ArticleMolecular systems biology2021
TATA and paused promoters active in differentiated tissues have distinct expression characteristics.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code.Nucleic acids research · 2026Article
- Beyond the mean: genetic control of gene expression fidelity and dispersion.bioRxiv : the preprint server for biology · 2026Article
- Mitotic reactivation and transcriptional bursting govern transcriptional noise in the early Drosophila embryo.Development (Cambridge, England) · 2026Article
- Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.Developmental cell · 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
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- Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.Genome biology · 2024Article
- A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus.BMC genomic data · 2023Article
- Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.Nature communications · 2023Article
- Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster.PLoS genetics · 2023Article
- CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity.Science advances · 2023Article
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.Nucleic acids research · 2023Article
- A bioinformatics screen reveals Hox and chromatin remodeling factors at thebioRxiv : the preprint server for biology · 2023Article
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- Genome-Wide Identification and Characterization ofFrontiers in genetics · 2022Article
- Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo.Genetics · 2021Article
- Histone variant H2A.Z regulates zygotic genome activation.Nature communications · 2021Article
- TATA and paused promoters active in differentiated tissues have distinct expression characteristics.Molecular systems biology · 2021Article
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4 authors.
Funding
Abstract
Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue-specific gene expression characteristics is not well understood. While promoters with Pol II pausing elements are active throughout development, TATA promoters are highly active in differentiated tissues. We therefore used a genomics approach on late-stage Drosophila embryos to analyze the properties of promoter types. Using tissue-specific Pol II ChIP-seq, we found that paused promoters have high levels of paused Pol II throughout the embryo, even in tissues where the gene is not expressed, while TATA promoters only show Pol II occupancy when the gene is active. The promoter types are associated with different chromatin accessibility in ATAC-seq data and have different expression characteristics in single-cell RNA-seq data. The two promoter types may therefore be optimized for different properties: paused promoters show more consistent expression when active, while TATA promoters have lower background expression when inactive. We propose that tissue-specific genes have evolved to use two different strategies for their differential expression across tissues.
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