Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization

Area of Science:

• Genomics
• Molecular Biology
• Human Genetics

Background:

• DNA replication timing is crucial for genome stability and gene regulation.
• Understanding allele-specific replication timing provides insights into genome organization and function.

Purpose of the Study:

• To develop and apply a novel genome-wide approach for characterizing allele-specific DNA replication timing in human primary basophilic erythroblasts.
• To identify genomic features and structural variations associated with replication asynchrony.

Main Methods:

• Genome-wide characterization of allele-specific DNA replication timing using a new approach.
• High-resolution TimEX profiling to detect timing variations (ripples).
• Nascent strand DNA profiling to identify replication origins.

Main Results:

• Approximately 88% of the genome shows synchronous replication between homologous chromosomes.
• Large structural variants and imprinted genes are associated with asynchronous replication domains.
• Identified ~600 megabase-sized asynchronously replicated domains, with smaller 'timing ripples' within them.
• Replication origins are strongly associated with G-quadruplexes, CpG islands, and transcription start sites.

Conclusions:

• Structural variants, parental imprinting, and X-inactivation contribute to replication asynchrony.
• Timing ripples represent reproducible variations in replication timing at the 100 kb scale, linked to origin clusters.
• Replication origin distribution and initiation frequency vary significantly across the S phase and are influenced by specific genomic features.