Abstract
The linker histone H1 is critical to maintenance of higher-order chromatin structures and to gene expression regulation. However, H1 dynamics and its functions in embryonic development remain unresolved. Here, we profiled gene expression, nucleosome positions, and H1 locations in early Drosophila embryos. The results show that H1 binding is positively correlated with the stability of beads-on-a-string nucleosome organization likely through stabilizing nucleosome positioning and maintaining nucleosome spacing. Strikingly, nucleosomes with H1 placement deviating to the left or the right relative to the dyad shift to the left or the right, respectively, during early Drosophila embryonic development. H1 occupancy on genic nucleosomes is inversely correlated with nucleosome distance to the transcription start sites. This inverse correlation reduces as gene transcription levels decrease. Additionally, H1 occupancy is lower at the 5′ border of genic nucleosomes than that at the 3′ border. This asymmetrical pattern of H1 occupancy on genic nucleosomes diminishes as gene transcription levels decrease. These findings shed new lights into how H1 placement dynamics correlates with nucleosome positioning and gene transcription during early Drosophila embryonic development.
Highlights
IntroductionDNA is packaged into chromatin through the formation of nucleosome
Introduction Eukaryotic genomicDNA is packaged into chromatin through the formation of nucleosome
In order to explore the pattern of H1 location on nucleosomes and the impact of its placement on nucleosome positioning, we generated genome-wide maps of H1 and nucleosome positions with mononucleosomal resolution in Drosophila embryos at 3–4 h after egg laying (AEL)
Summary
DNA is packaged into chromatin through the formation of nucleosome. Linker H1 histones typically comprises three parts: a central globular domain, a short N-terminal region, and a long unstructured C-terminal tail[10]. The N-terminal region is not important for H1 binding to nucleosome[6], whereas the C-terminal tail is required for H1 binding to chromatin in vivo[11]. The globular domain alone is sufficient for chromatosome formation and protects the same linker DNA in the native chromatin against micrococcal nuclease digestion as the full-length linker histone[10,12]. The studies of nucleosome recognition by linker histones have led to many conflicting models for how the globular domain binds to the nucleosome. Whether the globular domain interacts with both or only one linker DNA(s) is unresolved[15]. The position of linker histones in the nucleosome particle has remained controversial
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