4D Chromatin Dynamics Resolved During Early Random X Chromosome Inactivation

Area of Science:

• Genetics and Genomics
• Epigenetics and Chromatin Biology
• Developmental Biology

Background:

• X chromosome inactivation (XCI) is essential for dosage compensation in female mammals.
• XCI involves extensive three-dimensional (3D) chromatin reorganization.
• Understanding the dynamics of early XCI stages remains challenging.

Purpose of the Study:

• To investigate the four-dimensional (4D) chromatin dynamics during early XCI stages.
• To characterize single-cell inactivation trajectories and associated chromatin remodeling.
• To elucidate the role of Xist expression in XCI initiation.

Main Methods:

• Application of HiRES (Hi-C and RNA-seq simultaneously) multi-omics sequencing.
• Analysis of mouse embryonic stem cells undergoing induced random XCI.
• Single-cell resolution of 3D genome and transcriptome.

Main Results:

• Identified distinct inactivation trajectories at single-cell resolution.
• Discovered a transient structural state shared by both X chromosomes during biallelic Xist expression.
• Demonstrated that most chromatin remodeling accompanies or follows gene silencing.
• Revealed that topologically associating domain (TAD) attenuation initiates from anchor interaction loss.

Conclusions:

• Provides a detailed, fine-scale depiction of chromatin reorganization during XCI initiation.
• Highlights the dynamic interplay between 3D genome structure and gene silencing.
• Establishes HiRES as a powerful tool for studying dynamic multi-omics processes.