ArticleNature genetics2019
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization.
Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
59 citing papers in PubMed.
- Chromatin interaction landscape of epimorphic regeneration in teleost fish.Science advances · 2026Article
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes.Nature communications · 2026Article
- Re-establishment of TAD boundary organization during DNA replication.bioRxiv : the preprint server for biology · 2026Article
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains.Nature communications · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase.Nature communications · 2025Article
- HIRA defines early replication initiation zones independently of their genome compartment.Nature communications · 2025Article
- IVF and Thermal Manipulation at the First Cleavage Stage Alter Offspring Circadian Phenotype, Sleep, and Brain Epigenetics.International journal of molecular sciences · 2025Article
- Leishmania major chromosomes are replicated from a single high-efficiency locus supplemented by thousands of lower efficiency initiation events.Cell reports · 2025Article
- H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation.Epigenetics & chromatin · 2025Article
- KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition.Cell reports · 2025Article
- Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.Nature communications · 2025Article
- A tale of two strands: Decoding chromatin replication through strand-specific sequencing.Molecular cell · 2025Review
- Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Chromosome compartmentalization: causes, changes, consequences, and conundrums.Trends in cell biology · 2024Review
- The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In mammalian cells, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which exhibit early and late replication timing (RT), respectively. Here, we show that A/B compartments change coordinately with RT changes genome wide during mouse embryonic stem cell (mESC) differentiation. While A to B compartment changes and early to late RT changes were temporally inseparable, B to A changes clearly preceded late to early RT changes and transcriptional activation. Compartments changed primarily by boundary shifting, altering the compartmentalization of TADs facing the A/B compartment interface, which was conserved during reprogramming and confirmed in individual cells by single-cell Repli-seq. Differentiating mESCs altered single-cell Repli-seq profiles gradually but uniformly, transiently resembling RT profiles of epiblast-derived stem cells (EpiSCs), suggesting that A/B compartments might also change gradually but uniformly toward a primed pluripotent state. These results provide insights into how megabase-scale chromosome organization changes in individual cells during differentiation.
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