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ATAC-seq analysis of chromatin accessibility and nucleosome positioning in Drosophila melanogaster precellular blastoderm embryos

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE83851 | GEO | 2016/11/22

SECONDARY ACCESSION(S): PRJNA327205

REPOSITORIES: GEO

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Project description:Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2. There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2. There are also RNA-seq samples for each of these 10 samples.

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ATAC-seq analysis of chromatin accessibility and nucleosome positioning in Drosophila melanogaster precellular blastoderm embryos

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