Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

Area of Science:

• Cell Biology
• Epigenetics
• Genomics

Background:

• Centromeres are crucial for chromosome segregation during cell division.
• The precise organization and regulation of centromeric chromatin remain poorly understood.
• Centromeric chromatin is organized within satellite DNA arrays.

Purpose of the Study:

• To investigate the detailed sequence and chromatin architecture of human centromeres on individual haplotypes.
• To understand the organization of CENP-A (centromere protein A) within centromeric chromatin.
• To explore the role of DNA methylation in regulating centromere organization.

Main Methods:

• Utilized the T2T-HG002 diploid human genome benchmark.
• Employed adaptive-sampling-enriched, ultra-long-read DiMeLo-seq for single-molecule chromatin profiling.
• Analyzed centromeric sequence and chromatin architecture across all human centromeres.

Main Results:

• CENP-A forms multiple discrete subdomains within hypomethylated centromere dip regions (CDRs) on single chromatin fibers.
• CDRs are localized to sequence-homogeneous domains and show balanced CENP-A dosage across chromosomes and haplotypes.
• Bidirectional changes in DNA methylation correlate with alterations in centromeric chromatin architecture, including subdomain merging or consolidation.

Conclusions:

• DNA methylation is a principal regulator of human centromere organization.
• Changes in DNA methylation can lead to restructuring of centromeric chromatin, affecting CENP-A domain organization.
• These findings have implications for understanding centromere plasticity, epigenetic inheritance, and chromosomal instability.