to as C1) present at the C-terminus of all CIC proteins. The HMG-box and C1 domains are both necessary for binding specific TGAATGAA-like sites, do not function via dimerization, and are active in the absence of cofactors, suggesting that they form a bipartite structure for sequence-specific binding to DNA. We demonstrate that this binding mechanism operates throughout Drosophila development and in human cells, ensuring specific regulation of multiple CIC targets. It thus appears that HMG-box proteins generally depend on auxiliary DNA binding mechanisms for regulating their appropriate genomic targets, but that each sub-family has evolved unique strategies for this purpose. Finally, the key role of C1 in DNA binding also explains the fact that this domain is a hotspot for inactivating mutations in oligodendroglioma and other tumors, while being preserved in oncogenic CIC-DUX4 fusion chimeras associated to Ewing-like sarcomas.

A double‐edged sword: The world according to Capicua in cancer

“…The CIC HMG‐box is highly conserved among species and there are also additional conserved motifs, C1 and C2, in the C‐terminus and the central part, respectively . The in vitro DNA binding assay using mutant CIC constructs showed that the C1 motif is required for stable DNA binding by its interaction with the HMG box . Thus, both the HMG‐box and C1 motif contribute to the core function of CIC, as is also suggested by the mutation spectrum in human cancer (see below).…”

“…b). CIC recognizes chromatin through its consensus T(G/C)AATG(A/G)A sequence (also called CIC octamer) using an HMG‐box as a DNA‐binding motif, unlike other HMG class transcription factors most of which do not bind DNA in the sequence‐specific manner . The CIC HMG‐box is highly conserved among species and there are also additional conserved motifs, C1 and C2, in the C‐terminus and the central part, respectively .…”

Emerging entities in NUTM1‐rearranged neoplasms

“…However, NUTM1 has also recently emerged as a recurrent CIC fusion partner . CIC is a transcriptional repressor that interacts with DNA via a high motility group (HMG) box in conjunction with a C‐terminal C1 domain . It has also been shown to be a tumor suppressor in some lymphoid malignancies …”

Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation

“…Previous evidence suggests that Cic act primarily as a transcriptional repressor consisting of two highly conserved domains: the HMG-box which mediates DNA binding and nuclear localization, and a C-terminal motif C1 which co-operates with the HMG-box for DNA binding (12–16). In Drosophila, cic transduces the signaling of receptor tyrosine kinases (RTKs), Torso and the epidermal growth factor receptor (EGFR), and by doing so regulates cell proliferation and cell lineage specification during development (13,15,17–19).…”