Topological domains in mammalian genomes identified by analysis of chromatin interactions
Open accessAbstract
The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
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Eukaryotic chromosomes are partitioned into topologically associated domains (TADs).
“Second, it was demonstrated that eukaryotic chromosomes are partitioned into so-called topologically associated domains (TADs) [35,36,37], which appear to restrict the areas of enhancer action [38,39,40,41].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [36]
The Abstract reports topological domains as a pervasive feature of the human and mouse genomes and notes similar partitioning in Drosophila. It suggests this may be a fundamental principle of metazoan genomes, but does not establish the claim for eukaryotic chromosomes generally. (LLM, conf=0.85)
Experimental — accuracy not yet measuredMetazoan genomes are organised into megabase-scale segregated domains that are often invariant between cell types, termed TADs.
“metazoan genomes are organised into megabase-scale segregated domains that are often invariant between cell types, termed topologically associating domains (TADs) [432–434].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [432]
Loop extrusion mediated by cohesin and CTCF mediates the formation of chromatin loops and self-interacting TADs.
“loop extrusion mediated by cohesin and CTCF mediates the formation of chromatin loops and self-interacting Topologically Associating Domains (TADs)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [84]
The mouse α-globin cluster is located in close proximity to a cluster of 10 widely expressed genes near the boundary of a ~1Mb TAD as defined by Dixon et al.
“The mouse α-globin cluster is located in close proximity to a cluster of 10 widely expressed genes near the boundary of a ~1Mb TAD as defined by Dixon et al (Fig. 1A)12.”
From Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (2017) · cites this paper as [12]
Mammalian genomes are organized into a hierarchy of Megabase-scale topologically associating domains (TADs) and smaller, nested subTADs.
“Mammalian genomes are organized into a hierarchy of Megabase (Mb)-scale topologically associating domains (TADs) (Dixon et al., 2012; Nora et al., 2012) and smaller, nested subTADs (Dixon et al., 2012; Nora et al., 2012; Phillips-Cremins et al., 2013; Rao et al., 2014).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Dixon et al., 2012
There is enrichment for CTCF at human ES cell boundaries compared to loci internal to domains.
“Consistent with previous reports, we found enrichment for the architectural protein CCCTC-binding factor (CTCF) at human ES cell boundaries compared to loci internal to domains (Figure S6A-B) (Dixon et al., 2012; Nora et al., 2012; Phillips-Cremins et al., 2013).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Dixon et al., 2012
Topologically associating domains (TADs) exist at intermediate scales (100 kb to 1 Mb).
“At intermediate scales (100 kb to 1 Mb), a major discovery is the existence of topologically associating domains (TADs) (Dixon et al., 2012, Nora et al., 2012, Sexton et al., 2012).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Dixon et al., 2012
The third set of boundaries appears to represent repeats.
“The third set of boundaries appear to represent repeats (Figure 2B), consistent with previous findings (Dixon et al., 2012).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Dixon et al., 2012
Most TAD boundaries are conserved.
“Therefore, although we confirmed that most TAD boundaries are conserved (Dixon et al., 2012), novel borders can occur at promoters of developmentally regulated genes.”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Dixon et al., 2012
Mammalian chromosomes are structured into largely tissue-invariant TADs in which DNA interactions are more frequent within a given domain than with regions in other domains.
“Recent chromosome conformation studies have revealed that mammalian chromosomes are structured into largely tissue-invariant TADs in which the DNA interactions are more frequent within a given domain than with regions in other domains4,5.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [4]
Known TAD boundary signatures were observed around the boundary calls for each cell type.
“Furthermore, we observed known TAD boundary signatures4 around our boundary calls for each cell type (Extended Data Fig. 1c).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [4]
The median distance between the common boundaries was approximately 750 kb, consistent with the reported median TAD size in human cells.
“The median distance between the common boundaries was approximately 750 kb, consistent with the reported median TAD size in human cells4,19 (Extended Data Fig. 1e).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [4]
It has been suggested that SVs could lead to TAD fusions (also referred to as neo-TADs).
“Furthermore, it has also been suggested that SVs could lead to TAD fusions40 (also referred to as neo-TADs3,4);”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [4]
TADs were identified through Hi-C and their existence has been confirmed by alternative methods such as intrinsic 3C (i3C) and Genome Architecture Mapping (GAM).
“TADs were identified through Hi-C3,4 and their existence have since been confirmed by alternative methods such as intrinsic 3C (i3C),18 which avoids the cross-linking step and Genome Architecture Mapping (GAM),19 which avoids the ligation step.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [4]
TADs are somewhat conserved between different cell types and different species.
“TADs are somewhat conserved between different cell types and different species.4,20”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [4]
TADs are characterized by preferential contacts between loci inside the same TAD and insulation from loci in adjacent TADs.
“First, chromatin is organized into Topological Associating Domains (TADs) that are characterized by preferential contacts between loci inside the same TAD and insulation from loci in adjacent TADs.3,4”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [4]
CTCF and cohesin play an important functional role in TAD formation and maintenance.
“suggesting an important functional role of CTCF and cohesin in TAD formation and maintenance (Fig. 2A).”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [4]
∼18% of TAD boundaries appear to be partially resistant to CTCF loss, suggesting that additional boundary factors, such as active promoters and alternative architectural factors, may also play a role.
“Finally, ∼18% of TAD boundaries appear to be partially resistant to CTCF loss,10 suggesting that additional boundary factors, such as active promoters4 since engaged RNA Pol II can block cohesin extrusion46 as well as alternative architectural factors, may also play a role.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [4]
TAD boundaries are near universally enriched in CTCF and cohesin ChIP-Seq peaks.
“After TADs were discovered through Hi-C studies, it quickly became clear that TAD boundaries are near universally enriched in CTCF and cohesin ChIP-Seq peaks,3,4,16”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [4]
TADs constrain enhancer-gene interactions because most DNA contacts occur within the TADs.
“These TADs, which have similar boundaries in all human cell types examined, have been proposed to constrain enhancer-gene interactions because most DNA contacts occur within the TADs (Dixon et al., 2015; Dixon et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2012
TADs have similar boundaries in all human cell types examined.
“These TADs, which have similar boundaries in all human cell types examined, have been proposed to constrain enhancer-gene interactions because most DNA contacts occur within the TADs (Dixon et al., 2015; Dixon et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2012
Individual chromosomes are partitioned into megabase-sized topologically associating domains (TADs), regions with relatively high intradomain DNA interaction frequencies as measured by Hi-C chromosome conformation capture data.
“Furthermore, individual chromosomes are partitioned into megabase- sized topologically associating domains (TADs), regions with relatively high intradomain DNA interaction frequencies as measured by Hi-C chromosome conformation capture data (Dixon et al., 2012; Nora et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2012
TADs identified by processing Hi-C data with the Hidden Markov algorithm can also be identified when this algorithm is used to process cohesin ChIA-PET data.
“Nonetheless, the TADs identified by processing Hi-C data with the Hidden Markov algorithm (Dixon et al., 2012; Nora et al., 2012) can also be identified when this algorithm is used to process cohesin ChIA-PET data (Ji et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2012
Most TAD boundaries are shared by any two cell types.
“Studies on TADs have estimated that most TAD boundaries are shared by any two cell types (Dixon et al., 2015; Dixon et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2012
TAD boundaries are strikingly similar across cell types.
“the striking similarity of TAD boundaries across cell types (Dixon et al., 2015; Dixon et al., 2012)”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2012
Genome-wide, high-resolution understanding of chromosome cell-cycle dynamics is still limited by current technologies.
“genome-wide, high-resolution understanding of chromosome cell-cycle dynamics11 is still limited by current technologies”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [5]
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- Authors
- Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B.
- Affiliations
- Ludwig Cancer Research (BE)
- Harvard University (US)
- Corresponding author
- Ren, Bing
- Venue
- Nature
- Published
- 2012-04-11
- Volume
- 485
- Issue
- 7398
- Pages
- 376-380
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3356448
- OpenAlex
- W2070021921
- Cited by
- 6,829
- References
- 33
- Citations by year
- 2026: 356 · 2025: 432 · 2024: 550 · 2023: 544 · 2022: 567 · 2021: 690 · 2020: 661 · 2019: 629 · 2018: 568 · 2017: 524 · 2016: 423 · 2015: 351 · 2014: 237 · 2013: 220 · 2012: 66
- FWCI
- 112.45
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Centers for Disease Control and Prevention (R01GH003991)
- National Human Genome Research Institute (R01HG003991)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- topological domains, 3D genome organization, chromatin interactions, topologically associating domains, Hi-C, 5C, mouse X chromosome, X inactivation center, CTCF, heterochromatin, chromosome territories, embryonic stem cells, SINE retrotransposons
- MeSH terms
- CCCTC-Binding Factor, Animals, Binding Sites, Cell Differentiation, Chromatin, Chromosomes, Female, Heterochromatin, Humans, Male, Mammals, Repressor Proteins, RNA, Transfer, Genome, Evolution, Molecular, Genes, Essential, Short Interspersed Nucleotide Elements, Mice, Embryonic Stem Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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