DNA-binding transcription factors are crucial switches for modulating a wide variety of gene expression programs in a manner adapted to a cell’s needs in both time and space. The largest class of human transcription factors, comprising approximately 750 members, is formed by C2H2 zinc finger proteins (ZNF proteins). About half of them contain an N-terminal protein-protein interaction domain known as Krüppel-associated box (KRAB).

The canonical model for transcription regulation by KRAB-ZNF proteins posits that these transcription factors bind specifically to DNA via their zinc fingers and recruit multiprotein complexes via their KRAB domain. Ultimately, this DNA-bound complex converts the recognized gene locus into a state that is non-permissive for transcription (repression). A key cofactor in this model is the multidomain protein TRIM28 (synonym KAP1), which acts as a central hub to mediate interactions with proteins that modulate chromatin. Key interaction partners include heterochromatin proteins (HP1), the histone H3 lysine 9 methyltransferase SETDB1, and the “nucleosome remodeling and deacetylase” (NuRD) complex with its histone deacetylase activity.

The KRAB-ZNF/TRIM28 system plays a significant role in physiology and disease including stem cell biology, differentiation processes, the response to DNA damage, the suppression of retrotransposons and cancer.

The exact mechanisms by which a KRAB-ZNF/TRIM28 module regulates biological processes are far from fully elucidated. Open questions concern the regulation of the module, particularly which complexes influence gene regulation—when, how, under what biological conditions (cell type, cell cycle, endogenous and exogenous stimuli), in what manner, and at what level. The functions of the majority of KRAB-ZNF proteins remain equally unclear, particularly with regard to the identification of the target genes they regulate. The TRIM28/KRAB-ZNF system likely emerged during the evolution of tetrapods.

Elucidating the mechanisms of the TRIM28/KRAB-ZNF system and characterizing chemical compounds that influence this system are of great relevance for understanding and modulating programmable transrepressors such as dCas9-KRAB (CRISPRi methodology) in genetic engineering and gene therapy. In these fields, the KRAB domain of the KRAB-ZNF protein Kox1/ZNF10 is used to specifically silence genes.

Figure: A model for transcriptional regulation by a KRAB zinc finger protein in conjunction with TRIM28 complexes at a chromatin locus.

• Application of bioinformatics tools for phylogenetic analyses and gene expression analyses
• Use of knockout cell lines to investigate the function of components of gene regulatory processes
• Construction of custom eukaryotic expression vectors for transient and stable transfection of desired cell line models
• Elucidation of mechanisms of transcriptional control using reporter gene assays
• Study of protein complexes using co-immunoprecipitation or affinity chromatography followed by mass spectrometry (in collaboration with the Rostock Proteome Center)
• Analysis of gene expression profiles using quantitative real-time PCR

• General references on the topic of KRAB-ZNF/TRIM28
• Selected past work of our Institute