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| Status |
Public on Nov 23, 2023 |
| Title |
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network [PRO-seq] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Background
Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood.
Results
Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila DV patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues.
Conclusions
The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.
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| Overall design |
Examination of gene regulation during the establishment and maintenance of tissue-specific gene expression using the dorso-ventral (DV) patterning paradigm in early Drosophila embryogenesis.
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| Web link |
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03135-0
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| Contributor(s) |
Hunt G, Vaid R, Pirogov S, Pfab A, Ziegenhain C, Sandberg R, Reimegård J, Mannervik M |
| Citation(s) |
38166964 |
| |
| Submission date |
Aug 14, 2022 |
| Last update date |
Jan 06, 2024 |
| Contact name |
Mattias Mannervik |
| E-mail(s) |
mattias.mannervik@su.se
|
| Organization name |
Stockholm University
|
| Department |
Dept. of Molecular Biosciences
|
| Street address |
Svante Arrhenius väg 20C
|
| City |
Stockholm |
| ZIP/Postal code |
106 91 |
| Country |
Sweden |
| |
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| Platforms (1) |
| GPL22106 |
NextSeq 550 (Drosophila melanogaster) |
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| Samples (16)
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| This SubSeries is part of SuperSeries: |
| GSE211220 |
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network |
|
| Relations |
| BioProject |
PRJNA869359 |
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