Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 19, Pages 11121-11130Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx728
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Funding
- German Research Foundation [GE 2631/1-1]
- European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme [637987 ChromArch, 638573 SILENCE]
- German Research Foundation (Emmy Noether Programme) [UH 275 1/1]
- German Academic Scholarship Foundation
- Deutsche Forschungsgemeinschaft
- ERC
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Transcription comprises a highly regulated sequence of intrinsically stochastic processes, resulting in bursts of transcription intermitted by quiescence. In transcription activation or repression, a transcription factor binds dynamically to DNA, with a residence time unique to each factor. Whether the DNA residence time is important in the transcription process is unclear. Here, we designed a series of transcription repressors differing in their DNA residence time by utilizing the modular DNA binding domain of transcription activator-like effectors (TALEs) and varying the number of nucleotide-recognizing repeat domains. We characterized the DNA residence times of our repressors in living cells using single molecule tracking. The residence times depended non-linearly on the number of repeat domains and differed by more than a factor of six. The factors provoked a residence time-dependent decrease in transcript level of the glucocorticoid receptor-activated gene SGK1. Down regulation of transcription was due to a lower burst frequency in the presence of long binding repressors and is in accordance with a model of competitive inhibition of endogenous activator binding. Our single molecule experiments reveal transcription factor DNA residence time as a regulatory factor controlling transcription repression and establish TALE-DNA binding domains as tools for the temporal dissection of transcription regulation.
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