Abstract
SummaryChromatin organization is disrupted genome-wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naive histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is faithfully copied during DNA replication or the epigenome is perturbed. Here we develop chromatin occupancy after replication (ChOR-seq) to determine histone PTM occupancy immediately after DNA replication and across the cell cycle. We show that H3K4me3, H3K36me3, H3K79me3, and H3K27me3 positional information is reproduced with high accuracy on newly synthesized DNA through histone recycling. Quantitative ChOR-seq reveals that de novo methylation to restore H3K4me3 and H3K27me3 levels occurs across the cell cycle with mark- and locus-specific kinetics. Collectively, this demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
Highlights
The organization of eukaryotic genomes into chromatin influences all DNA-based processes, including gene expression and DNA repair
Using ChOR-seq to track H3K4me3, H3K36me3, H3K79me3, and H3K27me3, we find that post-translational modifications (PTMs) occupancy patterns are reproduced on newly replicated DNA with high accuracy in both repressed and active genomic regions, demonstrating that the positional information of histone marks is faithfully inherited to daughter strands during DNA replication
To inform on pre-replication histone PTM position, we used S phase synchronized HeLa S3 and carried out standard chromatin immunoprecipitation (ChIP)-seq of H3K4me3 and H3K27me3 in total chromatin prior to DNA labeling (Figure 1B; Figure S1A). These H3K4me3 and H3K27me3 enrichment profiles from S-phase-synchronized cells were largely identical to genome-wide maps of H3K4me3 and H3K27me3 in asynchronous HeLa S3 cells available from ENCODE (Bernstein et al, 2005) (Figure S1B), confirming that parental ChIP-seq is a suitable baseline for assessing our ChOR-seq data
Summary
The organization of eukaryotic genomes into chromatin influences all DNA-based processes, including gene expression and DNA repair. The basic mechanisms that ensure propagation of chromatin states during DNA replication and across cell division remain unclear (Alabert and Groth, 2012; Allis and Jenuwein, 2016; Almouzni and Cedar, 2016). The nucleosome is the basic unit of chromatin, in which 146 base pairs of DNA are wrapped around a histone core composed of a central histone H3-H4 tetramer flanked by two histone H2A-H2B dimers. Histones are decorated with a large variety of post-translational modifications (PTMs) that contribute to the establishment and maintenance of active and repressed chromatin states (Patel and Wang, 2013). Many of these regulatory modifications are found on histone H3. Tri-methylation of histone H3 lysine 27 (H3K27me3) demarcates larger, transcriptionally silent domains (Schuettengruber et al, 2017)
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