Abstract
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 how regions of activity are established during early embryogenesis, and if they are the product of spatially restricted or ubiquitous processes. To shed light on this question, we probed chromatin accessibility across the anterior-posterior axis (A-P) 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 highly similar between the two halves, with regions that manifest significant accessibility in one half of the embryo almost always accessible in the other half, even for promoters that are active in exclusively one half of the embryo. These data support previous studies that show that chromatin accessibility is not a direct result of activity, and point to a role for ubiquitous factors or processes in establishing chromatin accessibility at promoters in the early embryo. However, in concordance with similar works, we find that at enhancers active exclusively in one half of the embryo, we observe a significant skew towards greater accessibility in the region of their activity, highlighting the role of patterning factors such as Bicoid in this process.
Highlights
During early embryogenesis all animal genomes undergo a transition from a largely quiescent to a highly active state with widespread zygotic transcription [1]. This process, known as the maternal-to-zygotic transition (MZT), involves a major reorganization of chromatin, during which active and inactive regions are established which are distinguished by nucleosome composition, density and post-translational modifications [2,3,4,5,6]
In Drosophila melanogaster, zygotic transcription largely begins at the seventh syncytial mitotic cycle and gradually increases until the end of mitotic cycle 13, when the embryo has several thousand nuclei and widespread zygotic transcription is observed [10,11]
To determine the extent to which chromatin accessibility is spatially patterned along the A-P axis in the early embryo, we manually separated anterior and posterior embryo halves and performed a modified ATAC-seq [34] protocol on each half separately
Summary
During early embryogenesis all animal genomes undergo a transition from a largely quiescent to a highly active state with widespread zygotic transcription [1]. This process, known as the maternal-to-zygotic transition (MZT), involves a major reorganization of chromatin, during which active and inactive regions are established which are distinguished by nucleosome composition, density and post-translational modifications [2,3,4,5,6]. Many of the genes activated during the MZT produce mRNAs that have spatially restricted distributions These patterns are established through the activity of transcriptional enhancers, cis-regulatory sequences that integrate activating and repressive inputs from well-characterized, patterning transcription factors to produce novel, increasingly precise transcriptional outputs [12,13,14,15]
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