ArticleGenome research2015
Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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Who cites it
95 citing papers in PubMed.
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Nuclear compartmentalization at the G1/S transition plays a key role in DNA replication control.Nature communications · 2026Article
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Single cell multiomics approach to analyze replication timing and gene expression in mouse preimplantation embryos.Communications biology · 2025Article
- Control of epithelial homeostasis by apical polarity: it takes a network.Biochemical Society transactions · 2025Article
- Master transcription-factor binding sites constitute the core of early replication control elements.The EMBO journal · 2025Article
- Roles for the 3D genome in the cell cycle, DNA replication, and double strand break repair.Frontiers in cell and developmental biology · 2025Review
- Article
- Sex-specific DNA-replication in the early mammalian embryo.Nature communications · 2024Article
- Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner.Nature communications · 2024Article
- Article
- Genome folding dynamics during the M-to-G1-phase transition.Current opinion in genetics & development · 2023Review
- Origins of DNA replication in eukaryotes.Molecular cell · 2023Review
- Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1.Life science alliance · 2022Article
- Maintaining Transcriptional Specificity Through Mitosis.Annual review of genomics and human genetics · 2022Review
- Article
- Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.Cold Spring Harbor perspectives in biology · 2022Review
35 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating domains (TADs), which are the structural counterparts of replication domains. Hi-C also segregates inter-TAD contacts into defined 3D spatial compartments that align precisely to genome-wide replication timing profiles. Determinants of the replication-timing program are re-established during early G1 phase of each cell cycle and lost in G2 phase, but it is not known when TAD structure and inter-TAD contacts are re-established after their elimination during mitosis. Here, we use multiplexed 4C-seq to study dynamic changes in chromatin organization during early G1. We find that both establishment of TADs and their compartmentalization occur during early G1, within the same time frame as establishment of the replication-timing program. Once established, this 3D organization is preserved either after withdrawal into quiescence or for the remainder of interphase including G2 phase, implying 3D structure is not sufficient to maintain replication timing. Finally, we find that developmental domains are less well compartmentalized than constitutive domains and display chromatin properties that distinguish them from early and late constitutive domains. Overall, this study uncovers a strong connection between chromatin re-organization during G1, establishment of replication timing, and its developmental control.
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