Targeting of the Dosage-Compensated Male X-Chromosome during Early Drosophila Development

Abstract

Graphical AbstractHighlights d Establishment of a system to study dosage compensation before zygotic transcription starts d The Drosophila DCC binds genome-wide before enrichment at X chromosome binding sites d The CLAMP transcription factor binds to chromatin before zygotic transcription starts SUMMARY Dosage compensation, which corrects for the imbalance in X-linked gene expression between XX females and XY males, represents a model for how genes are targeted for coordinated regulation. However, the mechanism by which dosage compensation complexes identify the X chromosome during early development remains unknown because of the difficulty of sexing embryos before zygotic transcription using X-or Y-linked reporter transgenes. We used meiotic drive to sex Drosophila embryos before zygotic transcription and ChIP-seq to measure the dynamics of dosage compensation factor targeting. The Drosophila male-specific lethal dosage compensation complex (MSLc) requires the ubiquitous zinc-finger protein chromatin-linked adaptor for MSL proteins (CLAMP) to identify the X chromosome. We observe a multi-stage process in which MSLc first identifies CLAMP binding sites throughout the genome, followed by concentration at the strongest X-linked MSLc sites. We provide insight into the dynamics of binding site recognition by a large transcription complex during early development.

CLAMP and Zelda function together to promoteDrosophilazygotic genome activation

“…Therefore, our data support a model in which CLAMP functions early in the embryo prior to MSL complex assembly to open up specific chromatin regions for MSL complex recruitment later (J. Urban et al, 2017; Rieder et al, 2019). Moreover, ZLD likely functions primarily as an early pioneer factor whereas CLAMP has pioneering functions in both early and late embryos.…”

“…CLAMP is essential for early embryonic development (Rieder et al, 2017) and plays several key roles including: 1) recruiting the MSL dosage compensation complex to the male X-chromosome prior to ZGA (Rieder et al, 2019); 2) activating coordinated regulation of the histone genes (Rieder et al, 2017). Therefore, we hypothesized that CLAMP as a new GA-binding pioneer TF which regulates ZGA either interdependently with or independent of ZLD.…”

Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation

“…H4K16ac has a well-known role in X chromosome regulation (Akhtar and Becker, 2000;Gelbart et al, 2009;Hilfiker et al, 1997). Consistent with previous reports, our stage-specific ChIP-seq dataset revealed prominent H4K16ac enrichment on the X chromosome compared to autosomes from st7 onwards (Figures 3E, 4A, 7A, S3C, S4C, and S7A-S7C) (Franke et al, 1996;Rastelli et al, 1995;Rieder et al, 2019). However, the promoters of ''future'' dosage-compensated genes were already H4K16ac-positive at stages 3-4 ( Figure 7A).…”

GAF is essential for zygotic genome activation and chromatin accessibility in the earlyDrosophilaembryo

“…In addition to GAF and Zld, the transcription factor CLAMP is expressed in the early embryo and functions in chromatin accessibility and transcriptional activation (Rieder et al 2017;Soruco et al 2013;Urban et al 2017aUrban et al , 2017bRieder et al 2019). While CLAMP, like GAF, binds GAdinucleotide repeats, the two proteins preferentially bind to slightly different GA-repeats (Kaye et al 2018).…”