Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization.
We have developed a new approach to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronous replication. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. The longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed small variations termed timing ripples, which were undetected in previous, lower resolution analyses. Timing ripples reflect highly reproducible, variations of the timing of replication in the 100 kb-range that exist within the well-characterized megabase-sized replication timing domains. These ripples correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequencies during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Rituparna
R
Mukhopadhyay
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Julien
J
Lajugie
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Nicolas
N
Fourel
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Ari
A
Selzer
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Michael
M
Schizas
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Boris
B
Bartholdy
Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Jessica
J
Mar
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America.
Chii Mei
CM
Lin
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America.
Melvenia M
MM
Martin
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America.
Michael
M
Ryan
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America.
Mirit I
MI
Aladjem
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
Eric E
EE
Bouhassira
D000483:Alleles; D002478:Cells, Cultured; D004900:Erythroblasts / Q000378:metabolism*; D020869:Gene Expression Profiling; D015894:Genome, Human; D018392:Genomic Imprinting; D006801:Humans; D049951:X Chromosome Inactivation