Abstract
BackgroundTracking dynamic protein–chromatin interactions in vivo is key to unravel transcriptional and epigenetic transitions in development and disease. However, limited availability and heterogeneous tissue composition of in vivo source material impose challenges on many experimental approaches.ResultsHere we adapt cell-type-specific DamID-seq profiling for use in Drosophila imaginal discs and make FLP/FRT-based induction accessible to GAL driver-mediated targeting of specific cell lineages. In a proof-of-principle approach, we utilize ubiquitous DamID expression to describe dynamic transitions of Polycomb-binding sites during wing imaginal disc development and in a scrib tumorigenesis model. We identify Atf3 and Ets21C as novel Polycomb target genes involved in scrib tumorigenesis and suggest that target gene regulation by Atf3 and AP-1 transcription factors, as well as modulation of insulator function, plays crucial roles in dynamic Polycomb-binding at target sites. We establish these findings by DamID-seq analysis of wing imaginal disc samples derived from 10 larvae.ConclusionsOur study opens avenues for robust profiling of small cell population in imaginal discs in vivo and provides insights into epigenetic changes underlying transcriptional responses to tumorigenic transformation.
Highlights
Tracking dynamic protein–chromatin interactions in vivo is key to unravel transcriptional and epige‐ netic transitions in development and disease
We report here the co-regulation of multiple oncogenic genes by dynamic Pc-binding, while identifying at least two novel Pc target genes involved in scrib tumorigenesis
Only upon ubiquitous expression of a heat-shock-induced FLIP recombinase (FLP), we observed the characteristic DNA smear formed by the methylation-dependent PCR products amplified from genomic DNA extracted from wing imaginal discs (WIDs) (Fig. 1b, Additional file 1: Fig. S1A)
Summary
Tracking dynamic protein–chromatin interactions in vivo is key to unravel transcriptional and epige‐ netic transitions in development and disease. Like other in vivo model systems, the small size and the heterogeneous fate composition of Drosophila tissues still pose challenges to the detailed tracking of DNA binding sites in different cell populations and lineages in vivo. Chromatin immunoprecipitation (ChIP) protocols use fluorescenceactivated cell sorting (FACS) or immunoprecipitation (IP)-based methods to isolate Drosophila cell populations from tissues [1,2,3,4]. These approaches, still require a significant amount of input material for reproducible results, which has prevented these methods from being used in contexts where small source tissues, such as imaginal discs, are routinely isolated by manual dissection. M6A is only generated in cell types expressing DamID constructs; DamID protocols do not necessitate to
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