Transcription Factors Modulate c-Fos Transcriptional Bursts

• Published in: Cell reports (Cambridge) Vol. 8; no. 1; pp. 75 - 83
• Main Authors: Senecal, Adrien, Munsky, Brian, Proux, Florence, Ly, Nathalie, Braye, Floriane E., Zimmer, Christophe, Mueller, Florian, Darzacq, Xavier
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 10-07-2014; Elsevier
• Subjects: Alleles; Cell Line, Tumor; Cells, Cultured; Cellular Biology; DNA-Directed RNA Polymerases - metabolism; Humans; Life Sciences; Models, Genetic; Protein Structure, Tertiary; Proto-Oncogene Proteins c-fos - genetics; Proto-Oncogene Proteins c-fos - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Stochastic Processes; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptional Activation
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2014.05.053

Transcription is a stochastic process occurring mostly in episodic bursts. Although the local chromatin environment is known to influence the bursting behavior on long timescales, the impact of transcription factors (TFs)—especially in rapidly inducible systems—is largely unknown. Using fluorescence in situ hybridization and computational models, we quantified the transcriptional activity of the proto-oncogene c-Fos with single mRNA accuracy at individual endogenous alleles. We showed that, during MAPK induction, the TF concentration modulates the burst frequency of c-Fos, whereas other bursting parameters remain mostly unchanged. By using synthetic TFs with TALE DNA-binding domains, we systematically altered different aspects of these bursts. Specifically, we linked the polymerase initiation frequency to the strength of the transactivation domain and the burst duration to the TF lifetime on the promoter. Our results show how TFs and promoter binding domains collectively act to regulate different bursting parameters, offering a vast, evolutionarily tunable regulatory range for individual genes.
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•Single mRNA quantification and modeling reveal complex c-Fos regulation dynamics•Transcription factor concentrations control c-Fos burst activation frequencies•Transcription factor-DNA interaction controls burst duration•Strength of transactivation domains control initiation frequency
Transcription is a stochastic process mostly occurring in episodic bursts. The impact of transcription factors (TFs) on bursting behavior is largely unknown. Using FISH and computational modeling, Senecal et al. now link (1) TF concentration with transcription bursting frequency, (2) TF-DNA association with burst duration, and (3) TF transactivation domain strength with polymerase initiation frequency. This work shows how TFs regulate different bursting parameters, offering a vast, evolutionarily tunable regulatory range for individual genes.