Purpose: The goal of this study was to measure how chromatin accessibility and nucleosome positioning changes as embryos undergo the midblastula transition (MBT).
Methods: Single or paired embryos were collected at three minute intervals over the three cell cycles leading up to the MBT (nuclear cycles 11, 12, and 13). Embryos were subjected to ATAC-seq library preparation following established protocols. Thirteen total timepoints were collected. At least three biological replicates were collected per timepoint. Samples were subjected to paired end sequencing on an Illumina HiSeq 2500. Wild type (diploid) embryos were compared with haploid (sesame) embryos to determine whether changes in chromatin accessibility are governed by measurement of the nucleo-cytoplasmic ratio, a well known biological timer that controls the onset of the MBT.
Results: Chromatin accessibility changes dynamically during the period leading up to the MBT. Initially, genomic enhancer elements are accessible, but during NC12 and NC13, large scale chromatin remodeling results in a gain of accessibility for promoter elements and insulators. A substantial fraction of the dynamic chromatin accessibility is temporally regulated by the mechanism that measures the embryonic nuclear-cytoplasmic ratio, as determined by comparison between haploid and diploid embryos. A substantial fraction of open chromatin regions remain 'accessible' during mitotic metaphase.
Overall design
Embryos were collected in a three minute time course spanning three cell cycles and prepared for ATAC seq analysis. Triplicate biological replicates were collected per timepoint. Samples were subjected to paired end sequencing (2x 67bp) on an Illumina HiSeq 2500.
Please note that replicates were pooled for generating processed files, and each processed data file is linked to the first replicate sample (of the corresponding samples) (*_rep1).
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