ArticleProceedings of the National Academy of Sciences of the United States of America2008
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed.
- The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.Annual review of biochemistry · 2026Review
- Mitotic reactivation and transcriptional bursting govern transcriptional noise in the early Drosophila embryo.Development (Cambridge, England) · 2026Article
- Evolution of promoter-proximal pausing enabled a new layer of transcription control.Nature structural & molecular biology · 2026Article
- High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo.Research square · 2026Article
- High-resolution binding data of TFIID and cofactors show promoter-specific differencesbioRxiv : the preprint server for biology · 2025Article
- Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis.Nature communications · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function in vivo.Development (Cambridge, England) · 2024Article
- ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements.Bioinformatics (Oxford, England) · 2024Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.Genome biology · 2024Article
- DNA-sequence and epigenomic determinants of local rates of transcription elongation.bioRxiv : the preprint server for biology · 2023Article
- Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.Nature communications · 2023Article
- Polycomb Recruiters Inside and Outside of the Repressed Domains.International journal of molecular sciences · 2023Review
- Structural and developmental dynamics of Matrix associated regions in Drosophila melanogaster genome.BMC genomics · 2022Article
- A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos.Genes · 2022Review
- RNA Polymerase II "Pause" Prepares Promoters for Upcoming Transcription duringInternational journal of molecular sciences · 2022Article
- The control of transcriptional memory by stable mitotic bookmarking.Nature communications · 2022Article
- Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
64 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
RNA Polymerase II (Pol II) is bound to the promoter regions of many or most developmental control genes before their activation during Drosophila embryogenesis. It has been suggested that Pol II stalling is used to produce dynamic and rapid responses of developmental patterning genes to transient cues such as extracellular signaling molecules. Here, we present a combined computational and experimental analysis of stalled promoters to determine how they come to bind Pol II in the early Drosophila embryo. At least one-fourth of the stalled promoters contain a shared sequence motif, the "pause button" (PB): KCGRWCG. The PB motif is sometimes located in the position of the DPE, and over one-fifth of the stalled promoters contain the following arrangement of core elements: GAGA, Inr, PB, and/or DPE. This arrangement was used to identify additional stalled promoters in the Drosophila genome, and permanganate footprint assays were used to confirm that the segmentation gene engrailed contains paused Pol II as seen for heat-shock genes. We discuss different models for Pol II binding and gene activation in the early embryo.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.