Breaking TADs: Insights into Hierarchical Genome Organization

EpigenomicsVol. 7, No. 4 OpinionBreaking TADs: insights into hierarchical genome organizationPedro P Rocha, Ramya Raviram, Richard Bonneau & Jane A SkokPedro P Rocha Department of Pathology, New York University School of Medicine, New York, NY 10016, USA, Ramya Raviram Department of Pathology, New York University School of Medicine, New York, NY 10016, USA, Richard Bonneau Department of Biology, New York University, New York, NY 10003, USA Department of Computer Science, Courant Institute of Mathematical Sciences, New York, NY 10003, USA Simons Center for Data Analysis, New York, NY 10010, USA & Jane A Skok*Author for correspondence: E-mail Address: jane.skok@med.nyu.edu Department of Pathology, New York University School of Medicine, New York, NY 10016, USAPublished Online:25 Jun 2015https://doi.org/10.2217/epi.15.25AboutSectionsView ArticleView Full TextPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareShare onFacebookTwitterLinkedInReddit View articleKeywords: chromosome confirmation capturegene regulationHi-Cnuclear organizationTADsReferences1 Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2(4), 292–301 (2001).Crossref, Medline, CAS, Google Scholar2 Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 295(5558), 1306–1311 (2002).Crossref, Medline, CAS, Google Scholar3 Lieberman-Aiden E, Van Berkum NL, Williams L et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289–293 (2009).Crossref, Medline, CAS, Google Scholar4 Nora EP, Lajoie BR, Schulz EG et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398), 381–385 (2012).Crossref, Medline, CAS, Google Scholar5 Dixon JR, Selvaraj S, Yue F et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398), 376–380 (2012).Crossref, Medline, CAS, Google Scholar6 Sexton T, Yaffe E, Kenigsberg E et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148(3), 458–472 (2012).Crossref, Medline, CAS, Google Scholar7 Schoenfelder S, Furlan-Magaril M, Mifsud B et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 25(4), 582–597 (2015).Crossref, Medline, CAS, Google Scholar8 Dowen JM, Fan ZP, Hnisz D et al. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159(2), 374–387 (2014).Crossref, Medline, CAS, Google Scholar9 Dixon JR, Jung I, Selvaraj S et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518(7539), 331–336 (2015).Crossref, Medline, CAS, Google Scholar10 Le Dily F, Bau D, Pohl A et al. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev. 28(19), 2151–2162 (2014).Crossref, Medline, CAS, Google Scholar11 Van Bortle K, Nichols MH, Li L et al. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol. 15(6), R82 (2014).Crossref, Medline, Google Scholar12 Andrey G, Montavon T, Mascrez B et al. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 340(6137), 1234167 (2013).Crossref, Medline, CAS, Google Scholar13 Narendra V, Rocha PP, An D et al. Transcription. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science 347(6225), 1017–1021 (2015).Crossref, Medline, CAS, Google Scholar14 Vietri Rudan M, Barrington C, Henderson S et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 10(8), 1297–1309 (2015).Crossref, Medline, CAS, Google Scholar15 Phillips-Cremins JE, Sauria ME, Sanyal A et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153(6), 1281–1295 (2013).Crossref, Medline, CAS, Google Scholar16 Rao SS, Huntley MH, Durand NC et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7), 1665–1680 (2014).Crossref, Medline, CAS, Google Scholar17 Giorgetti L, Galupa R, Nora EP et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157(4), 950–963 (2014).Crossref, Medline, CAS, Google Scholar18 Lajoie BR, Dekker J, Kaplan N. The Hitchhiker's guide to Hi-C analysis: practical guidelines. Methods 72, 65–75 (2015).Crossref, Medline, CAS, Google Scholar19 Noordermeer D, De Wit E, Klous P et al. Variegated gene expression caused by cell-specific long-range DNA interactions. Nat. Cell Biol. 13(8), 944–951 (2011).Crossref, Medline, CAS, Google Scholar20 Chaumeil J, Micsinai M, Ntziachristos P et al. The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage. Nat. Commun. 4, 2231 (2013).Crossref, Medline, Google ScholarFiguresReferencesRelatedDetailsCited ByUmifenovir Epigenetically Targets the IL-10 Pathway in Therapy against Coxsackievirus B4 InfectionMicrobiology Spectrum, Vol. 11, No. 1MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal networkCell Reports Methods, Vol. 3, No. 1A comparison of topologically associating domain callers over mammals at high resolution12 April 2022 | BMC Bioinformatics, Vol. 23, No. 1Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages23 July 2022 | Nature Communications, Vol. 13, No. 1Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants19 August 2022 | Frontiers in Cell and Developmental Biology, Vol. 10Multi-Omic Epigenetic-Based Model Reveals Key Molecular Mechanisms Associated with Palmitic Acid Lipotoxicity in Human Astrocyte30 March 2022A comparison of topologically associating domain callers based on Hi-C dataIEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 10Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastomaComputational and Structural Biotechnology Journal, Vol. 20CASPIAN: A method to identify chromatin topological associated domains based on spatial density clusterComputational and Structural Biotechnology Journal, Vol. 20SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information25 January 2021 | Genome Biology, Vol. 22, No. 1Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C28 August 2021 | Epigenetics & Chromatin, Vol. 14, No. 1Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches18 August 2021 | Human Genetics, Vol. 140, No. 10Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis3 June 2021 | Genome Research, Vol. 31, No. 7The chicken model organism for epigenomic researchGenome, Vol. 64, No. 4A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C16 March 2021 | PLOS Computational Biology, Vol. 17, No. 3Super enhancers—Functional cores under the 3D genome17 December 2020 | Cell Proliferation, Vol. 54, No. 2Wheat chromatin architecture is organized in genome territories and transcription factories29 April 2020 | Genome Biology, Vol. 21, No. 1Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection22 January 2019 | BMC Genomics, Vol. 20, No. 1Hi-C analysis: from data generation to integration20 December 2018 | Biophysical Reviews, Vol. 11, No. 1Comparison of computational methods for the identification of topologically associating domains10 December 2018 | Genome Biology, Vol. 19, No. 1Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate13 December 2018 | Genome Biology, Vol. 19, No. 1Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries7 February 2018 | Nature Communications, Vol. 9, No. 1Epigenetic Regulation in Neurodegenerative DiseasesTrends in Neurosciences, Vol. 41, No. 9Condensin Depletion Causes Genome Decompaction Without Altering the Level of Global Gene Expression in Saccharomyces cerevisiae1 September 2018 | Genetics, Vol. 210, No. 1Genome-wide profiling of transcribed enhancers during macrophage activation23 October 2017 | Epigenetics & Chromatin, Vol. 10, No. 1The role of human host genetics in tuberculosis resistance20 July 2017 | Expert Review of Respiratory Medicine, Vol. 11, No. 9A critical assessment of topologically associating domain prediction tools2 March 2017 | Nucleic Acids Research, Vol. 45, No. 6Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution23 April 2018 | Cold Spring Harbor Symposia on Quantitative Biology, Vol. 82Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions20 July 2016 | Nucleic Acids Research, Vol. 44, No. 18CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci25 May 2016 | Nature Communications, Vol. 7, No. 1RAG Off-Target Activity Is in the LoopTrends in Molecular Medicine, Vol. 21, No. 12 Vol. 7, No. 4 Follow us on social media for the latest updates Metrics Downloaded 431 times History Published online 25 June 2015 Published in print June 2015 Information© Future Medicine LtdKeywordschromosome confirmation capturegene regulationHi-Cnuclear organizationTADsFinancial & competing interests disclosurePP Rocha is supported by an ASH fellowship. R Bonneau is supported by the Simons Foundation. JA Skok is a Leukemia and Lymphoma Society (LLS) scholar and is supported by NIH grants R01 GM086852, NIAID R56 A1099111, R21AI107069 and R01GM112192. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.No writing assistance was utilized in the production of this manuscript.PDF download