Transcription-coupled structural dynamics of topologically associating domains regulate replication origin...

Area of Science:

• Cell Biology
• Genetics
• Molecular Biology

Background:

• Metazoan cells use a limited set of DNA replication origins per cell cycle.
• Origin selection is crucial for cell growth, differentiation, and managing replication stress.
• Despite links to genetic and epigenetic factors, the precise mechanism of origin selection remains unclear.

Purpose of the Study:

• To investigate the spatial distribution and selection mechanism of DNA replication origins within topologically associating domains (TADs).
• To understand how chromatin organization influences replication origin efficiency.

Main Methods:

• Dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging was used to map origin distribution.
• Analysis of origin spatial organization within TADs during different cell cycle phases.
• Investigated the role of transcription and CTCF in origin relocalization.

Main Results:

• Replication origins initiate at TAD boundaries at the start of S phase.
• High-efficiency origins relocate to the TAD periphery during G1 phase, while low-efficiency origins remain distributed.
• Origin relocalization is dependent on transcription and CTCF-mediated chromatin structure.
• Proliferating Cell Nuclear Antigen (PCNA) forms immobile clusters at TADs, promoting peripheral origin firing.

Conclusions:

• Replication origin efficiency is determined by physical distribution within chromatin domains, influenced by transcription-dependent structural reorganization.
• This mechanism explains the correlation between origin efficiency and active transcription marks.
• The coordination of DNA replication, transcription, and chromatin organization within TADs offers insights into chromatin dynamics.