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.
MeSH terms
-
Amino Acid Motifs / genetics
-
Amino Acid Sequence
-
Animals
-
Animals, Genetically Modified
-
Base Sequence
-
Binding Sites / genetics
-
DNA / genetics*
-
DNA / metabolism
-
Drosophila / embryology
-
Drosophila / genetics
-
Drosophila / metabolism
-
Drosophila Proteins / genetics*
-
Drosophila Proteins / metabolism
-
Embryo, Nonmammalian / cytology
-
Embryo, Nonmammalian / embryology
-
Embryo, Nonmammalian / metabolism
-
HEK293 Cells
-
HMG-Box Domains / genetics
-
HMGB Proteins / genetics*
-
HMGB Proteins / metabolism
-
High Mobility Group Proteins / genetics*
-
High Mobility Group Proteins / metabolism
-
Homeodomain Proteins / genetics
-
Homeodomain Proteins / metabolism
-
Humans
-
Immunohistochemistry
-
Microscopy, Confocal
-
Models, Genetic
-
Mutation*
-
Neoplasms / genetics*
-
Neoplasms / metabolism
-
Protein Binding
-
Repressor Proteins / genetics*
-
Repressor Proteins / metabolism
-
Sequence Homology, Amino Acid
-
Sequence Homology, Nucleic Acid
Substances
-
DUX4L1 protein, human
-
Drosophila Proteins
-
HMGB Proteins
-
High Mobility Group Proteins
-
Homeodomain Proteins
-
Repressor Proteins
-
cic protein, Drosophila
-
DNA
Grants and funding
This work was funded by grants from the Spanish Ministry of Economy and Competitiveness (MINECO) (BFU2011-23611 and BFU2014-52863-P) to GJ; the European Research Council (ERC-AG/ 250297-RAS AHEAD), the EU-Framework Programme (LSHG-CT-2007-037665/CHEMORES, HEALTH-F2-2010-259770/LUNGTARGET and HEALTH-2010-260791/EUROCANPLATFORM), the MINECO (SAF2011-30173 and SAF2014-59864-R), the Autonomous Community of Madrid (S2011/BDM-2470/ONCOCYCLE) to MB; and the Fundació La Marató de TV3 (20131730/1). LSC was supported by a fellowship from the Programa de Formación de Personal Investigador (FPI, MINECO). MB is a recipient of an Endowed Chair from the AXA Research Fund. GJ is an ICREA investigator. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.