Transcriptional and Epigenetic Signatures of Zygotic Genome Activation During Early Drosophila Embryogenesis
Supplementary material
Elodie Darbo, Carl Herrmann, Thomas Lecuit, Denis Thieffry and Jacques van Helden
Abstract
Background: In all Metazoa, transcription is inactive during the first mitotic cycles after fertilization. In Drosophila melanogaster, Zygotic Genome Activation (ZGA) occurs in two waves, starting respectively at mitotic cycles 8 (approximately 60 genes) and 14 (over a thousand genes). The regulatory mechanisms underlying these drastic transcriptional changes remain largely unknown. We combined several publicly available transcriptome and ChIP-seq datasets in a computational work flow to identify novel molecular actors and cis-regulatory modules putatively involved in ZGA control. Method: We developed an original gene clustering method based on discretized transition profiles, and applied it to datasets from three landmark early embryonic transcriptome studies in order to identify a cluster of ZGA-responding genes. We ran de novo motif discovery in the corresponding non-coding regions (upstream, introns, UTR)and used the significant motifs to detect putative cis-regulatory modules (CRMs) in ZGA genes. These CRMs were further compared with various epigenetic marks characterized by ChIP-seq. Results: We identified 417 genes significantly up-regulated during ZGA. De novo motif discovery returned nine motifs over-represented in their non-coding sequences, three of which correspond to previously known transcription factors: Zelda, Tramtrack and Trithorax-like (Trl). The 9 discovered motifs were combined to scan ZGA-associated regions and predict 900 putative cis-regulatory modules. The fact that Trl is known to act as chromatin remodeling factor suggested that epigenetic regulation might play an important role in zygotic genome activation. We thus systematically compared the locations of predicted CRMs with ChIP-seq profiles for various transcription factors, 38 epigenetic marks from ModENCODE, and DNAse1 accessibility profiles. This analysis highlighted a strong and specific enrichment of predicted ZGA-associated CRMs for Zelda, CBP, Trl binding sites, as well as for histone marks associated with active enhancers (H3K4me1) and for open chromatin regions. Conclusion: Based on the results of our computational analyses, we suggest a temporal model explaining the onset of zygotic genome activation by the combined action of transcription factors and epigenetic signals. Although this study is mainly based on the analysis of publicly available transcriptome and CHIP-seq datasets, the model enlights the mechanisms that underly the coordinated activation of several hundreds genes at a precise time point during embryonic development.Data and results