ArticlePLoS genetics2014
Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 64 citations in OpenAlex.
- Atlas of imprinted and allele-specific DNA methylation in the human body.Nature communications · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins.eLife · 2024Article
- Review
- Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers.Nature cancer · 2024Article
- Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes.Nucleus (Austin, Tex.) · 2023Review
- Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.Nature protocols · 2023Review
- Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon.BMC biology · 2023Article
- Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability.Nature communications · 2022Article
- Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods.Journal of visualized experiments : JoVE · 2021Article
- Dynamics of replication origin over-activation.Nature communications · 2021Article
- Chromosomal coordination and differential structure of asynchronous replicating regions.Nature communications · 2021Article
- BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks.Epigenetics & chromatin · 2020Article
- Genomic methods for measuring DNA replication dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- Control of DNA replication timing in the 3D genome.Nature reviews. Molecular cell biology · 2019Review
- Involvement of G-quadruplex regions in mammalian replication origin activity.Nature communications · 2019Article
- Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase.Nucleic acids research · 2019Article
- Genome-wide stability of the DNA replication program in single mammalian cells.Nature genetics · 2019Article
- Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.Cell systems · 2018Article
- Mechanisms of establishment and functional significance of DNA demethylation during erythroid differentiation.Blood advances · 2018Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.