Comprehensive interrogation of aDrosophilaembryonic patterning network reveals the impact of chromatin state on tissue-specific burst kinetics and RNA Polymerase II promoter-proximal pause release

Abstract

Formation of tissue-specific transcriptional programs underlies multicellular development, but how the chromatin landscape influences transcription is not fully understood. Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila dorsoventral (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. 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.

Modulation of transcription burst amplitude underpins dosage compensation in theDrosophilaembryo

“…One option for inferring burst parameters for multiple X chromosome genes would be to exploit an approach for burst inference based on the two state model that was described for allele specific scRNA-seq 66 and has recently been used with Drosophila scRNA-seq data. 67 This approach can estimate k on and burst size ( k ini / k off ), although estimation of the individual k ini and k off parameters is less reliable. 66 However, as noted 68 , the sparsity of reads in existing scRNA-seq data from the Drosophila embryo 68,69 makes sexing the nuclei difficult.…”

Modulation of transcription burst amplitude underpins dosage compensation in the Drosophila embryo

“…One option for inferring burst parameters for multiple X chromosome genes would be to exploit an approach for burst inference based on the two-state model that was described for allele-specific single-cell RNA-seq (scRNA-seq) 66 and that has recently been used with Drosophila scRNA-seq data. 67 This approach can estimate k on and burst size ( k ini / k off ), although estimation of the individual k ini and k off parameters is less reliable. 66 However, as noted, 68 the sparsity of reads in existing scRNA-seq data from the Drosophila embryo 68 , 69 makes sexing the nuclei difficult.…”