First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α
Samuel Zambrano,
Alessia Loffreda,
Elena Carelli,
Giacomo Stefanelli,
Federica Colombo,
Edouard Bertrand,
Carlo Tacchetti,
Alessandra Agresti,
Marco E. Bianchi,
Nacho Molina,
Davide Mazza
Affiliations
Samuel Zambrano
School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy; Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Corresponding author
Alessia Loffreda
Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
Elena Carelli
Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
Giacomo Stefanelli
Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
Federica Colombo
Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan 20133, Italy
Edouard Bertrand
Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier 34293, France
Carlo Tacchetti
School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy; Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
Alessandra Agresti
Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
Marco E. Bianchi
School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy; Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
Nacho Molina
Institut de Génétique et Biologie Moléculaire Cellulaire, Illkirch-Graffenstaden 67404, France; Corresponding author
Davide Mazza
Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Corresponding author
Summary: Nuclear factor (NF)-κB controls the transcriptional response to inflammatory signals by translocating into the nucleus, but we lack a single-cell characterization of the resulting transcription dynamics. Here we show that upon tumor necrosis factor (TNF)-α transcription of NF-κB target genes is heterogeneous in individual cells but results in an average nascent transcription profile that is prompt (i.e., occurs almost immediately) and sharp (i.e., increases and decreases rapidly) compared with NF-κB nuclear localization. Using an NF-κB-controlled MS2 reporter we show that the single-cell nascent transcription is more heterogeneous than NF-κB translocation dynamics, with a fraction of synchronized “first responders” that shape the average transcriptional profile and are more prone to respond to multiple TNF-α stimulations. A mathematical model combining NF-κB-mediated gene activation and a gene refractory state is able to reproduce these features. Our work shows how the expression of target genes induced by transcriptional activators can be heterogeneous across single cells and yet time resolved on average.