The 3D genome

How chromosomes are positioned and folded within the nucleus has implications for gene regulation. In this Review, Kempfer and Pombo describe and evaluate methods for studying chromosome architecture and outline the insights they are providing about nuclear organization.

Different genomic regions are replicated at different times during the S phase of the cell cycle, forming early- and late-replicating domains that occupy different locations in the nucleus. The recent identification of specific DNA sequences and long non-coding RNAs that regulate DNA replication timing is providing key insights into the roles of replication timing and into timing and 3D organization.

The 3D organization of the genome is crucial for gametogenesis, embryogenesis and cell differentiation through its modulation of transcription, DNA replication and cell division. Recent studies have highlighted the roles of 3D chromatin dynamics, such as the formation of enhancer–promoter interactions in mammalian development.

For appropriate control of gene expression, enhancers must communicate with the right target genes at the right time, typically over large genomic distances. In this Review, Schoenfelder and Fraser discuss our latest understanding of long-range enhancer–promoter crosstalk, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.

Genome organization can regulate gene expression, but can gene expression regulate genome organization? Recent studies reveal that, although not required for higher-level genome organization, transcription has a role in the formation and stabilization of genomic subdomains and enhancer–promoter interactions.

High-resolution studies of chromosome conformation are revealing that the 3D genome is organized into smaller structural features than was previously supposed and is primarily composed of compartmental domains and CTCF loops. In this Perspectives article Rowley and Corces describe the latest views on the organizational drivers and principles of the 3D genome, and the interplay between genome activity and organization.

Mechanical cues from the microenvironment can be efficiently transmitted to the nucleus to engage in the regulation of genome organization and gene expression. Recent technological and theoretical progress sheds new light on the relationships between cell mechanics, nuclear and chromosomal architecture and gene transcription.

This Review summarizes our understanding of plant chromatin organization and positioning beyond the nucleosomal level, advanced by up-to-date chromatin conformation capture methods and visualization techniques, as well as discusses future directions.

The three-dimensional (3D) organization of eukaryote chromosomes regulates genome function and nuclear processes such as DNA replication, transcription and DNA-damage repair. Experimental and computational methodologies for 3D genome analysis have been rapidly expanding, with a focus on high-throughput chromatin conformation capture techniques and on data analysis.

Recent studies show that structural variation can alter the genome architecture, leading to changes in the regulation of gene expression that cause disease. The authors review the role of genetic structural variation in disease and the pathogenic potential of changes to the 3D genome.

The 4D Nucleome Network aims to map the spatial and dynamic organization of the human and mouse genomes to gain insight into the structure and biological functions of the nucleus.

Genome-wide mapping of regulatory elements will improve our understanding of how genetic variation in the noncoding genome affects disease phenotypes.

In this Review, the authors compare commonly used chromosome conformation capture techniques, describing their respective strengths and weaknesses, and provide advice for the end user on which approach and analysis method to use.

Mechanistic insights are emerging into how long non-coding RNAs (lncRNAs) regulate gene expression by coordinating regulatory proteins, localizing to genomic loci and shaping nuclear organization. Interestingly, lncRNAs can perform functions that cannot be carried out by DNA elements or proteins alone, such as amplifying regulatory signals in the nucleus.

Three-dimensional genome organization can shape gene expression by facilitating interactions between regulatory elements. The authors review the process of X-chromosome inactivation with a focus on chromatin organization and subnuclear localization of the active and inactive X chromosomes, as well as the potential roles of long non-coding RNAs.

Mutations in non-coding parts of the genome can cause disease. Technological advances are providing unprecedented detail on genome organization and folding, and have revealed that enhancer–target gene coupling is spatially restricted, as it occurs within topologically associated domains (TADs), and that disrupting such organization can lead to disease-associated gene dysregulation.

Job Dekker asserts that cases in which data from microscopy- and 3C-based methods appear discordant about genome organization will provide opportunities to improve our models of chromatin folding.

Genome-wide mapping of chromatin contacts reveals the structural and organizational changes that the metazoan genome undergoes during cell differentiation. These changes involve entire chromosomes, which are influenced by contacts with nuclear structures such as the lamina, and local interactions mediated by transcription factors and chromatin looping.

In this article the authors review current knowledge on chromatin architecture and the molecular mechanisms that underlie it. They discuss how three-dimensional (3D) organization of chromatin relates to gene expression, development and disease, and consider its effect on genome evolution.

Synthetic biology approaches to characterize gene regulation have largely used transcription factor circuits in bacteria. However, the multilayered regulation of genes by chromatin in eukaryotes provides opportunities for more sophisticated control of gene expression. This Review describes diverse approaches for engineering eukaryotic chromatin states, the insights gained into physiological gene regulation principles, and the broad potential applications throughout biomedical research and industry.

The evolution of genes is influenced by regional variation in mutation rates (RViMR). Chromatin organization affects RViMR, although the correlation between chromatin state and mutation types and rates is complex. This Review describes recent research on RViMR and chromatin organization, and the emerging findings from investigations of both germline and somatic mutations.

Promoter–enhancer loopings and other features of the 3D genome are dynamically regulated in the brain. In this Review, Akbarian and colleagues discuss how neuronal and glial gene expression is governed by the 3D genome, with implications for cognition and neuropsychiatric disease.

In this Review, Aifantis and colleagues describe recent insights into the epigenetic dysregulation of malignant blood stem cell differentiation.

The authors analyze time-resolved changes in genome topology, gene expression, transcription-factor binding, and chromatin state during iPSC generation. They conclude that 3D genome reorganization generally precedes gene expression changes and that removal of locus-specific topological barriers explains why pluripotency genes are activated sequentially during reprogramming.

Risk loci for breast cancer have been identified by genome-wide association studies. Here, the authors use Capture Hi-C to identify 110 putative target genes at 33 loci and assessed associations of gene expression, SNP genotype, and survival, providing evidence of mechanisms that may influence the prognosis and risk of breast cancer.

Transcriptional regulation is coupled with chromosomal positioning and chromatin architecture. Here the authors develop a transcriptional decomposition approach to separate expression associated with genome structure from independent effects not directly associated with genomic positioning.

Super-enhancers (SEs) are important regulatory elements for gene expression, but their intrinsic properties remain poorly understood. Here the authors analyse Hi-C and ChIP-seq data and find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers.

3DNetMod identifies nested topologically associating domains (TADs) and subTADs from Hi-C data.

Knowledge of three-dimensional (3D) genome structure and how polyploidization shapes it remains poor. A study now characterizes and compares 3D genomes for diploid and tetraploid cotton, showing how allopolyploidization affects 3D genome architecture and transcriptional regulation.

Transcriptome, DNA methylome and Hi-C profiling of peri- and post-implantation mouse cell lineages identified allele- and lineage-specific methylation patterns. Global demethylation and remethylation correlate with megabase chromatin compartments.

Baarlink et al. identify a transient pool of nuclear F-actin, the dynamics of which are controlled by cofilin-1 that accumulates after mitosis and is important for chromatin reorganization in G1.

Topologically associating domains (TADs) detected by Hi-C technologies are megabase-scale areas of highly interacting chromatin. Here Gong, Lazaris et al. develop a computational approach to improve the reproducibility of Hi-C contact matrices and stratify TAD boundaries based on their insulating strength.

Analysis of the 3D genomic organization of Schizosaccharomyces pombe during the cell cycle reveals that condensin mediates formation of large domains that serve as chromosomal compaction units, whereas cohesin forms smaller, more stable domains.

Genome-wide analyses of somatic mutations across six cancer types show that mutation frequencies differ between chromosomal regions located at the nuclear core versus the periphery, and thus mutational patterns are influenced by nuclear architecture.

Depletion of chromosome-associated cohesin leads to loss of topologically associating domains in interphase chromosomes, without affecting segregation into compartments, and instead, it unmasks a finer compartment structure that reflects local chromatin and transcriptional activity.

Topologically associating domain (TAD) boundaries in flies seem to be different from those in mammals. Here, the authors use Hi-C with sub-kb resolution to identify about 4000 TADs in flies, most demarcated by the insulator complexes BEAF-32/CP190 or BEAF-32/Chromator like CTCF/cohesin in mammals.

Although topologically associating domains (TADs) have been extensively investigated, it is not clear to what extent DNA sequence contributes to their formation. Here the authors develop software to identify high-resolution TAD boundaries and reveal their relationship to underlying DNA motifs.

High-resolution contact maps of active enhancers and target genes generated by H3K27ac HiChIP in primary human cells provide rational guides to link noncoding disease-associated risk variants to candidate causal genes. Genes are validated by CRISPR activation and interference at connected enhancers and eQTL analysis, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.

Spatial organization of the genome plays a crucial role in regulating gene expression. Here the authors introduce GMAP, the Gaussian Mixture model And Proportion test, to identify topologically associating domains and subdomains in Hi-C data.

Proximity-ligation methods like Hi-C map DNA-DNA interactions and reveal its organization into topologically associating domains (TADs). Here the authors describe PSYCHIC, a computational approach for analysing Hi-C data that allows the identification of promoter-enhancer interactions.

Chromosome conformation capture techniques enable the study of genome organization in cancer cells. Here, the authors use Hi-C, WGS, and RNA-seq to study the 3D genome of multiple myeloma and find that genome disorganization is associated with copy number variations and changes in gene expression.

Schalbetter et al. show by Hi-C and modelling that mitotic chromosome compaction in budding yeast occurs by cis-looping of chromatin, and reveal distinct roles for cohesin and condensin depending on chromatin context.

Adam Rubin, Brook Barajas, Mayra Furlan-Magaril and colleagues studied dynamic chromatin across the genome of differentiating human skin keratinocytes, identifying both stable and reorganizing classes of transcriptional enhancers.

Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic architecture.

Hanssen et al. show that CTCF–cohesin binding sites at the α-globin gene cluster function as boundaries to restrict the interaction of enhancers with the flanking chromatin, thus preventing abnormal gene expression.

Chromatin looping plays an important role in gene regulation and the ability to manipulate loops would aid in understanding how this occurs. Here the authors present CLOuD9, a system that uses dimerized Cas9 complexes to selectively and reversibly establish chromatin loops.

A low-input Hi-C method is used to show that chromatin organization is markedly relaxed in pre-implantation mouse embryos after fertilization and that the subsequent maturation of 3D chromatin architecture is surprisingly slow.

New analyses reveal that TERRA transcripts arising from the subtelomeric pseudoautosomal (PAR) region of sex chromosomes nucleate pairing of X alleles in mouse ES cells.

Single-cell Hi-C analysis in thousands of mouse embryonic stem cells shows that chromosomal compartments, topological-associated domains and long-range loops all have distinct cell-cycle dynamics.

Six tools to call chromatin interactions and seven tools for topologically associating domain calling are systematically compared with real and simulated data. The strengths and weaknesses of each tool are discussed.

This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.

Homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber, rather than CTCF occupancy, explain the 3D HoxB folding pattern.

The distribution of cohesin in the mouse genome depends on CTCF, transcription and the cohesin release factor Wapl.

Regulatory elements for specific human genes are rapidly identified with CRISPR epigenome editing.

Chatzinikolaou et al. show that the nucleotide excision repair complex ERCC1–XPF cooperates with the chromatin organizer CTCF, cohesin subunits and ATRX to facilitate the silencing of a subset of imprinted genes in the developing liver.

Using a single-nucleus Hi-C protocol, the authors find that spatial organization of chromatin during oocyte-to-zygote transition differs between paternal and maternal nuclei within a single-cell zygote.

A chromosome conformation capture method in which single cells are first imaged and then processed enables intact genome folding to be studied at a scale of 100 kb, validated, and analysed to generate hypotheses about 3D genomic interactions and organisation.

A technique called genome architecture mapping (GAM) involves sequencing DNA from a large number of thin nuclear cryosections to develop a map of genome organization without the limitations of existing 3C-based methods.

Capture Hi-C analysis reveals that DNA double-strand breaks within transcriptionally active regions of the human genome form clusters that exhibit delayed repair in the G1 phase of the cell cycle.

Single-cell combinatorial indexed Hi-C (sciHi-C) is a streamlined protocol for generating thousands of high-quality single-cell chromosome conformation data sets that resemble bulk Hi-C data in aggregate.

A conformation capture sequencing method is developed to link multiple genomic loci into three-dimensional proximity chains called chromosomal walks (C-walks), adding to our understanding of how higher-order chromosomal structures participate in genome regulation.

High-resolution three-dimensional maps of chromatin contacts in the developing human brain help to identify enhancer–promoter contacts, many of which are associated with human cognitive function and disease.

Genomic duplications in the SOX9 region are associated with human disease phenotypes; a study using human cells and mouse models reveals that the duplications can cause the formation of new higher-order chromatin structures called topologically associated domains (TADs) thereby resulting in changes in gene expression.

An in-depth analysis of the structure, chromatin accessibility and expression status of the mouse inactive X (Xi) chromosome provides insights into the regulation of Xi chromosome structure, its dependence on the macrosatellite DXZ4 region, the Xist non-coding RNA, as well as the basis for topologically associating domain (TAD) formation on the Xi.

Using super-resolution imaging to directly observe the three-dimensional organization of Drosophila chromatin at a scale spanning sizes from individual genes to entire gene regulatory domains, the authors find that transcriptionally active, inactive and Polycomb-repressed chromatin states each have a distinct spatial organisation.

An epigenetic mechanism in which gain-of-function IDH mutations promote gliomagenesis by disrupting chromosomal topology is presented, with IDH mutations causing the binding sites of the methylation-sensitive insulator CTCF to become hypermethylated; disruption of a CTCF boundary near the glioma oncogene PDGFRA allows a constitutive enhancer to contact and activate the oncogene aberrantly.

Genome-wide chromosome conformation capture analysis in C. elegans reveals that the dosage compensation complex, a condensin complex, remodels the X chromosomes of hermaphrodites into a sex-specific topology distinct from autosomes while regulating gene expression chromosome-wide.

Michael Talkowski and colleagues analyze balanced chromosomal abnormalities in 273 individuals by whole-genome sequencing. Their findings suggest that sequence-level resolution improves prediction of clinical outcomes for balanced rearrangements and provides insight into pathogenic mechanisms such as altered gene regulation due to changes in chromosome topology.

Sean Whalen and colleagues present a computational method, TargetFinder, for reconstructing three-dimensional regulatory landscapes using one-dimensional genomic features. TargetFinder identifies the minimal set of features necessary to predict individual interacting enhancer–promoter pairs and accurately distinguishes them from non-interacting pairs.

José Luis Gómez-Skarmeta, Hector Escrivá, Ignacio Maeso, Damien Devos and colleagues perform 4C-seq profiling of the Hox cluster in amphioxus embryos and find that, unlike in vertebrate embryos, the cluster is organized into a single chromatin interaction domain. They suggest that the vertebrate Hox bipartite regulatory system is an evolutionary novelty.

Sarah Elderkin and colleagues show that PRC1 acts as a master regulator of genome architecture in mouse embryonic stem cells by organizing genes in three-dimensional interaction networks. They find that the strongest spatial network is composed of the four Hox clusters and key early developmental transcription factor genes, and they propose that selective release of genes from this spatial network underlies cell fate specification during embryonic development.

Nicholas Luscombe, Cameron Osborne and colleagues report the use of Capture Hi-C (CHi-C) to detect the long-range interactions of almost 22,000 promoters in 2 human cell types. They found that transcriptionally inactive genes interact with previously uncharacterized elements that may act as long-range silencers.

Douglas Higgs and colleagues functionally test the α-globin super-enhancer in mice by genetically deleting its constituent enhancers. They find that the individual regulatory elements seem to act independently and in an additive way with respect to hematological phenotype, gene expression, and chromatin structure and conformation.

Peter Scacheri and colleagues identify ‘outside’ SNPs that physically interact with GWAS risk SNPs as part of a target gene's regulatory circuitry. Their findings suggest a model whereby outside variants and GWAS SNPs that physically interact collude to influence target transcript levels as well as clinical risk.

Ken-ichi Noma and colleagues use ChIA-PET to identify genome-wide associations mediated by condensin and cohesin in fission yeast. They find that cohesin and condensin generate small and larger chromatin domains, respectively, and that condensin, but not cohesin, connects cell cycle–regulated genes bound by mitotic transcription factors.

B lineage development requires the transcription factors E2A, EBF1, Foxo1 and Ikaros. Murre and colleagues show that these factors gain access to lineage-specific enhancer sites by the action of the chromatin remodeler Brg1.

Tcra and Tcrd segments are embedded within a single locus but undergo distinct temporal rearrangements. Krangel and colleagues show that chromatin looping mediated by CTCF regulates the availability of variable gene segments to the RAG recombinase.

The covalent insertion of fluorophore-labeled DNA adaptors by Tn5 transposase into open chromatin allows its imaging and subsequent analysis by sequencing from exactly the same samples.

HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest.

The combination of short and long crosslinkers during chromosome conformation capture allows the interrogation of structure from the nucleosome to the chromosome-wide level in yeast.

UMI-4C is a rapid, simplified barcoding approach to targeted chromatin conformation capture that produces high-complexity libraries from low sample input, is easily multiplexed and gives a quantitative, statistically defined readout.

Targeted DNase Hi-C uses DNase I instead of restriction enzymes for chromatin fragmentation and improves the resolution of chromatin interaction maps.

Pooling barcoded 3C libraries and simultaneously capturing interactions at many loci of interest generates reproducible cis- and trans-interaction maps at high resolution from low amounts of input material. This allows for the comparison of interactions in different cell types using common software designed for differential analysis of sequence count data, rather than requiring software specifically designed for 3C experiments.

Retroviruses such as HIV integrate into the host genome as an essential step prior to their replication. Here Lelek et al. identify nuclear pore complex proteins that are essential for HIV nuclear import and productive integration, and show that the intranuclear protein Tpr influences integration into transcriptionally active chromatin.

Nuclear lamins mediate interactions between chromatin and the nuclear envelope, however they are also found throughout the nucleoplasm. By measuring the dynamics of different genomic loci, Bronshtein et al.show that lamin A is also required for the stability of the nuclear interior.

Polycomb Group (PcG) proteins regulate gene expression and genome architecture. Using super-resolution microscopy and molecular simulations, Waniet al. describe the organization of PcG proteins into hundreds of nano-scale protein clusters and suggest these clusters shape genome architecture.

The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in 3D space. Here, Zhang et al.present an algorithm integrating ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs.

Chromosome conformation is a dynamic process, especially in brain. Here, Mitchell and colleagues devise a method they call NeuroDam that can prospectively tag chromosome conformation in the mouse brain in vivo, and longitudinally assess long range chromosome looping weeks and months later.

Chromatin architecture is a key regulator of transcriptional processes, however current methods to investigate it have technical limitations. Here, the authors describe a novel chromatin capture technique, CATCH, which can be used to identify and characterize complex genomic interaction networks.

This protocol describes targeted chromatin capture (T2C), a high-resolution method to interrogate 3D chromatin organization and genomic interactions at sub-kilobase-pair resolution that requires minimal cell numbers and sequencing depth.

This protocol describes how to prepare samples for labeling nuclei of cultured mammalian cells for 3D structured illumination microscopy of nuclear structures. Image acquisition, registration and downstream image analysis are also described.

Li et al. provide a protocol for long-read ChIA-PET, a technique for mapping chromatin interactions. The longer paired-end tags, which are generated by tagmentation, provide sufficient coverage to determine haplotype-specific chromatin interactions at single-nucleotide resolution.

Ramani et al. describe a protocol for in situ DNase Hi-C as an alternative to traditional Hi-C methods that use restriction enzymes. The use of DNase I for chromatin digestion circumvents the resolution limit imposed when relying on genomic restriction sites.