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Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

ABSTRACT: Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

PROVIDER: PRJNA414230 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6171263_1.fastq.gz	Fastqsanger.gz
	SRR6171263_2.fastq.gz	Fastqsanger.gz
	SRR6171264_1.fastq.gz	Fastqsanger.gz
	SRR6171264_2.fastq.gz	Fastqsanger.gz
	SRR6171265_1.fastq.gz	Fastqsanger.gz

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Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

Project description:As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of “open” chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. Recent work has implicated the ubiquitously expressed maternal factor Zelda in this process. To assess the relative contribution of activity in the establishment of open chromatin , we have probed chromatin accessibility across the anterior-posterior axis of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is remarkably similar between the two halves. Promoters and enhancers that are active in exclusively one half of the embryo have open chromatin in the other half, demonstrating that chromatin accessibility is not a direct result of activity. However there is a small skew at enhancers that drive transcription exclusively in either the anterior or posterior half of the embryo, with greater accessibility in the region of activity. Taken together these data support a model in which regions of chromatin accessibility are defined and established by ubiquitous factors, and fine tuned subsequently by activity.

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Project description:Establishment of spatial coordinates during early Drosophila embryogenesis relies on differential activity of axis patterning enhancers. Concentration gradients along the embryonic axes of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. In order to receive the TF input, an enhancer must be accessible. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization in not well understood. Notably, it is unclear whether chromatin organization of axis patterning enhancers is uniform across the embryo or varies regionally with their differential activity. We profiled chromatin accessibility with ATAC-seq in narrow, genetically tagged domains along the antero-posterior (AP) axis in the Drosophila blastoderm. In a series of transgenic strains, we drove expression of a nuclear tag (nuclear-envelope marker UNC84-3xFLAG) under control of well-characterised enhancers of the AP gene regulatory network. Tagged nuclei were subsequently isolated from the whole-embryo homogenate by anti-FLAG antibody pull-down, followed by Tn5 transposase digestion of the native chromatin (ATAC-seq). We demonstrate that one quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable regions and their accessibility changes correlate with their regulatory activity. When receiving a net activating input and promoting transcription, an enhancer displays elevated accessibility in comparison to the region of the embryo where it receives a net repressive input.

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