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Replication Timing Uncovers a Novel Two-Compartment Arrangement of Maize Interphase Euchromatin.

ABSTRACT: The time within S phase when a given genomic region replicates is measurable and referred to as Replication Timing (RT). We previously proposed a "mini-domain" chromatin fiber RT model for maize euchromatin's spatial architecture. 3D quantitative cytology showed that euchromatin is subdivided into two compartments during S-phase, distinguished by chromatin condensation and replication timing: Early-S and Middle-S. A key gap remains in understanding whether this compartmentalization is a general feature throughout the cell cycle, which could greatly impact our knowledge of genome architecture and gene regulation. To investigate this, we conducted two orthogonal assays, Hi-C for genome-wide interaction data and 3D FISH for direct visualization of chromatin organization. The Hi-C-derived eigenvalues and insulation scores significantly concord with Early-S and Middle-S regions. Early-S regions showed negative insulation scores with more long-range contacts, whereas Middle-S regions displayed the opposite, positive insulation scores with fewer long-range contacts. Compared to Middle-S regions, the Early-S regions showed much stronger correlations with epigenomic signatures of open and transcriptionally active chromatin. Oligo FISH painting with RT-specific probes demonstrated that Early-S and Middle-S regions occupied adjacent but largely non-overlapping nucleoplasmic regions throughout all stages of interphase, including G1. These findings validate our model while establishing that the global "A" compartment of euchromatin actually consists of two spatially and epigenetically distinct substructures – now referred to as Early-S and Middle-S compartments. Given the strong correlation between replication timing and Hi-C data from root tips, we examined the conservation of Hi-C architecture in both root tip and earshoot tissues and found them to be remarkably similar. Overall, our findings highlight the importance of replication timing as a conserved feature of chromatin architecture, reflecting broader principles of genome organization.

ORGANISM(S): Zea mays

PROVIDER: GSE287128 | GEO | 2026/01/10

REPOSITORIES: GEO

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Project description:Extensive changes in replication timing occur during early mouse development, but their biological significance remains uncertain. To identify evolutionarily conserved features of replication timing and their relationships to epigenetic properties in humans, we profiled replication timing genome-wide in four human embryonic stem cell (hESC) lines, hESC-derived neural precursor cells (NPCs), lymphoblastoid cells, and two independently derived human induced pluripotent stem cell lines (hiPSCs). Results confirm the conservation of coordinately replicated megabase-sized units of chromosomes (replication domains) with stable cell type specific molecular boundaries that consolidate into larger replication domains during differentiation. Replication timing changes encompassed units of 400-800 kb and were coordinated with changes in transcription similar to mouse. Moreover, significant cell-type specific conservation of replication timing profiles was observed across regions of conserved synteny, despite significant species variation in the alignment of replication timing to isochore GC/LINE-1 content. Replication profiling also revealed a closer genome-wide epigenetic alignment of hESCs to mouse epiblast-derived stem cells (mEpiSCs) than to mouse ESCs. Finally, we identify a signature of chromatin modifications marking the boundaries of early replicating domains and a remarkably strong link between spatial proximity of chromatin as measured by Hi-C analysis and replication timing. Together, our results reveal evolutionarily conserved elements of the replication program in mammalian early development, demonstrate the power of replication profiling to identify important epigenetic distinctions between closely related stem cell populations (e.g. ESCs vs. EpiSCs), and strengthen the hypothesis that replication domains are structural and functional units of 3D chromosomal architecture. 8 cell types, with a total of 13 individual replicates (i.e. 5 in duplicates, 3 in single replicates)

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Replication Timing Uncovers a Novel Two-Compartment Arrangement of Maize Interphase Euchromatin.

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