GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

Gaskill, Marissa M; Gibson, Tyler J.; Larson, Elizabeth D; Harrison, Melissa M.

doi:10.7554/elife.66668

Cited by 84 publications

(108 citation statements)

References 105 publications

(195 reference statements)

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“…We next determined whether GAF alters chromatin accessibility at loci at which depletion of CLAMP or ZLD individually alters accessibility (Type IV) and are bound by all three factors. Indeed, we found that approximately 10% of loci that require GAF for their chromatin accessibility (n=104) (Gaskill et al, 2021) TFs coordinately regulate early zygotic chromatin accessibility during ZGA (Hamm and Harrison, 2018) Together, our results reveal the CLAMP and ZLD regulate chromatin accessibility, which alters the occupancy of both factors and regulates zygotic transcription. Furthermore, GAF and/or other TFs might function at sites that are not altered by depleting CLAMP or ZLD individually, suggesting that multiple TFs promote chromatin accessibility during ZGA.…”

Section: Clamp and Zld Regulate Gene Expression Via Modulating Chromatin Accessibilitymentioning

confidence: 53%

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

Duan

Rieder

Colonnetta

et al. 2021

eLife

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During the essential and conserved process of zygotic genome activation (ZGA), chromatin accessibility must increase to promote transcription. Drosophila is a well-established model for defining mechanisms that drive ZGA. Zelda (ZLD) is a key pioneer transcription factor (TF) that promotes ZGA in the Drosophila embryo. However, many genomic loci that contain GA-rich motifs become accessible during ZGA independent of ZLD. Therefore, we hypothesized that other early TFs that function with ZLD have not yet been identified, especially those that are capable of binding to GA-rich motifs such as CLAMP. Here, we demonstrate that Drosophila embryonic development requires maternal CLAMP to: 1) activate zygotic transcription; 2) increase chromatin accessibility at promoters of specific genes that often encode other essential TFs; 3) enhance chromatin accessibility and facilitate ZLD occupancy at a subset of key embryonic promoters. Thus, CLAMP functions as a pioneer factor which plays a targeted yet essential role in ZGA.

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Section: Clamp and Zld Regulate Gene Expression Via Modulating Chromatin Accessibilitymentioning

confidence: 53%

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

Duan

Rieder

Colonnetta

et al. 2021

eLife

View full text Add to dashboard Cite

show abstract

Section: Clamp and Zld Regulate Gene Expression Via Modulating Chromatin Accessibilitymentioning

confidence: 93%

“…C. Upper panel: Venn diagram showing the number of overlapping sites between GAFdependent DA sites (Gaskill et al, 2021), ZLD non-DA with ZLD bound, and CLAMP non-DA with CLAMP bound peaks.…”

Section: Figure 5 Clamp and Zld Regulate Gene Expression Via Modulating Chromatin Accessibilitymentioning

confidence: 99%

“…Lower panel: Venn diagram showing the number of overlapping sites between GAFdependent DA sites (Gaskill et al, 2021), ZLD non-DA, and CLAMP non-DA peaks. CLAMP and ZLD function together at promoters to regulate each other's occupancy and gene expression of genes encoding other key TFs.…”

Section: Figure 5 Clamp and Zld Regulate Gene Expression Via Modulating Chromatin Accessibilitymentioning

confidence: 99%

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CLAMP and Zelda function together to promote Drosophila zygotic genome activation

Duan

Rieder

Colonnetta

et al. 2020

Preprint

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Because zygotic genome activation (ZGA) is an essential process across metazoans, it is key to evolve multiple pioneer transcription factors (TFs) to protect organisms from loss of a single factor. Pioneer TF Zelda (ZLD) is the only known factor which increases accessibility of chromatin to promote ZGA in the early Drosophila embryo. However, many genomic loci remain accessible without ZLD and have GA-rich motifs. Therefore, we hypothesized that other pioneer TFs that function with ZLD have not yet been identified in early embryos, especially those that bind to GA-rich motifs, such as CLAMP (Chromatin-linked adaptor for Male-specific lethal MSL proteins). Here, we determine that CLAMP is a novel pioneer TF which interacts directly with nucleosomes, regulates zygotic genome transcription, promotes chromatin accessibility, and facilitates the binding of ZLD to promoters. Thus, the maternal factor CLAMP functions with ZLD as a pioneer TF to open chromatin and drive zygotic genome activation.

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“…GAGA factor (GAF) is known to interact with Mod(mdg4) to regulate su(Hw) insulators [44]. GAF also interacts with chromatin remodelers, transcription machinery, and polycomb response elements (PREs) [45], and GAF is necessary for the maternal-to-zygotic transition in embryos [46]. GAF, like M1BP, has many functions throughout the genome.…”

Section: Insulator Proteins Involved In Tad Formation Regulation and Maintenancementioning

confidence: 99%

Multi-Scale Organization of the Drosophila melanogaster Genome

Peterson

Samuelson

Hanlon

2021

Genes

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Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome.

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GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

Cited by 84 publications

References 105 publications

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

Multi-Scale Organization of the Drosophila melanogaster Genome

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