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The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors.

ABSTRACT: Sox proteins are widely believed to team up with other transcription factors as partner proteins to perform their many essential functions during development. In this study, yeast two-hybrid screens identified transcription factors as a major group of interacting proteins for Sox8 and Sox10. Interacting transcription factors were very similar for these two group E Sox proteins and included proteins with different types of DNA-binding domains, such as homeodomain proteins, zinc finger proteins, basic helix-loop-helix and leucine zipper proteins. In all cases analyzed, the interaction involved the DNA-binding domain of the transcription factor which directly contacted the C-terminal part of the high-mobility-group (HMG) domain. In particular, the C-terminal tail region behind helix 3 of the HMG domain was shown by mutagenesis to be essential for interaction and transcription factor recruitment. The HMG domain thus not only possesses DNA-binding and DNA-bending but also protein-interacting ability which may be equally important for the architectural function of Sox proteins on their target gene promoters.

SUBMITTER: Wissmuller S

PROVIDER: S-EPMC1421504 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors.

Wissmüller Sandra S Kosian Thomas T Wolf Michael M Finzsch Markus M Wegner Michael M

Nucleic acids research 20060331 6

Sox proteins are widely believed to team up with other transcription factors as partner proteins to perform their many essential functions during development. In this study, yeast two-hybrid screens identified transcription factors as a major group of interacting proteins for Sox8 and Sox10. Interacting transcription factors were very similar for these two group E Sox proteins and included proteins with different types of DNA-binding domains, such as homeodomain proteins, zinc finger proteins, b ...[more]

PMID: 16582099

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Project description:BackgroundThe enhanceosome is an enhancer located upstream of the human interferon β gene, bound by transcription factor (TF) complex of extremely rigid structure. Within these rigid constraints, even a slight change of distances between transcription factor binding sites (TFBS) results in loss of functionality of the enhanceosome. We hypothesized that smaller subunits of the enhanceosome may entail TF complex formation in other regulatory regions.ResultsIn order to verify this hypothesis we systematically searched for dimerization preferences of the TFs that have TFBS in the enhanceosome. For this we utilized our recently developed tool, TACO. We performed this computational experiment in a cell-type-specific manner by utilizing cell-type-specific DNase-seq data for 105 human cell types. We also used 20 TRANSFAC motifs comprising not only the usual TFs constituting the enhanceosome but also the architectural proteins of High Mobility Group I(Y) (HMG I). A similar experiment used 42 DNase-seq data sets for mouse cell types. We found 137 statistically significant dimer predictions in the human genome, and 37 predictions in the mouse genome, that matched the positioning on the enhanceosome with ±2 bp tolerance. To characterize these predicted TF dimers, we performed functional analysis (Gene Ontology enrichment) for sets of genes which were in the neighbourhood of predicted dimer instances. A notable feature of these instances is that (1) most of them are located in introns of genes, (2) they are enriched in regulatory states, and (3) those instances that are located near transcription start sites are enriched for inclusion in computationally predicted enhancers. We also investigated similarity of dimer predictions between human and mouse.ConclusionsIt follows from our experiments that, except for homodimer formed by IRF proteins, the rest of the dimers were formed exclusively between one of the transcriptional activators (ATF-2/c-Jun and IRF) and a HMG I protein. NF- κB did not participate in forming dimers with other proteins. Dimers predicted in mouse were fully contained in those predicted in human, with exactly the same spacing and orientation. Intriguingly, in most of the cases the enhanceosome motifs have 1 bp wider spacing than the corresponding dimers predicted genome-wide, which is likely caused by the overall 3D structure constraints of the enhanceosome-bound complex.

Dataset Information

The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors.

Publications

The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors.

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