Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin

Area of Science:

• Genomics
• Cell Biology
• Epigenetics

Background:

• Replication timing (RT) regulates genome duplication during S phase.
• Previous models suggested maize euchromatin subcompartmentalization based on chromatin condensation and RT.
• The persistence of this compartmentalization throughout the cell cycle remained unclear.

Purpose of the Study:

• To investigate the spatial organization of maize euchromatin.
• To determine if proposed subcompartments persist throughout the cell cycle.
• To redefine the maize euchromatin 'A' compartment based on RT and spatial organization.

Main Methods:

• Genome-wide interaction data using Hi-C.
• Direct visualization of chromatin organization using 3D FISH painting.
• Analysis of epigenomic signatures associated with replication timing.

Main Results:

• Hi-C revealed distinct interaction patterns for early-S (negative insulation, long-range contacts) and middle-S regions.
• Early-S regions correlated strongly with open, transcriptionally active chromatin.
• 3D FISH confirmed early-S and middle-S regions occupy adjacent, non-overlapping nuclear sub-territories throughout interphase.

Conclusions:

• Maize euchromatin 'A' compartment comprises two spatially distinct subcompartments.
• These subcompartments are defined by high-frequency RT transitions along the genome.
• RT is a critical feature defining genome organization and has implications for chromatin-templated processes.