Abstract
Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge in transcription is understanding how promoter composition dictates bursting, particularly in multicellular organisms. We investigate two key Drosophila developmental promoter motifs, the TATA box (TATA) and the Initiator (INR). Using live imaging in Drosophila embryos and new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds to minutes. TATA-containing promoters and INR-containing promoters exhibit distinct dynamics, with one or two separate rate-limiting steps respectively. A TATA box is associated with long active states, high rates of polymerase initiation, and short-lived, infrequent inactive states. In contrast, the INR motif leads to two inactive states, one of which relates to promoter-proximal polymerase pausing. Surprisingly, the model suggests pausing is not obligatory, but occurs stochastically for a subset of polymerases. Overall, our results provide a rationale for promoter switching during zygotic genome activation.
Highlights
Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states
This approach allows for a direct comparison of core promoter activity since differences caused by variations in cis-regulatory context, genomic positioning, and mRNA sequence are eliminated
The core promoters were selected based on the presence of known core promoter motifs[49], such as a TATA box in sna or an INR in kruppel and Insulin-like peptide 4 (Ilp4) (Fig. 1a, Supplementary Fig. 1, and Supplementary Movies 1 and 5)
Summary
Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. Transcription of active genes into RNA requires the controlled assembly of multiple protein complexes at promoters[1] This includes the sequential recruitment of general transcription factors to form the pre-initiation complex (PIC), followed by the recruitment of RNA Polymerase II (Pol II) at the transcriptional start site (TSS)[2,3,4] of promoters. How core-promoter motifs affect this ratelimiting step is still unknown, in the context of a developing embryo In parallel to these genomics approaches, single-cell imaging revealed that transcription is not a continuous process over time but occurs through stochastic fluctuations between periods of transcriptional activity and periods of inactivity, called bursting[22]. Relatively less attention has been given to the impact of core promoter motifs on transcriptional bursting
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
