Activation of proto-oncogenes by disruption of chromosome neighborhoods
Open accessAbstract
The spread of bad neighborhoods: Our genomes have complex three-dimensional (3D) arrangements that partition and regulate gene expression. Cancer cells frequently have their genomes grossly rearranged, disturbing this intricate 3D organization. Hnisz et al. show that the disruption of these 3D neighborhoods can bring oncogenes under the control of regulatory elements normally kept separate from them (see the Perspective by Wala and Beroukim). These novel juxtapositions can result in the inappropriate activation of oncogenes. Science , this issue p. 1454 ; see also p. 1398
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Genetic perturbation of CTCF binding has been shown to result in misregulation of gene expression in various cell lines and cancer.
“While genetic perturbation of CTCF binding has been shown to result in misregulation of gene expression in various cell lines and cancer9–11,28”
From Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (2017) · cites this paper as [10]
Boundary disruption has been linked to cancer and diseases of limb development.
“Boundary disruption has recently been linked to cancer and diseases of limb development (Flavahan et al., 2016; Hnisz et al., 2016; Lupianez et al., 2015)”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Hnisz et al., 2016
Recent high-resolution Chromosome-Conformation-Capture sequencing studies have revealed that TAD boundaries are perturbed in rare human limb malformation diseases and certain types of cancers, leading to enhancer miswiring and pathogenic disruption of gene expression.
“Recent high-resolution Chromosome-Conformation-Capture sequencing studies have revealed that TAD boundaries are perturbed in rare human limb malformation diseases (Lupianez et al., 2015) and certain types of cancers (Flavahan et al., 2016; Hnisz et al., 2016), leading to enhancer miswiring and pathogenic disruption of gene expression.”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Hnisz et al., 2016
Several other studies have reported the deregulation of chromatin folding structures in different cancer types.
“Several other studies have reported the deregulation of chromatin folding structures in different cancer types11,15,16.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [15]
CRISPR/Cas9 deletion of CTCF binding sites at the anchors of insulated neighborhoods produces changes in the expression of genes within the neighborhoods and immediately adjacent to the deleted neighborhood boundary.
“In a dozen loci and in multiple cell types, CRISPR/Cas9 deletion of CTCF binding sites at the anchors of insulated neighborhoods have been shown to produce changes in the expression of genes within the neighborhoods and immediately adjacent to the deleted neighborhood boundary.”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
Somatic mutations occur frequently and recurrently in the loop anchors of oncogene-containing insulated neighborhoods in a variety of cancer cells.
“Somatic mutations occur frequently and recurrently in the loop anchors of oncogene-containing Insulated neighborhoods in a variety of cancer cells (Figure 2E).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
In T cell leukemia cells, ~90% of all enhancer or promoter-related DNA loops occur within insulated neighborhood boundaries.
“Similarly, in T cell leukemia cells, ~90% of all enhancer or promoter-related DNA loops occur within insulated neighborhood boundaries (Hnisz et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
Silent proto-oncogenes typically occur within insulated neighborhoods and genetic modification of the neighborhood loop anchors can cause activation of these oncogenes.
“Silent proto-oncogenes typically occur within insulated neighborhoods and genetic modification of the neighborhood loop anchors can cause activation of these oncogenes (Flavahan et al., 2016; Hnisz et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
The vast majority of enhancer-gene interactions occur within insulated neighborhoods.
“The vast majority of enhancer-gene interactions occur within insulated neighborhoods (Dowen et al., 2014; Hnisz et al., 2016; Ji et al., 2016; Phillips-Cremins et al., 2013).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
Mutations that alter the loop anchor sites of oncogene-containing insulated neighborhoods make an important contribution to the misregulation of gene expression that is inherent to the cancer state.
“These observations are consistent with the idea that mutations that alter the loop anchor sites of oncogene-containing insulated neighborhoods make an important contribution to the misregulation of gene expression that is inherent to the cancer state (Flavahan et al., 2016; Hnisz et al., 2016; Katainen et al., 2015).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
Chromosomal rearrangements such as translocations or deletions which activate oncogenes also disrupt insulated neighborhoods around those genes without altering the sequence of the gene itself.
“Furthermore, chromosomal rearrangements such as translocations or deletions which activate oncogenes also disrupt insulated neighborhoods around those genes without altering the sequence of the gene itself (Groschel et al., 2014; Hnisz et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
Approximately 80% of insulated neighborhood boundaries are shared by any two cell types.
“Studies on insulated neighborhoods have estimated that approximately 80% of neighborhood boundaries of shared by any two cell types (Hnisz et al., 2016; Ji et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2016
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“Transcriptional enhancers normally interact with their target genes through the formation of DNA loops (5-7), which typically are constrained within larger CTCF-cohesin mediated loops called insulated neighborhoods (8-10), which in turn can form clusters that contribute to topologically associating domains (TADs) (11,…”
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“Transcriptional enhancers normally interact with their target genes through the formation of DNA loops (5-7), which typically are constrained within larger CTCF-cohesin mediated loops called insulated neighborhoods (8-10), which in turn can form clusters that contribute to topologically associating domains (TADs) (11,…”
BackgroundMolecular Genetics of Acute Lymphoblastic Leukemia
Armstrong, S. A., & Look, A. T. (2005) · Journal of Clinical Oncology · doi:10.1200/jco.2005.05.047 · Cited by 358 · cited 1× · see citing works
“A T-cell acute lymphoblastic leukemia (TALL) cell (Jurkat) was selected for these studies because key T-ALL oncogenes and genetic alterations are well-known (13, 14).”
BackgroundSite‐specific recombination of the tal‐1 gene is a common occurrence in human T cell leukemia.
Brown, J. L., Cheng, J. T., Chen, Q., Siciliano, M. J., Crist, W., Buchanan, G., & Baer, R. J. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07535.x · Cited by 339 · cited 4× · see citing works
“Several patient deletions, however, retained the TAL1 promoter SCIENCE sciencemag.org 25 MARCH 2016 • VOL 351 ISSUE 6280 1455 TAL1 9 8 ChIA-PET interactions: 40k 10 kb CTCF H3K27Ac RNA-Seq 72 kb 9 8 ChIA-PET interactions: 40k 115 kb 10 kb CTCF H3K27Ac RNA-Seq LMO2 Insulated neighborhood: Insulated neighborhood: LMO2 C…”
BackgroundInfluentialKieffer-Kwon, K.-R., Tang, Z., Mathé, E. A., Qian, J., Sung, M., Li, G., Resch, W., Baek, S., Pruett, N. D., Grøntved, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.039 · Cited by 326 · see citing works
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions
Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.048 · Cited by 319 · cited 3× · see citing works
“We have analyzed our ChIA-PET data using two analytical approaches: one that estimates the background contact frequency based on the genomic proximity bias (Mango pipeline) adapted from previous reports (24, 30, 40), and an analytical approach that estimates the background contact frequency based on the ligation frequ…”
BackgroundMethodSeitan, V. C., Faure, A. J., Zhan, Y., McCord, R. P., Lajoie, B. R., Ing-Simmons, E., Lenhard, B., Giorgetti, L., Heard, E., Fisher, A. G., et al. (2013) · Genome Research · doi:10.1101/gr.161620.113 · Cited by 318 · cited 3× · see citing works
“at the CD3 and GATA3 loci (41, 42) (Table S2A-B).”
BackgroundSelf-citationChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Li, G., Fullwood, M. J., Han, X., Mulawadi, F. H., Velkov, S., Vega, V. B., Ariyaratne, P. N., Mohamed, Y. B., Ooi, H.-S., Tennakoon, C., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-2-r22 · Cited by 316 · cited 3× · see citing works
“pipeline was adapted from a previous report (8) and was recently developed based on multiple previous studies (15, 32, 39).”
MethodInfluentialRoss-Innes, C. S., Becq, J., Warren, A., Cheetham, R. K., Northen, H., O’Donovan, M., Malhotra, S., di Pietro, M., Ivakhno, S., He, M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3357 · Cited by 299 · see citing works
Genome-wide map of regulatory interactions in the human genome
Heidari, N., Phanstiel, D. H., He, C., Grubert, F., Jahanbani, F., Kasowski, M., Zhang, M. Q., & Snyder, M. P. (2014) · Genome Research · doi:10.1101/gr.176586.114 · Cited by 278 · cited 2× · see citing works
“A recent study noted that mutations in CTCF binding sites occur frequently in cancers (23), but it is unclear if mutations in boundaries are common as only a subset of CTCF sites form insulated neighborhoods (8, 10, 24).”
BackgroundExploring long-range genome interactions using the WashU Epigenome Browser
Zhou, X., Lowdon, R. F., Li, D., Lawson, H. A., Madden, P. A. F., Costello, J., & Wang, T. (2013) · Nature Methods · doi:10.1038/nmeth.2440 · Cited by 209 · see citing works
Analysis of long-range chromatin interactions using Chromosome Conformation Capture
Naumova, N., Smith, E. M., Zhan, Y., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.07.022 · Cited by 178 · cited 1× · see citing works
“Generation of 5C libraries 3C was performed with HindIII restriction enzyme as previously described with some minor modifications (34, 57).”
MethodSelf-citationVlierberghe, P. V., van Grotel, M., Beverloo, H. B., Lee, C., Helgason, T., Buijs-Gladdines, J. G. C. A. M., Passier, M., van Wering, E. R., Veerman, A. J. P., Kamps, W. A., et al. (2006) · Blood · doi:10.1182/blood-2006-04-019927 · Cited by 172 · cited 13× · see citing works
“3G); a previous study proposed that deletion of cryptic repressors located in the deleted region enables activation of LMO2 (21).”
BackgroundInfluentialMechanisms of transcription factor deregulation in lymphoid cell transformation
O’Neil, J., & Look, A. T. (2007) · Oncogene · doi:10.1038/sj.onc.1210766 · Cited by 122 · cited 2× · see citing works
“The LMO2 gene encodes a transcription factor that is overexpressed and oncogenic in some forms of T-ALL (14, 20).”
BackgroundMango: a bias-correcting ChIA-PET analysis pipeline
Phanstiel, D. H., Boyle, A. P., Heidari, N., & Snyder, M. P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv336 · Cited by 113 · cited 5× · see citing works
“Several computational pipelines have thus been developed to estimate background contact frequencies based on this “genomic proximity bias,” both for chromosome conformation capture data (35, 36) and ChIA-PET data (30, 37).”
BackgroundMethodInfluentialMy5C: web tools for chromosome conformation capture studies
Lajoie, B. R., van Berkum, N. L., Sanyal, A., & Dekker, J. (2009) · Nature Methods · doi:10.1038/nmeth1009-690 · Cited by 88 · cited 2× · see citing works
“5C read mapping Sequencing data were obtained from both an Illumina MiSeq and an Illumina HiSeq 2000 machine and was processed by a custom pipeline to map and assemble 5C interactions, as previously described (55, 56).”
MethodSelf-citationWang, J., Li, J.-W., Wang, X.-C., Zheng, C., & Ma, W.-D. (2013) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1016/j.bbrc.2013.08.032 · Cited by 81 · cited 1× · see citing works
“4G, 4H) the following evidence indicated activation of the genes in the cancer types the mutations were documented in: FGFR1 was found overexpressed in liver carcinoma in previous studies (70, 71).”
BackgroundA statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
Paulsen, J., Rødland, E. A., Holden, L., Holden, M., & Hovig, E. J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku738 · Cited by 61 · cited 1× · see citing works
“Several computational pipelines have thus been developed to estimate background contact frequencies based on this “genomic proximity bias,” both for chromosome conformation capture data (35, 36) and ChIA-PET data (30, 37).”
MethodFrom cells to chromatin: Capturing snapshots of genome organization with 5C technology
Ferraiuolo, M. A., Sanyal, A., Naumova, N., Dekker, J., & Dostie, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.10.011 · Cited by 50 · see citing works
Self-citationAn NK and T Cell Enhancer Lies 280 Kilobase Pairs 3′ to the Gata3 Structural Gene
Hosoya-Ohmura, S., Lin, Y.-H., Herrmann, M., Kuroha, T., Rao, A. U. K., Moriguchi, T., Lim, K.-C., Hosoya, T., & Engel, J. D. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05065-11 · Cited by 45 · cited 1× · see citing works
“at the CD3 and GATA3 loci (41, 42) (Table S2A-B).”
BackgroundChromatin looping defines expression of TAL1, its flanking genes, and regulation in T-ALL
Zhou, Y., Kurukuti, S., Saffrey, P., Vukovic, M., Michie, A. M., Strogantsev, R., West, A. G., & Vetrie, D. L. P. (2013) · Blood · doi:10.1182/blood-2013-02-483875 · Cited by 34 · see citing works
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Coactivator condensation at super-enhancers links phase separation and gene control
Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., Abraham, B. J., Hannett, N. M., Zamudio, A. V., Manteiga, J. C., et al. (2018) · Science · doi:10.1126/science.aar3958 · Cited by 2,595 · see citing works
Self-citationHiGlass: web-based visual exploration and analysis of genome interaction maps
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“This highlights the crucial role of boundaries in mediating the physical insulation of neighboring chromosome domains, with important implications for disease-causing chromosomal rearrangements in humans (Flavahan et al., 2016; Franke et al., 2016; Hnisz et al., 2016).”
Self-citationA Phase Separation Model for Transcriptional Control
Hnisz, D., Shrinivas, K., Young, R. A., Chakraborty, A. K., & Sharp, P. A. (2017) · Cell · doi:10.1016/j.cell.2017.02.007 · Cited by 1,753 · see citing works
Self-citationEpigenetic plasticity and the hallmarks of cancer
Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science · doi:10.1126/science.aal2380 · Cited by 1,340 · see citing works
“Indeed, frequentmutations of CTCFmotifs in the vicinity of oncogenes have been reported in colorectal, liver, and esophageal cancer (50, 51).”
BackgroundOrganization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174 · see citing works
Transcriptional Addiction in Cancer
Bradner, J. E., Hnisz, D., & Young, R. A. (2017) · Cell · doi:10.1016/j.cell.2016.12.013 · Cited by 1,188 · see citing works
“Thus, the CTCF DNA-binding motif in loop anchor regions is among the most altered human transcription factor-binding sequences in cancer cells (Hnisz et al., 2016b; Ji et al., 2016; Katainen et al., 2015).”
InfluentialSelf-citationThe chromatin accessibility landscape of primary human cancers
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230 · see citing works
“However, these mutations were relatively rare and often had only small effects on the accessibility of the CTCF motif site despite a known enrichment of somatic mutations in CTCF motif sites in cancer (51, 52).”
BackgroundLong-range enhancer–promoter contacts in gene expression control
Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102 · see citing works
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Weintraub, A. S., Li, C. H., Zamudio, A. V., Sigova, A. A., Hannett, N. M., Day, D. S., Abraham, B. J., Cohen, M. A., Nabet, B., Buckley, D. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.008 · Cited by 992 · see citing works
“Insulators: Insulators were defined by downloading the called insulated neighborhoods from (Hnisz et al., 2016a) (available at: http://younglab. wi.mit.edu/ insulatedneighborhoods.htm).”
InfluentialSelf-citationHigh-resolution TADs reveal DNA sequences underlying genome organization in flies
Ramírez, F., Bhardwaj, V., Arrigoni, L., Lam, K. C., Grüning, B. A., Villaveces, J. M., Habermann, B. H., Akhtar, A., & Manke, T. (2018) · Nature Communications · doi:10.1038/s41467-017-02525-w · Cited by 974 · see citing works
“Interestingly, mutations of the CTCF binding motif at TAD boundaries are particularly abundant in cancer, causing dysregulation of oncogenes (Hnisz et al. 2016).”
BackgroundChromatin Domains: The Unit of Chromosome Organization
Dixon, J. R., Gorkin, D. U., & Ren, B. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.018 · Cited by 811 · see citing works
Structural variation in the 3D genome
Spielmann, M., Lupiáñez, D. G., & Mundlos, S. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0007-0 · Cited by 719 · see citing works
The role of 3D genome organization in development and cell differentiation
Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works
Circular ecDNA promotes accessible chromatin and high oncogene expression
Wu, S., Turner, K. M., Nguyen, N., Raviram, R., Erb, M. L., Santini, J., Luebeck, J., Rajkumar, U., Diao, Y., Li, B., et al. (2019) · Nature · doi:10.1038/s41586-019-1763-5 · Cited by 651 · see citing works
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613 · see citing works
“…domain boundaries by deletion or silencing of CTCF binding sites allows abnormal contact between previously separated enhancers and promoters, which can induce aberrant gene activation leading to cancer (Flavahan et al., 2015; Hnisz et al., 2016a) or developmental defects (Lupianez et al., 2015).”
BackgroundPrinciples of genome folding into topologically associating domains
Szabo, Q., Bantignies, F., & Cavalli, G. (2019) · Science Advances · doi:10.1126/sciadv.aaw1668 · Cited by 594 · see citing works
The Energetics and Physiological Impact of Cohesin Extrusion
Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.072 · Cited by 581 · see citing works
Transcription factors and 3D genome conformation in cell-fate decisions
Stadhouders, R., Filion, G. J. P., & Graf, T. (2019) · Nature · doi:10.1038/s41586-019-1182-7 · Cited by 519 · see citing works
CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation
Merkenschlager, M., & Nora, E. P. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022339 · Cited by 505 · see citing works
“CTCF binding site mutations can disrupt the binding of CTCF and cohesin and are common in colorectal cancer (67), acute T cell leukemia (59), and other types of cancer.”
BackgroundThe structural basis for cohesin–CTCF-anchored loops
Li, Y., Haarhuis, J. H. I., Sedeño Cacciatore, Á., Oldenkamp, R., van Ruiten, M. S., Willems, L., Teunissen, H., Muir, K. W., de Wit, E., Rowland, B. D., et al. (2020) · Nature · doi:10.1038/s41586-019-1910-z · Cited by 459 · see citing works
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
Hug, C. B., Grimaldi, A. G., Kruse, K., & Vaquerizas, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.03.024 · Cited by 466 · see citing works
Methods for mapping 3D chromosome architecture
Kempfer, R., & Pombo, A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0195-2 · Cited by 502 · see citing works
Integrative detection and analysis of structural variation in cancer genomes
Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardımcı, G. G., Chakraborty, A., Bann, D. V., Wang, Y., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0195-8 · Cited by 452 · see citing works
Self-citationRegulation of genome organization and gene expression by nuclear mechanotransduction
Uhler, C., & Shivashankar, G. V. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.101 · Cited by 449 · see citing works
CRISPR in cancer biology and therapy
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Metabolic control of epigenetics in cancer
Kinnaird, A. S., Zhao, S., Wellen, K. E., & Michelakis, E. D. (2016) · Nature reviews. Cancer · doi:10.1038/nrc.2016.82 · Cited by 419 · see citing works
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
Hnisz, D., Day, D. S., & Young, R. A. (2016) · Cell · doi:10.1016/j.cell.2016.10.024 · Cited by 420 · see citing works
“A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript within insulated neighborhoods and genetic modification of the neighborhood loop anchors can cause activation of these oncogenes (Flavahan et al., 2016; Hnisz et al., 2016).”
InfluentialSelf-citationNonlinear control of transcription through enhancer–promoter interactions
Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04570-y · Cited by 415 · see citing works
Weischenfeldt, J., Dubash, T., Drainas, A. P., Mardin, B. R., Chen, Y., Stütz, A. M., Waszak, S. M., Bosco, G., Halvorsen, A. R., Raeder, B., et al. (2017) · Nature Genetics · doi:10.1038/ng.3722 · Cited by 404 · see citing works
The role of enhancers in cancer
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The Three-Dimensional Organization of Mammalian Genomes
Yu, M., & Ren, B. (2017) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100616-060531 · Cited by 366 · see citing works
“Perturbation of the anchors by genetic engineering and/or naturally occurred mutations led to gene dysregulation (Dowen et al. 2014, Hnisz et al. 2016b, Ji et al. 2016).”
BackgroundOn the existence and functionality of topologically associating domains
Beagan, J. A., & Phillips‐Cremins, J. E. (2020) · Nature Genetics · doi:10.1038/s41588-019-0561-1 · Cited by 357 · see citing works
Viswanathan, S. R., Ha, G., Hoff, A. M., Wala, J. A., Carrot-Zhang, J., Whelan, C. W., Haradhvala, N. J., Freeman, S. S., Reed, S. C., Rhoades, J., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.036 · Cited by 365 · see citing works
The second decade of 3C technologies: detailed insights into nuclear organizationPreprint
Denker, A., & de Laat, W. L. (2016) · Genes & Development · doi:10.1101/gad.281964.116 · Cited by 346 · see citing works
Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
Ghavi-Helm, Y., Jankowski, A., Meiers, S., Viales, R. R., Korbel, J. O., & Furlong, E. E. M. (2019) · Nature Genetics · doi:10.1038/s41588-019-0462-3 · Cited by 354 · see citing works
Regulation of disease-associated gene expression in the 3D genome
Krijger, P. H. L., & de Laat, W. L. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.138 · Cited by 316 · see citing works
Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
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Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
Phanstiel, D. H., Van Bortle, K., Spacek, D., Hess, G. T., Shamim, M. S., Machol, I., Love, M. I., Aiden, E. L., Bassik, M. C., & Snyder, M. P. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.08.006 · Cited by 299 · see citing works
CTCF: making the right connectionsPreprint
Ghirlando, R., & Felsenfeld, G. (2016) · Genes & Development · doi:10.1101/gad.277863.116 · Cited by 292 · see citing works
“CTCF-binding sites are major hot spots for mutations in the cancer genome (Katainen et al. 2015), and oncogenes can be activated by mutations that disrupt CTCF binding at the boundaries of loop domains (Hnisz et al. 2016).”
BackgroundYY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
Beagan, J. A., Duong, M. T., Titus, K. R., Zhou, L., Cao, Z., Ma, J., Lachanski, C. V., Gillis, D. R., & Phillips-Cremins, J. E. (2017) · Genome Research · doi:10.1101/gr.215160.116 · Cited by 299 · see citing works
“TAD structural integrity is critical for proper gene expression; perturbation of TAD boundaries leads to ectopic enhancer looping and aberrant activation of nontarget genes (Dowen et al. 2014; Lupiáñez et al. 2015; Narendra et al. 2015; Flavahan et al. 2016; Hnisz et al. 2016).”
InfluentialNano-based delivery of RNAi in cancer therapy
Xin, Y., Huang, M., Guo, W. W., Huang, Q., Zhang, L. Z., & Jiang, G. (2017) · Molecular Cancer · doi:10.1186/s12943-017-0683-y · Cited by 296 · see citing works
Predicting 3D genome folding from DNA sequence with Akita
Fudenberg, G., Kelley, D. R., & Pollard, K. S. (2020) · Nature Methods · doi:10.1038/s41592-020-0958-x · Cited by 292 · see citing works
Nakayama, R. T., Pulice, J. L., Valencia, A. M., McBride, M. J., McKenzie, Z. M., Gillespie, M. A. K., Ku, W. L., Teng, M., Cui, K., Williams, R. T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3958 · Cited by 291 · see citing works
“0 369 1,599 3,717 4,698 13,516 (12) (41) (13) (22) (20) (20) (29) (25) (30) (29) GO term analysis of upregulated genes (435) biological processes Collagen catabolic process Extracellular matrix organization Nephron development Ossification Kidney development Renal system development Actin cytoskeleton organization Blo…”
BackgroundDisruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0564-y · Cited by 283 · see citing works
Self-citationCardozo Gizzi, A. M., Cattoni, D. I., Fiche, J.-B., Espinola, S. M., Gurgo, J., Messina, O., Houbron, C., Ogiyama, Y., Papadopoulos, G. L., Cavalli, G., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.011 · Cited by 258 · see citing works
Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs
Flavahan, W. A., Drier, Y., Johnstone, S. E., Hemming, M. L., Tarjan, D. R., Hegazi, E., Shareef, S. J., Javed, N. M., Raut, C. P., Eschle, B. K., et al. (2019) · Nature · doi:10.1038/s41586-019-1668-3 · Cited by 253 · see citing works
Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries
Sun, J. H., Zhou, L., Emerson, D. J., Phyo, S. A., Titus, K. R., Gong, W., Gilgenast, T. G., Beagan, J. A., Davidson, B. L., Tassone, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.005 · Cited by 249 · see citing works
“CTCF Occupancy at the FMR1 daSTR Is Ablated in Fragile X Syndrome CTCF occupancy is disrupted at boundaries that lose structural integrity in diseases of limb development and cancer (Flavahan et al., 2016; Hnisz et al., 2016; Lupiáñez et al., 2015).”
InfluentialDissecting super-enhancer hierarchy based on chromatin interactions
Huang, J., Li, K., Cai, W., Liu, X., Zhang, Y., Orkin, S. H., Xu, J., & Yuan, G.-C. (2018) · Nature Communications · doi:10.1038/s41467-018-03279-9 · Cited by 241 · see citing works
TAD disruption as oncogenic driver
Valton, A.-L., & Dekker, J. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.03.008 · Cited by 226 · see citing works
Self-citationTranscriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism
Schuijers, J., Manteiga, J. C., Weintraub, A. S., Day, D. S., Zamudio, A. V., Hnisz, D., Lee, T. I., & Young, R. A. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.056 · Cited by 232 · see citing works
“CTCF ChIP-seq peaks are depicted as purple rectangles, super-enhancers are depicted as red rectangles, and typical enhancers are depicted as gray rectangles (data from this study; Hnisz et al., 2016a; Pope et al., 2014).”
BackgroundMethodInfluentialSelf-citationTranscription shapes 3D chromatin organization by interacting with loop extrusion
Banigan, E. J., Tang, W., van den Berg, A. A., Stocsits, R. R., Wutz, G., Brandão, H. B., Busslinger, G. A., Peters, J., & Mirny, L. A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2210480120 · Cited by 216 · see citing works
Polymer physics predicts the effects of structural variants on chromatin architecture
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Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors
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Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma
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Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia
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“Frequent loss of TAD boundary insulation has been previously observed in human cancer, including T-ALL 49 .”
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DeepC: predicting 3D genome folding using megabase-scale transfer learning
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“…E u r op e P M C F und e r s A u t ho r M a nu s c r i p t s E u r op e P M C F und e r s A u t ho r M a nu s c r i p t s kb CRISPR-mediated deletion in HEK293T cells, encompassing four CTCF sites at the LMO2 locus, leads to a local rearrangement of the chromatin structure as confirmed by 5C 31 .”
BackgroundMethodInfluentialCuartero, S., Weiss, F. D., Dharmalingam, G., Guo, Y., Ing-Simmons, E., Masella, S., Robles-Rebollo, I., Xiao, X., Wang, Y.-F., Barozzi, I., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0184-1 · Cited by 210 · see citing works
Hallmarks of cancer—the new testament
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“Verhaak R et al. 2010 Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.”
BackgroundInfluentialDNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner
Collins, P. L., Purman, C. E., Porter, S. I., Nganga, V. K., Saini, A., Hayer, K. E., Gurewitz, G. L., Sleckman, B. P., Bednarski, J. J., Bassing, C. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16926-x · Cited by 215 · see citing works
Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
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Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Biggs, D., Preece, C., Downes, D. J., Gosden, M., Sharpe, J. A., Sloane-Stanley, J. A., Hughes, J. R., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3573 · Cited by 219 · see citing works
CRISPR off-target analysis in genetically engineered rats and mice
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McCord, R. P., Kaplan, N., & Giorgetti, L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.021 · Cited by 204 · see citing works
“If the repair of DNA damage disrupts a TAD boundary, enhancers and promoters that are normally segregated may become juxtaposed, causing misregulation of oncogenes (Hnisz et al. 2016).”
BackgroundLandscape of cohesin-mediated chromatin loops in the human genome
Grubert, F., Srivas, R., Spacek, D. V., Kasowski, M. M., Ruiz-Velasco, M., Sinnott-Armstrong, N., Greenside, P., Narasimha, A. M., Liu, Q., Geller, B. S., et al. (2020) · Nature · doi:10.1038/s41586-020-2151-x · Cited by 201 · see citing works
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Circulating tumor cells: from new biological insights to clinical practice
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“403 The proto-oncogene TAL1 is activated by microdeletions that obliterate TAD boundaries in T-ALL.”
BackgroundCTCF-mediated topological boundaries during development foster appropriate gene regulationPreprint
Narendra, V. K., Bulajić, M., Dekker, J., Mazzoni, E. O., & Reinberg, D. (2016) · Genes & Development · doi:10.1101/gad.288324.116 · Cited by 172 · see citing works
“Relocating a gene or genomic segment from one side of a topological boundary to the other dramatically changes its regulatory associations and thus transcriptional output (Hnisz et al. 2016; Neijts et al. 2016).”
Self-citationThe Epigenetic Hallmarks of Cancer
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Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning
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Position effects influence HIV latency reversal
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Targeting transcription cycles in cancer
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Topologically associating domain boundaries are required for normal genome function
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“…by the overall depletion of structural variants at TAD boundaries observed in the general human population 26 , while disruptions and rearrangements of TAD structure have been implicated in the mis-expression of genes and are associated with developmental and cancer phenotypes 1 – 3, 29, 30 .”
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Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions
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Self-citationHiCcompare: an R-package for joint normalization and comparison of HI-C datasets
Stansfield, J. C., Cresswell, K. G., Vladimirov, V. I., & Dozmorov, M. G. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2288-x · Cited by 147 · see citing works
Aberrant Super‐Enhancer Landscape in Human Hepatocellular Carcinoma
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Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
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Beagan, J. A., Pastuzyn, E. D., Fernandez, L. R., Guo, M. H., Feng, K., Titus, K. R., Chandrashekar, H., Shepherd, J. D., & Phillips-Cremins, J. E. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0634-6 · Cited by 143 · see citing works
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Genome control by SMC complexes
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CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioningPreprint
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“We investigated the same regions as previously described and we used the same primer pool (Hnisz et al. 2016).”
InfluentialSelf-citationGenetic–epigenetic interactions in cis: a major focus in the post-GWAS era
Do, C., Shearer, A., Suzuki, M., Terry, M. B., Gelernter, J. E., Greally, J. M., & Tycko, B. (2017) · Genome biology · doi:10.1186/s13059-017-1250-y · Cited by 141 · see citing works
Developing in 3D: the role of CTCF in cell differentiation
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“…Eukaryotic chromosomes are organized in the three-dimensional (3D) nuclear space and this folding is important for processes such as DNA replication, repair, recombination and transcription (Franke et al., 2016; Hnisz et al., 2016; Hu et al., 2015; Lupiáñez et al., 2015; Pope et al., 2014).”
BackgroundAcute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping
Hyle, J. W., Zhang, Y., Wright, S., Xu, B., Shao, Y., Easton, J. B., Tian, L., Feng, R., Xu, P., & Li, C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz462 · Cited by 140 · see citing works
Self-citationA critical assessment of topologically associating domain prediction tools
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Amaral, P., Leonardi, T., Han, N., Viré, E. A., Gascoigne, D. K., Arias‐Carrasco, R., Büscher, M., Pandolfini, L., Zhang, A., Pluchino, S., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1405-5 · Cited by 137 · see citing works
“Finally, considering the recent involvement of CTCF and architectural mutations in activation of oncogenes in specific tumours [58, 59], which represent hitherto overlooked potential causative mutations, we performed a mutational analysis of CTCF motifs associated with tapRNA loci.”
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LADL: light-activated dynamic looping for endogenous gene expression control
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Radiation-induced DNA damage and repair effects on 3D genome organization
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Pediatric T‐cell acute lymphoblastic leukemia
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“…chromosomal structures, and long-range chromatin interactions (Janssen et al., 1993; Mansour et al., 2014; Patel et al., 2014; Navarro et al., 2015; Hnisz et al., 2016), LMO2 by 11p12-13 deletions (Van Vlierberghe et al., 2006), TLX3 by a translocation to BCL11B (MacLeod et al., 2003), MYB by gene…”
Background
- Authors
- Hnisz, D., Weintraub, A. S., Day, D. S., Valton, A.-L., Bak, R. O., Li, C. H., Goldmann, J., Lajoie, B. R., Fan, Z. P., Sigova, A. A., Reddy, J., Borges-Rivera, D., Lee, T. I., Jaenisch, R., Porteus, M. H., Dekker, J., & Young, R. A.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- University of Massachusetts Chan Medical School (US)
- Stanford Medicine (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Hnisz, Denes
- Weintraub, Abraham S.
- Young, Richard A.
- ORCID
- Venue
- Science
- Published
- 2016-03-25
- Volume
- 351
- Issue
- 6280
- Pages
- 1454-1458
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4884612
- OpenAlex
- W2303393194
- Cited by
- 1,042
- References
- 73
- Citations by year
- 2026: 48 · 2025: 67 · 2024: 90 · 2023: 106 · 2022: 90 · 2021: 124 · 2020: 129 · 2019: 132 · 2018: 102 · 2017: 104 · 2016: 48
- FWCI
- 66.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship@UMassChan (submittedVersion)
- HAL (submittedVersion)
- Funders
- Austrian Science Fund (J3490)
- Ludwig Graduate Fellowship
- Laurie Kraus Lacob Faculty Scholar Award in Pediatric Translational Research
- Hyundai Hope on Wheels
- Danish Council for Independent Research, Medical Sciences
- Sapere Aude Research Talent (DFF-1331-00735B)
- National Human Genome Research Institute (R01 HG003143, U54 HG007010, U01 HG007910)
- National Cancer Institute (U54 CA193419)
- NIH (HG002668, CA109901, NS088538, MH104610, AI120766, U54 DK107980, U01 DA 040588)
- National Institute of General Medical Sciences (R01 GM 112720)
- National Institute of Allergy and Infectious Diseases (U01 R01 AI 117839)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- proto-oncogenes, oncogene activation, T-cell acute lymphoblastic leukemia, microdeletion, chromosome structure, cancer genetics, gene expression regulation
- MeSH terms
- Chromosome Aberrations, Chromosome Mapping, Humans, Mutation, Proto-Oncogenes, Translocation, Genetic, Transcriptional Activation, Gene Expression Regulation, Leukemic, Sequence Deletion, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, HEK293 Cells
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