DNA residence time is a regulatory factor of transcription repression

• Published in: Nucleic acids research 2017-11, Vol.45 (19), p.11121-11130
• Main Authors: Clauß, Karen, Popp, Achim P, Schulze, Lena, Hettich, Johannes, Reisser, Matthias, Escoter Torres, Laura, Uhlenhaut, N Henriette, Gebhardt, J Christof M
• Format: Article
• Language: English
• Subjects: Binding Sites - genetics; Blotting, Western; Cell Line, Tumor; DNA - genetics; DNA - metabolism; Gene Expression Regulation; Gene regulation, Chromatin and Epigenetics; Humans; Immediate-Early Proteins - genetics; Immediate-Early Proteins - metabolism; Microscopy, Fluorescence; Protein Binding; Protein-Serine-Threonine Kinases - genetics; Protein-Serine-Threonine Kinases - metabolism; Reverse Transcriptase Polymerase Chain Reaction; Transcription Activator-Like Effectors - genetics; Transcription Activator-Like Effectors - metabolism; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkx728

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.