Regions outside the DNA-binding domain are critical for proper in vivo specificity of an archetypal zinc finger transcription factor
| Autor: | Wooi F. Lim, Richard C. M. Pearson, Alister P. W. Funnell, Merlin Crossley, Ka Sin Mak, Crisbel M. Artuz, Jon Burdach, Lit Yeen Tan, Beeke Wienert |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Kruppel-Like Transcription Factors
Biology Gene Regulation Chromatin and Epigenetics Cell Line Mice Consensus Sequence Genetics Animals Promoter Regions Genetic Transcription factor Zinc finger Zinc finger transcription factor Binding Sites Base Sequence DNA-binding domain DNA Chromatin Cell biology Protein Structure Tertiary Gene Expression Regulation Mutation Chromatin immunoprecipitation Corepressor Binding domain Protein Binding |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | Transcription factors (TFs) are often regarded as being composed of a DNA-binding domain (DBD) and a functional domain. The two domains are considered separable and autonomous, with the DBD directing the factor to its target genes and the functional domain imparting transcriptional regulation. We examined an archetypal zinc finger (ZF) TF, Kruppel-like factor 3 with an N-terminal domain that binds the corepressor CtBP and a DBD composed of three ZFs at its C-terminus. We established a system to compare the genomic occupancy profile of wild-type Kruppel-like factor 3 with two mutants affecting the N-terminal functional domain: a mutant unable to contact the cofactor CtBP and a mutant lacking the entire N-terminal domain, but retaining the ZFs intact. Chromatin immunoprecipitation followed by sequencing was used to assess binding across the genome in murine embryonic fibroblasts. Unexpectedly, we observe that mutations in the N-terminal domain generally reduced binding, but there were also instances where binding was retained or even increased. These results provide a clear demonstration that the correct localization of TFs to their target genes is not solely dependent on their DNA-contact domains. This informs our understanding of how TFs operate and is of relevance to the design of artificial ZF proteins. |
| Databáze: | OpenAIRE |
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