3D chromatin architecture and transcription regulation in cancer

Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer–promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.

• Publication year

  2022

• Venue

  Journal of Hematology & Oncology

• Publication date

  2022-05-04

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/s13045-022-01271-xPMID 35509102PMCID 9069733
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

  2023cited by this paper
• HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.

  2022cited by this paper
• Hallmarks of Cancer: New Dimensions.

  2022cited by this paper
• Liquid–liquid phase separation drives cellular function and dysfunction in cancer

  2022cited by this paper
• The noncanonical role of EZH2 in cancer

  2021cited by this paper
• Cohesin Mutations in Cancer: Emerging Therapeutic Targets

  2021cited by this paper
• In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin

  2021cited by this paper
• Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation.

  2021cited by this paper
• Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability.

  2021cited by this paper
• Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

  2021cited by this paper
• Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression.

  2021cited by this paper
• STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma.

  2021cited by this paper
• Acute depletion of CTCF rewires genome-wide chromatin accessibility

  2021cited by this paper
• Enhancers navigate the three-dimensional genome to direct cell fate decisions.

  2021cited by this paper
• ecDNA hubs drive cooperative intermolecular oncogene expression

  2021cited by this paper
• The Role of Polycomb Group Protein BMI1 in DNA Repair and Genomic Stability

  2021cited by this paper
• Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

  2021cited by this paper
• Phase separation of EML4–ALK in firing downstream signaling and promoting lung tumorigenesis

  2021cited by this paper
• Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.

  2021cited by this paper
• Genome folding through loop extrusion by SMC complexes

  2021cited by this paper
• SIRT3 consolidates heterochromatin and counteracts senescence

  2021cited by this paper
• SMARCA2 Is a Novel Interactor of NSD2 and Regulates Prometastatic PTP4A3 through Chromatin Remodeling in t(4;14) Multiple Myeloma

  2021cited by this paper
• CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

  2021cited by this paper
• CTCF and EGR1 suppress breast cancer cell migration through transcriptional control of Nm23-H1

  2021cited by this paper
• PDS5A and PDS5B in Cohesin Function and Human Disease

  2021cited by this paper
• Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation

  2021cited by this paper
• 3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia

  2021cited by this paper
• Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2

  2021cited by this paper
• Transcriptional enhancers and their communication with gene promoters

  2021cited by this paper
• CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells

  2021cited by this paper
• Histo-molecular characterization of pancreatic cancer with microsatellite instability: intra-tumor heterogeneity, B2M inactivation, and the importance of metastatic sites

  2021cited by this paper
• Going beyond Polycomb: EZH2 Functions in Prostate Cancer

  2021cited by this paper
• Distinct nuclear compartment-associated genome architecture in the developing mammalian brain

  2021cited by this paper
• CTCF binding modulates UV damage formation to promote mutation hot spots in melanoma

  2021cited by this paper
• ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

  2021cited by this paper
• Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

  2021cited by this paper
• The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis

  2021cited by this paper
• DamID to Map Genome-Protein Interactions in Preimplantation Mouse Embryos.

  2021cited by this paper
• Small ring has big potential: insights into extrachromosomal DNA in cancer

  2021cited by this paper
• LINC complex regulation of genome organization and function.

  2021cited by this paper
• Mammalian SWI/SNF continuously restores local accessibility to chromatin

  2021cited by this paper
• CTCF Mediates Replicative Senescence Through POLD1

  2021cited by this paper
• Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer.

  2021cited by this paper
• Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions

  2021cited by this paper
• A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression

  2021cited by this paper
• On the choreography of genome folding: A grand pas de deux of cohesin and CTCF.

  2021cited by this paper
• The Nuclear Lamina.

  2021cited by this paper
• Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization

  2021cited by this paper
• The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts

  2021cited by this paper
• 3D chromatin architecture and epigenetic regulation in cancer stem cells

  2021cited by this paper
• Glycogen accumulation and phase separation drives liver tumor initiation.

  2021cited by this paper
• Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4

  2021cited by this paper
• Promoter-proximal CTCF-binding promotes long-range-enhancer dependent gene activation

  2021cited by this paper
• Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures

  2021cited by this paper
• Increased ACTL6A Occupancy Within mSWI/SNF Chromatin Remodelers Drives Human Squamous Cell Carcinoma

  2021cited by this paper
• CTCF and transcription influence chromatin structure re-configuration after mitosis

  2021cited by this paper
• HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

  2021cited by this paper
• The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization

  2021cited by this paper
• Cohesin mutations in myeloid malignancies.

  2021cited by this paper
• CTCF as a regulator of alternative splicing: new tricks for an old player

  2021cited by this paper
• Phase separation drives aberrant chromatin looping and cancer development

  2021cited by this paper
• Assessing acute myeloid leukemia susceptibility in rearrangement‐driven patients by DNA breakage at topoisomerase II and CCCTC‐binding factor/cohesin binding sites

  2021cited by this paper
• Nuclear lamin phosphorylation: an emerging role in gene regulation and pathogenesis of laminopathies

  2020cited by this paper
• Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture.

  2020cited by this paper
• Novel insights into extrachromosomal DNA: redefining the onco-drivers of tumor progression

  2020cited by this paper
• A complex regulatory landscape involved in the development of mammalian external genitals

  2020cited by this paper
• EZH2-Targeted Therapies in Cancer: Hype or a Reality

  2020cited by this paper
• ARID2 Chromatin Remodeler in Hepatocellular Carcinoma

  2020cited by this paper
• Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure

  2020cited by this paper
• CTCF and CTCFL in cancer.

  2020cited by this paper
• The meiosis-specific cohesin component stromal antigen 3 promotes cell migration and chemotherapeutic resistance in colorectal cancer.

  2020cited by this paper
• Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

  2020cited by this paper
• Probing multi-way chromatin interaction with hypergraph representation learning

  2020cited by this paper
• H3K79me2/3 controls enhancer–promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells

  2020cited by this paper
• Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction

  2020cited by this paper
• Risk SNP-Mediated Enhancer–Promoter Interaction Drives Colorectal Cancer through Both FADS2 and AP002754.2

  2020cited by this paper
• The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage

  2020cited by this paper
• Enhancer–promoter interactions and transcription

  2020cited by this paper
• Revisiting 3D chromatin architecture in cancer development and progression

  2020cited by this paper
• HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

  2020cited by this paper
• Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ

  2020cited by this paper
• The Self-Organizing Genome: Principles of Genome Architecture and Function.

  2020cited by this paper
• A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells

  2020cited by this paper
• Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

  2020cited by this paper
• Progresses in the plant 3D chromatin architecture.

  2020cited by this paper
• Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin.

  2020cited by this paper
• Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)

  2020cited by this paper
• Loop competition and extrusion model predicts CTCF interaction specificity

  2020cited by this paper
• Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation.

  2020cited by this paper
• Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication.

  2020cited by this paper
• Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation

  2020cited by this paper
• BRD9 Is a Critical Regulator of Androgen Receptor Signaling and Prostate Cancer Progression

  2020cited by this paper
• The 3D Genome as a Target for Anticancer Therapy.

  2020cited by this paper
• ARID2 deficiency correlates with the response to immune checkpoint blockade in melanoma.

  2020cited by this paper
• EZH2: a novel target for cancer treatment

  2020cited by this paper
• Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML

  2020cited by this paper
• Downregulation of APRIN expression increases cancer cell proliferation via an interleukin-6/STAT3/cyclin D axis

  2020cited by this paper
• Regulation of 3D chromatin organization by CTCF.

  2020cited by this paper
• Post-translational modifications of EZH2 in cancer

  2020cited by this paper
• Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation

  2020cited by this paper

• Chromatin architecture and physical constriction cooperate in phenotype switching and cancer cell dissemination

  2026cites this paper
• Nucleosome Clustering as a Biomarker and Mechanistic Switch for Reprogramming Cells

  2026cites this paper
• The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity

  2025cites this paper
• RAD21-mediated epigenetic regulation promotes lung adenocarcinoma progression and sensitizes cancer cells to ERK-targeted therapy.

  2025cites this paper
• Repeats Influence Structural DNA Properties Around Functional Annotations Associated with 3D Organization and Transcription

  2025cites this paper
• Trans-Scale Insights into Variability in Radiation Cancer Risk Across Tissues, Individuals, and Species

  2025cites this paper
• Enhancer regulation in cancer: from epigenetics to m6A RNA modification

  2025cites this paper
• DNA methylation variations of DNA damage response in glioblastoma: NSUN5 modulates tumor-intrinsic cytosolic DNA-sensing and microglial behavior

  2025cites this paper
• DNA Methylation Concurrence, Independent of DNA Methylation Ratios, Is Associated with Chromatin Accessibility and 3D Genome Architecture

  2025cites this paper
• Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy

  2025cites this paper
• Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications

  2025cites this paper
• Satb1 integrates cohesin mediated genome organization and transcriptional regulation during T cell development

  2025cites this paper
• Nuclear envelope proteins, mechanotransduction, and their contribution to breast cancer progression

  2025cites this paper
• Generating three-dimensional genome structures with a variational quantum algorithm

  2025cites this paper
• Unveiling chromatin dynamics with virtual epigenome

  2025influential citation
• At the nucleus of cancer: how the nuclear envelope controls tumor progression

  2025cites this paper
• Interplay Between 3D Chromatin Architecture and Gene Regulation at the APOE Locus Contributes to Alzheimer’s Disease Risk

  2025cites this paper
• Development of high-titer class-switched antibody responses to phosphorylated amino acids is prevalent in pancreatic ductal adenocarcinoma

  2025cites this paper
• Beyond the DNA sequence: mapping the dynamic epigenetic landscape for risk stratification and therapeutic intervention in acute myeloid leukemia

  2025cites this paper
• Interaction of CTCF and CTCFL in genome regulation through chromatin architecture during the spermatogenesis and carcinogenesis

  2024cites this paper
• Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer

  2024cites this paper
• Crosstalk between colorectal CSCs and immune cells in tumorigenesis, and strategies for targeting colorectal CSCs

  2024cites this paper
• Alteration of chromosome structure impacts gene expressions implicated in pancreatic ductal adenocarcinoma cells

  2024cites this paper
• Epigenetic dynamics of aging and cancer development: current concepts from studies mapping aging and cancer epigenomes

  2024cites this paper
• Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells

  2024influential citation
• Building Haplotype‐Resolved 3D Genome Maps of Chicken Skeletal Muscle

  2024cites this paper
• Advances in the multimodal analysis of the 3D chromatin structure and gene regulation

  2024cites this paper
• 3C methods in cancer research: recent advances and future prospects

  2024cites this paper
• Integrated enhancer regulatory network by enhancer–promoter looping in gastric cancer

  2024cites this paper
• Molecular insights into regulatory RNAs in the cellular machinery

  2024cites this paper
• Exploring the molecular basis of diapause I induction in the annual killifish Garcialebias charrua: a transcriptomic approach

  2024cites this paper
• CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection

  2024cites this paper
• Reversible acetylation of HDAC8 regulates cell cycle

  2024cites this paper
• The uncertainties and certainties of gene transcription in a human tumor cell

  2024cites this paper
• A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer–promoter communication

  2024cites this paper
• SATB2 and circ3915 RNA chromatin dysregulation drive KRAS-like oncogenic transformation

  2024cites this paper
• HTAD: a human-in-the-loop framework for supervised chromatin domain detection

  2024cites this paper
• Epigenetic therapies in cancer treatment: Opportunities and challenges

  2024cites this paper
• The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update.

  2023cites this paper
• Epigenetic remodelling under hypoxia.

  2023cites this paper
• Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations

  2023cites this paper
• How a disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization

  2023cites this paper
• Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis

  2023cites this paper
• Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review.

  2023cites this paper
• Targeting Transcription Factor YY1 for Cancer Treatment: Current Strategies and Future Directions

  2023cites this paper
• Three‐dimensional genome structure and function

  2023cites this paper
• Chromosome conformation capture technologies as tools to detect structural variations and their repercussion in chromatin 3D configuration

  2023cites this paper
• Embryonic transcription and epigenetics: root of the evil

  2023cites this paper
• Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1

  2023cites this paper
• Epigenetically programmed resistance to chemo- and immuno-therapies.

  2023cites this paper
• Regulation of loop extrusion on the interphase genome

  2023cites this paper
• Characterization of network hierarchy reflects cell state specificity in genome organization

  2022cites this paper
• AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization

  2022cites this paper
• Recent advances in the chromatin-based mechanism of FLOWERING LOCUS C repression through autonomous pathway genes

  2022cites this paper
• Restructuring of Lamina-Associated Domains in Senescence and Cancer

  2022cites this paper