Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking
Open accessAbstract
Extensive prior research focused on somatic copy-number alterations (SCNAs) affecting cancer genes, yet the extent to which recurrent SCNAs exert their influence through rearrangement of cis-regulatory elements (CREs) remains unclear. Here we present a framework for inferring cancer-related gene overexpression resulting from CRE reorganization (e.g., enhancer hijacking) by integrating SCNAs, gene expression data and information on topologically associating domains (TADs). Analysis of 7,416 cancer genomes uncovered several pan-cancer candidate genes, including IRS4, SMARCA1 and TERT. We demonstrate that IRS4 overexpression in lung cancer is associated with recurrent deletions in cis, and we present evidence supporting a tumor-promoting role. We additionally pursued cancer-type-specific analyses and uncovered IGF2 as a target for enhancer hijacking in colorectal cancer. Recurrent tandem duplications intersecting with a TAD boundary mediate de novo formation of a 3D contact domain comprising IGF2 and a lineage-specific super-enhancer, resulting in high-level gene activation. Our framework enables systematic inference of CRE rearrangements mediating dysregulation in cancer.
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The integrity of domain structures is important for the proper regulation of genes.
“Therefore, the integrity of the domain structures is important for the proper regulation of genes8–12.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [11]
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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248 · see citing works
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 9,540 · see citing works
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works
Comprehensive molecular characterization of human colon and rectal cancer
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11252 · Cited by 8,499 · see citing works
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works
Comprehensive molecular profiling of lung adenocarcinoma
The Cancer Genome Atlas Research Network (2014) · Nature · doi:10.1038/nature13385 · Cited by 5,732 · see citing works
Mutational landscape and significance across 12 major cancer types
Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., et al. (2013) · Nature · doi:10.1038/nature12634 · Cited by 4,419 · see citing works
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works
The landscape of somatic copy-number alteration across human cancers
Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017 · see citing works
Comprehensive genomic characterization of squamous cell lung cancers
The Cancer Genome Atlas Research Network (2012) · Nature · doi:10.1038/nature11404 · Cited by 3,994 · see citing works
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662 · see citing works
Discovery and saturation analysis of cancer genes across 21 tumour types
Lawrence, M. S., Stojanov, P., Mermel, C. H., Robinson, J. T., Garraway, L. A., Golub, T. R., Meyerson, M., Gabriel, S. B., Lander, E. S., & Getz, G. (2014) · Nature · doi:10.1038/nature12912 · Cited by 3,096 · see citing works
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works
Primer3Plus, an enhanced web interface to Primer3
Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., & Leunissen, J. A. M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm306 · Cited by 2,761 · see citing works
Massive genomic rearrangement acquired in a single catastrophic event during cancer development
Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., Pleasance, E. D., Lau, K. W., Beare, D., Stebbings, L. A., et al. (2011) · Cell · doi:10.1016/j.cell.2010.11.055 · Cited by 2,414 · see citing works
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Beneš, V., & Korbel, J. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts378 · Cited by 2,384 · see citing works
Self-citationDisruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132 · see citing works
Pan-cancer patterns of somatic copy number alteration
Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhang, C., Wala, J. A., Mermel, C. H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2760 · Cited by 1,843 · see citing works
A comprehensive catalogue of somatic mutations from a human cancer genome
Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordóñez, G. R., Bignell, G. R., et al. (2010) · Nature · doi:10.1038/nature08658 · Cited by 1,696 · see citing works
CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
Hark, A. T., Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., & Tilghman, S. M. (2000) · Nature · doi:10.1038/35013106 · Cited by 1,547 · see citing works
The long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D. J., Dunford-Shore, B. H., McGrath, S. D., Hickenbotham, M. T., et al. (2008) · Nature · doi:10.1038/nature07485 · Cited by 1,415 · see citing works
Emerging landscape of oncogenic signatures across human cancers
Ciriello, G., Miller, M. L., Aksoy, B. A., Şenbabaoğlu, Y., Schultz, N. D., & Sander, C. (2013) · Nature Genetics · doi:10.1038/ng.2762 · Cited by 1,382 · see citing works
A map of the cis-regulatory sequences in the mouse genome
Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · see citing works
Punctuated Evolution of Prostate Cancer Genomes
Baca, S. C., Prandi, D., Lawrence, M. S., Mosquera, J. M., Romanel, A., Drier, Y., Park, K., Kitabayashi, N., MacDonald, T. Y., Ghandi, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.03.021 · Cited by 1,300 · see citing works
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome
Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., et al. (2007) · Science · doi:10.1126/science.1149504 · Cited by 1,163 · see citing works
Self-citationIdentification of genomic alterations in oesophageal squamous cell cancer
Song, Y., Li, L., Ou, Y., Gao, Z., Li, E., Li, X., Zhang, W., Wang, J., Xu, L., Zhou, Y., et al. (2014) · Nature · doi:10.1038/nature13176 · Cited by 1,081 · see citing works
Beroukhim, R., Getz, G. A., Nghiemphu, L., Barretina, J., Hsueh, T., Linhart, D., Vivanco, I., Lee, J. C., Huang, J. H. Y., Alexander, S., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710052104 · Cited by 1,055 · see citing works
Self-citationActivation of proto-oncogenes by disruption of chromosome neighborhoods
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., et al. (2016) · Science · doi:10.1126/science.aad9024 · Cited by 1,042 · see citing works
Rausch, T., Jones, D. T. W., Zapatka, M., Stütz, A. M., Zichner, T., Weischenfeldt, J., Jäger, N., Remke, M., Shih, D., Northcott, P. A., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.013 · Cited by 865 · see citing works
Self-citationThe Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
Davis, C., Ricketts, C. J., Wang, M., Yang, L., Cherniack, A. D., Shen, H., Buhay, C., Kang, H.-J., Kim, S. C., Fahey, C. C., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.014 · Cited by 844 · see citing works
Dissecting the genomic complexity underlying medulloblastoma
Jones, D. T. W., Jäger, N., Kool, M., Zichner, T., Hutter, B., Sultan, M., Cho, Y.-J., Pugh, T. J., Hovestadt, V., Stütz, A. M., et al. (2012) · Nature · doi:10.1038/nature11284 · Cited by 839 · see citing works
Self-citationComplex landscapes of somatic rearrangement in human breast cancer genomes
Stephens, P. J., McBride, D. J., Lin, M., Varela, I., Pleasance, E., Simpson, J. T., Stebbings, L. A., Leroy, C., Edkins, S., Mudie, L. J., et al. (2009) · Nature · doi:10.1038/nature08645 · Cited by 833 · see citing works
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma
Jones, D., Hutter, B., Jäger, N., Korshunov, A., Kool, M., Warnatz, H.-J., Zichner, T., Lambert, S. R., Ryzhova, M. V., Khuong-Quang, D.-A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2682 · Cited by 819 · see citing works
Self-citationNon-coding recurrent mutations in chronic lymphocytic leukaemia
Puente, X. S., Beà, S., Valdés‐Mas, R., Villamor, N., Gutiérrez‐Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., et al. (2015) · Nature · doi:10.1038/nature14666 · Cited by 813 · see citing works
An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element
Mansour, M. R., Abraham, B. J., Anders, L., Berezovskaya, A., Gutierrez, A., Durbin, A. D., Etchin, J., Lawton, L., Sallan, S. E., Silverman, L. B., et al. (2014) · Science · doi:10.1126/science.1259037 · Cited by 801 · see citing works
Independent filtering increases detection power for high-throughput experiments
Bourgon, R., Gentleman, R. C., & Huber, W. K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914005107 · Cited by 731 · see citing works
Signatures of mutation and selection in the cancer genome
Bignell, G. R., Greenman, C. D., Davies, H., Butler, A. P., Edkins, S., Andrews, J. M., Buck, G., Chen, L., Beare, D., Latimer, C., et al. (2010) · Nature · doi:10.1038/nature08768 · Cited by 707 · see citing works
A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia
Gröschel, S., Sanders, M. A., Hoogenboezem, R., de Wit, E., Bouwman, B. A. M., Erpelinck, C., van der Velden, V. H. J., Havermans, M., Avellino, R., van Lom, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.019 · Cited by 687 · see citing works
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
Northcott, P. A., Lee, C., Zichner, T., Stütz, A. M., Erkek, S., Kawauchi, D., Shih, D. J. H., Hovestadt, V., Zapatka, M., Sturm, D., et al. (2014) · Nature · doi:10.1038/nature13379 · Cited by 642 · see citing works
Self-citationMad2 Overexpression Promotes Aneuploidy and Tumorigenesis in Mice
Sotillo, R., Hernando, E., Díaz-Rodríguez, E., Teruya-Feldstein, J., Cordón-Cardo, C., Lowe, S. W., & Benezra, R. (2007) · Cancer Cell · doi:10.1016/j.ccr.2006.10.019 · Cited by 612 · see citing works
Self-citationTelomerase activation by genomic rearrangements in high-risk neuroblastoma
Peifer, M., Hertwig, F., Roels, F., Dreidax, D., Gartlgruber, M., Menon, R., Krämer, A., Roncaioli, J. L., Sand, F., Heuckmann, J. M., et al. (2015) · Nature · doi:10.1038/nature14980 · Cited by 595 · see citing works
Self-citationFast and efficient QTL mapper for thousands of molecular phenotypes
Ongen, H., Buil, A., Brown, A. A., Dermitzakis, E. T., & Delaneau, O. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv722 · Cited by 571 · see citing works
Genomic inflation factors under polygenic inheritance
Yang, J., Weedon, M. N., Purcell, S., Lettre, G., Estrada, K., Willer, C. J., Smith, A. V., Ingelsson, E., O’Connell, J. R., Mangino, M., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.39 · Cited by 560 · see citing works
Genome-wide chromatin state transitions associated with developmental and environmental cues
Zhu, J., Adli, M., Zou, J., Verstappen, G., Coyne, M. J., Zhang, X.-L., Durham, T. J., Miri, M., Deshpande, V., Jager, P. D., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.033 · Cited by 553 · see citing works
Non-coding recurrent mutations in chronic lymphocytic leukaemia
Puente, X. S., Beà, S., Valdés‐Mas, R., Villamor, N., Gutiérrez‐Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., et al. (2016) · Nature · doi:10.1038/nature18910 · Cited by 546 · see citing works
Enhancer loops appear stable during development and are associated with paused polymerase
Ghavi-Helm, Y., Klein, F. A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W., & Furlong, E. E. M. (2014) · Nature · doi:10.1038/nature13417 · Cited by 536 · see citing works
Narendra, V., Rocha, P. P., An, D., Raviram, R., Skok, J. A., Mazzoni, E. O., & Reinberg, D. (2015) · Science · doi:10.1126/science.1262088 · Cited by 535 · see citing works
Topology of mammalian developmental enhancers and their regulatory landscapes
de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521 · see citing works
Genome-wide analysis of noncoding regulatory mutations in cancer
Weinhold, N., Jacobsen, A., Schultz, N., Sander, C., & Lee, W. (2014) · Nature Genetics · doi:10.1038/ng.3101 · Cited by 484 · see citing works
Functional and topological characteristics of mammalian regulatory domains
Symmons, O., Uslu, V. V., Tsujimura, T., Ruf, S., Nassari, S., Schwarzer, W., Ettwiller, L., & Spitz, F. (2014) · Genome Research · doi:10.1101/gr.163519.113 · Cited by 455 · see citing works
The landscape and therapeutic relevance of cancer-associated transcript fusions
Yoshihara, K., Wang, Q., Torres-Garcia, W., Zheng, S., Vegesna, R., Kim, H., & Verhaak, R. G. W. (2015) · Oncogene · doi:10.1038/onc.2014.406 · Cited by 450 · see citing works
Transcriptional Enhancers in Animal Development and Evolution
Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.06.070 · Cited by 449 · see citing works
Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture
Li, X., Nadauld, L. D., Ootani, A., Corney, D. C., Pai, R. K., Gevaert, O., Cantrell, M. A., Rack, P. G., Neal, J. T., Chan, C. W. M., et al. (2014) · Nature Medicine · doi:10.1038/nm.3585 · Cited by 443 · see citing works
An enhancer deletion affects both H19 and Igf2 expression.Preprint
Leighton, P. A., Saam, J. R., Ingram, R. S., Stewart, C. L., & Tilghman, S. M. (1995) · Genes & Development · doi:10.1101/gad.9.17.2079 · Cited by 399 · see citing works
TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors
Valentijn, L. J., Köster, J., Zwijnenburg, D. A., Hasselt, N. E., Sluis, P. V., Volckmann, R., van Noesel, M. M., George, R. E., Tytgat, G. A. M., Molenaar, J. J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3438 · Cited by 398 · see citing works
Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
Zhang, X., Choi, P. S., Francis, J. M., Imielinski, M. B., Watanabe, H., Cherniack, A. D., & Meyerson, M. M. (2015) · Nature Genetics · doi:10.1038/ng.3470 · Cited by 341 · see citing works
Weischenfeldt, J., Simon, R., Feuerbach, L., Schlangen, K., Weichenhan, D., Minner, S. J. P., Wuttig, D., Warnatz, H.-J., Stehr, H., Rausch, T., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.01.002 · Cited by 319 · see citing works
Self-citationStructural and functional diversity of Topologically Associating Domains
Dekker, J., & Heard, É. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.08.044 · Cited by 313 · see citing works
Distinct types of tumor-initiating cells form human colon cancer tumors and metastases
Dieter, S. M., Ball, C. R., Hoffmann, C. M., Nowrouzi, A., Herbst, F., Zavidij, O., Abel, U., Arens, A., Weichert, W., Brand, K., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.08.010 · Cited by 297 · see citing works
Self-citationMaternal imprinting at the H19-Igf2 locus maintains adult haematopoietic stem cell quiescence
Venkatraman, A., He, X. C., Thorvaldsen, J. L., Sugimura, R., Perry, J. M., Tao, F., Zhao, M., Christenson, M. K., Sanchez, R., Yu, J. Y., et al. (2013) · Nature · doi:10.1038/nature12303 · Cited by 296 · see citing works
Fredriksson, N. J., Ny, L., Nilsson, J. A., & Larsson, E. (2014) · Nature Genetics · doi:10.1038/ng.3141 · Cited by 282 · see citing works
4C Technology: Protocols and Data Analysis
van de Werken, H. J. G., de Vree, P. J. P., Splinter, E., Holwerda, S. J. B., Klous, P., de Wit, E., & de Laat, W. L. (2012) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-391938-0.00004-5 · Cited by 240 · see citing works
Recurrent somatic mutations in regulatory regions of human cancer genomes
Melton, C. A., Reuter, J., Spacek, D. V., & Snyder, M. P. (2015) · Nature Genetics · doi:10.1038/ng.3332 · Cited by 230 · see citing works
Splinter, E., de Wit, E., van de Werken, H. J. G., Klous, P., & de Laat, W. L. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.009 · Cited by 224 · see citing works
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans
Waszak, S. M., Delaneau, O., Gschwind, A. R., Kilpinen, H., Raghav, S. K., Witwicki, R. M., Orioli, A., Wiederkehr, M., Panousis, N. I., Yurovsky, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.001 · Cited by 214 · see citing works
Self-citationGenomics of uterine leiomyomas: insights from high-throughput sequencing
Mehine, M. M., Mäkinen, N., Heinonen, H.-R., Aaltonen, L. A., & Vahteristo, P. (2014) · Fertility and Sterility · doi:10.1016/j.fertnstert.2014.06.050 · Cited by 201 · see citing works
Mechanisms of FGFR-mediated carcinogenesis
Ahmad, I., Iwata, T., & Leung, H. Y. (2012) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2012.01.004 · Cited by 185 · see citing works
Chromosomal translocations in cancer
Nambiar, M., Kari, V., & Raghavan, S. C. (2008) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2008.07.005 · Cited by 180 · see citing works
DiBind : Dierential binding analysis of ChIP-Seq peak data
Stark, R., & Brown, G. (2016) · Cited by 179 · see citing works
Roy, N., Malik, S., Villanueva, K. E., Urano, A., Lu, X., Von Figura, G., Seeley, E. S., Dawson, D. W., Collisson, E. A., & Hebrok, M. (2015) · Genes & Development · doi:10.1101/gad.256628.114 · Cited by 155 · see citing works
A cell‐based model system links chromothripsis with hyperploidy
Mardin, B. R., Drainas, A. P., Waszak, S. M., Weischenfeldt, J., Isokane, M., Stütz, A. M., Raeder, B., Efthymiopoulos, T., Buccitelli, C., Segura‐Wang, M., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156505 · Cited by 140 · see citing works
Self-citationIGF2 signaling and regulation in cancer
Brouwer‐Visser, J., & Huang, G. S. (2015) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2015.01.002 · Cited by 118 · see citing works
Data analysis: Create a cloud commons
Stein, L. D., Knoppers, B. M., Campbell, P. J., Getz, G. A., & Korbel, J. O. (2015) · Nature · doi:10.1038/523149a · Cited by 110 · see citing works
Self-citationTyrosine Phosphoproteomics of Fibroblast Growth Factor Signaling
Hinsby, A. M., Olsen, J. V., & Mann, M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m404537200 · Cited by 98 · see citing works
FourCSeq: analysis of 4C sequencing data
Klein, F. A., Pakozdi, T., Anders, S., Ghavi-Helm, Y., Furlong, E. E. M., & Huber, W. K. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv335 · Cited by 94 · see citing works
Mapping the Shh long-range regulatory domain
Anderson, E., Devenney, P. S., Hill, R., & Lettice, L. (2014) · Development · doi:10.1242/dev.108480 · Cited by 86 · see citing works
Attiyeh, E. F., Diskin, S. J., Attiyeh, M. A., Mossé, Y. P., Hou, C., Jackson, E. M., Kim, C., Glessner, J., Hakonarson, H. H., Biegel, J. A., et al. (2009) · Genome Research · doi:10.1101/gr.075671.107 · Cited by 80 · see citing works
Lingohr, M. K. (2003) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2003.08.003 · Cited by 69 · see citing works
IRS-4 Mediates Protein Kinase B Signaling during Insulin Stimulation without Promoting Antiapoptosis
Uchida, T., Myers, M. G., & White, M. F. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.1.126-138.2000 · Cited by 67 · see citing works
Insulin Receptor Substrate-4 Enhances Insulin-like Growth Factor-I-induced Cell Proliferation
Qu, B.-H., Karas, M., Koval, A. P., & LeRoith, D. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.44.31179 · Cited by 59 · see citing works
Effect of IRS4 Levels on PI 3-Kinase Signalling
Hoxhaj, G., Dissanayake, K., & MacKintosh, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0073327 · Cited by 41 · see citing works
Insulin Receptor Substrate-4 Binds to Slingshot-1 Phosphatase and Promotes Cofilin Dephosphorylation
Homma, Y., Kanno, S., Sasaki, K., Nishita, M., Yasui, A., Asano, T., Ohashi, K., & Mizuno, K. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.565945 · Cited by 24 · see citing works
Shimwell, N. J., Martin, A., Bruton, R. K., Blackford, A. N., Sedgwick, G. G., Gallimore, P. H., Turnell, A. S., & Grand, R. J. A. (2008) · Oncogene · doi:10.1038/onc.2008.417 · Cited by 18 · see citing works
Proliferation and migration of hepatoblastoma cells are mediated by IRS-4 via PI3K/Akt pathways.
Xia, Z., Zhang, N., & Ding, D. (2014) · PubMed · Cited by 11 · see citing works
When Deletions Gain Functions: Commandeering Epigenetic Mechanisms
Chen, J., & Weiss, W. A. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.021 · Cited by 6 · see citing works
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The whole-genome landscape of medulloblastoma subtypes
Northcott, P. A., Buchhalter, I., Morrissy, A. S., Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Gröbner, S., Segura-Wang, M., Zichner, T., Rudneva, V. A., et al. (2017) · Nature · doi:10.1038/nature22973 · Cited by 1,112 · see citing works
Self-citationStructural 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
Structural variation in the sequencing era
Ho, S. S., Urban, A. E., & Mills, R. E. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0180-9 · Cited by 608 · see citing works
Principles 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., et al. (2020) · Nature · doi:10.1038/s41586-020-1965-x · Cited by 597 · see citing works
Kim, H., Nguyen, N., Turner, K. M., Wu, S., Gujar, A. D., Luebeck, J., Liu, J., Deshpande, V., Rajkumar, U., Namburi, S., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0678-2 · Cited by 596 · see citing works
Widespread and Functional RNA Circularization in Localized Prostate Cancer
Chen, S., Huang, V., Xu, X., Livingstone, J., Soares, F., Jeon, J., Zeng, Y., Hua, J. T., Petricca, J., Guo, H., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.025 · Cited by 544 · 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
Understanding 3D genome organization by multidisciplinary methods
Jerković, I., & Cavalli, G. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00362-w · Cited by 389 · 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
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
Self-citationSuper-Enhancer-Driven Transcriptional Dependencies in Cancer
Sengupta, S., & George, R. E. (2017) · Trends in cancer · doi:10.1016/j.trecan.2017.03.006 · Cited by 349 · see citing works
Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
Verhaak, R. G. W., Bafna, V., & Mischel, P. S. (2019) · Nature reviews. Cancer · doi:10.1038/s41568-019-0128-6 · Cited by 324 · see citing works
Takeda, D. Y., Spisák, S., Seo, J.-H., Bell, C., O’Connor, E., Korthauer, K., Ribli, D., Csabai, I., Solymosi, N., Szállási, Z., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.037 · Cited by 317 · see citing works
Despang, A., Schöpflin, R., Franke, M., Ali, S., Jerković, I., Paliou, C., Chan, W.-L., Timmermann, B., Wittler, L., Vingron, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0466-z · Cited by 306 · see citing works
Disruption 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-citationMedulloblastomics revisited: biological and clinical insights from thousands of patients
Hovestadt, V., Ayrault, O., Swartling, F. J., Robinson, G. W., Pfister, S. M., & Northcott, P. A. (2020) · Nature Reviews Cancer · doi:10.1038/s41568-019-0223-8 · Cited by 271 · see citing works
Self-citationSignal Transduction Pathways in Breast Cancer: The Important Role of PI3K/Akt/mTOR
Ortega, M. A., Fraile‐Μartinez, O., Asúnsolo, Á., Buján, J., García‐Honduvilla, N., & Coca, S. (2020) · Journal of Oncology · doi:10.1155/2020/9258396 · Cited by 241 · see citing works
Ly, P., Brunner, S. F., Shoshani, O., Kim, D. H., Lan, W., Pyntikova, T., Flanagan, A. M., Behjati, S., Page, D. C., Campbell, P. J., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0360-8 · Cited by 220 · see citing works
Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma
Helmsauer, K., Valieva, M. E., Ali, S., González, R. C., Schöpflin, R., Röefzaad, C., Bei, Y., García, H. D., Rodríguez-Fos, E., Puiggròs, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19452-y · Cited by 227 · see citing works
Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia
Kloetgen, A., Thandapani, P., Ntziachristos, P., Ghebrechristos, Y. E., Nomikou, S., Lazaris, C., Chen, X., Hu, H., Bakogianni, S., Wang, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0602-9 · Cited by 219 · see citing works
Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D
Robson, M. I., Ringel, A. R., & Mundlos, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.032 · Cited by 188 · see citing works
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis
Kragesteen, B. K., Spielmann, M., Paliou, C., Heinrich, V., Schöpflin, R., Esposito, A., Annunziatella, C., Bianco, S., Chiariello, A. M., Jerković, I., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0221-x · Cited by 183 · see citing works
Enhancers in disease: molecular basis and emerging treatment strategies
Claringbould, A., & Zaugg, J. B. (2021) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2021.07.012 · Cited by 171 · see citing works
The Epigenetic Hallmarks of Cancer
Esteller, M., Dawson, M. A., Kadoch, C., Rassool, F. V., Jones, P. A., & Baylin, S. B. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-0296 · Cited by 184 · see citing works
Krefting, J., Andrade-Navarro, M. A., & Ibn-Salem, J. (2018) · BMC Biology · doi:10.1186/s12915-018-0556-x · Cited by 162 · see citing works
Thandapani, P. (2019) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2019.02.014 · Cited by 163 · see citing works
Wang, X., Xu, J., Zhang, B., Hou, Y., Song, F., Lyu, H., & Yue, F. (2021) · Nature Methods · doi:10.1038/s41592-021-01164-w · Cited by 152 · see citing works
Aberrant Super‐Enhancer Landscape in Human Hepatocellular Carcinoma
Tsang, F. H., Law, C., Tang, T. C. C., Cheng, C. L., Chin, D. W., Tam, V., Wei, L., Wong, C. C., Ng, I. O., & Wong, C. (2019) · Hepatology · doi:10.1002/hep.30544 · Cited by 153 · see citing works
Collier, M. D., Sungalee, S., Zufferey, M., Tavernari, D., Katanayeva, N., Battistello, E., Mina, M., Douglass, K. M., Rey, T., Raynaud, F., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0338-y · Cited by 147 · see citing works
Wang, X., Luan, Y., & Yue, F. (2022) · Science Advances · doi:10.1126/sciadv.abn9215 · Cited by 148 · see citing works
Super-enhancer function and its application in cancer targeted therapy
Tang, F., Yang, Z., Tan, Y., & Li, Y. (2020) · npj Precision Oncology · doi:10.1038/s41698-020-0108-z · Cited by 143 · see citing works
Gong, Y., Lazaris, C., Sakellaropoulos, T., Lozano, A. C., Kambadur, P., Ntziachristos, P., Aifantis, I., & Tsirigos, A. (2018) · Nature Communications · doi:10.1038/s41467-018-03017-1 · Cited by 140 · see citing works
Rubin, M. A., Bristow, R. G., Thienger, P., Dive, C., & Imielinski, M. B. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.10.033 · Cited by 136 · see citing works
Wu, P., Li, T., Li, R., Jia, L., Zhu, P., Liu, Y., Chen, Q., Tang, D., Yu, Y., & Li, C. (2017) · Nature Communications · doi:10.1038/s41467-017-01793-w · Cited by 130 · see citing works
The three-dimensional genome: regulating gene expression during pluripotency and development
Andrey, G., & Mundlos, S. (2017) · Development · doi:10.1242/dev.148304 · Cited by 129 · see citing works
Pongor, L. S., Schultz, C. W., Rinaldi, L., Wangsa, D., Redon, C. E., Takahashi, N., Fialkoff, G., Desai, P. A., Zhang, Y., Burkett, S. S., et al. (2023) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0796 · Cited by 128 · see citing works
Computational analysis of cancer genome sequencing data
Cortés‐Ciriano, I., Gulhan, D., Lee, J. J.-K., Melloni, G. E. M., & Park, P. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00431-y · Cited by 116 · see citing works
Pan-cancer analysis of whole genomesPreprint
Campbell, P., Getz, G., Stuart, J. M., Korbel, J., & Stein, L. D. (2017) · bioRxiv · doi:10.1101/162784 · Cited by 343 · see citing works
Self-citationLaugsch, M., Bartusel, M., Rehimi, R., Alirzayeva, H., Karaolidou, A., Crispatzu, G., Zentis, P., Nikolić, M., Bleckwehl, T., Kolovos, P., et al. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.03.004 · Cited by 106 · see citing works
Structural variations in cancer and the 3D genome
Dubois, F. P. B., Sidiropoulos, N., Weischenfeldt, J., & Beroukhim, R. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00488-9 · Cited by 110 · see citing works
Self-citationChromatin features constrain structural variation across evolutionary timescales
Fudenberg, G., & Pollard, K. S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1808631116 · Cited by 106 · see citing works
Patterns and mechanisms of structural variations in human cancer
Yi, K., & Ju, Y. S. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0112-3 · Cited by 101 · see citing works
CCND2 and CCND3 hijack immunoglobulin light-chain enhancers in cyclin D1− mantle cell lymphoma
Martin‐García, D., Navarro, A., Valdés‐Mas, R., Clot, G., Gutiérrez‐Abril, J., Prieto, M., Ribera‐Cortada, I., Woroniecka, R., Rymkiewicz, G., Bens, S., et al. (2018) · Blood · doi:10.1182/blood-2018-07-862151 · Cited by 107 · see citing works
Structural variants drive context-dependent oncogene activation in cancer
Xu, Z., Lee, D.-S., Chandran, S., Le, V. T., Bump, R., Yasis, J., Dallarda, S., Marcotte, S., Clock, B., Haghani, N. K., et al. (2022) · Nature · doi:10.1038/s41586-022-05504-4 · Cited by 97 · see citing works
Structural Variation in Cancer: Role, Prevalence, and Mechanisms
Cosenza, M. R., Rodríguez–Martín, B., & Korbel, J. O. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120121-101149 · Cited by 92 · see citing works
Self-citationOncogenic super-enhancer formation in tumorigenesis and its molecular mechanisms
Jia, Q., Chen, S., Tan, Y., Li, Y., & Tang, F. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0428-7 · Cited by 90 · see citing works
Cancer Evolution: A Multifaceted Affair
Ciriello, G., Magnani, L., Aitken, S. J., Akkari, L., Behjati, S., Hanahan, D., Landau, D. A., López-Bigas, N., Lupiáñez, D. G., Marine, J., et al. (2023) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-0530 · Cited by 89 · see citing works
Illuminating the noncoding genome in cancer
Zhang, X., & Meyerson, M. M. (2020) · Nature Cancer · doi:10.1038/s43018-020-00114-3 · Cited by 85 · see citing works
The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization
Ibrahim, D. M., & Mundlos, S. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.02.015 · Cited by 79 · see citing works
Zhang, Y., Yang, L., Kucherlapati, M. H., Chen, F., Hadjipanayis, A. G., Pantazi, A., Bristow, C. A., Lee, E. A., Mahadeshwar, H. S., Tang, J., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.025 · Cited by 80 · see citing works
Kasprzak, A., & Adamek, A. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20194915 · Cited by 82 · see citing works
Zhang, Y., Chen, F., Fonseca, N. A., He, Y., Fujita, M., Nakagawa, H., Zhang, Z., Brāzma, A., PCAWG Transcriptome Working Group, Amin, S. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13885-w · Cited by 74 · see citing works
Self-citationUnderstanding the 3D genome: Emerging impacts on human disease
Krumm, A., & Duan, Z. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.004 · Cited by 75 · see citing works
Tian, B., Zhao, Y., Liang, T., Ye, X., Li, Z., Yan, D., Fu, Q., & Li, Y. (2017) · Journal of drug targeting · doi:10.1080/1061186x.2017.1306535 · Cited by 76 · see citing works
Yang, M., Safavi, S., Woodward, E. L., Duployez, N., Olsson, L., Ungerbäck, J., Sigvardsson, M., Zaliova, M. K., Zuna, J., Fioretos, T., et al. (2020) · Blood · doi:10.1182/blood.2019004684 · Cited by 76 · see citing works
Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
Orlando, G., Law, P., Cornish, A. J., Dobbins, S. E., Chubb, D., Broderick, P., Litchfield, K., Hariri, F., Pastinen, T., Osborne, C. S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0211-z · Cited by 73 · see citing works
Order and disorder: abnormal 3D chromatin organization in human disease
Anania, C., & Lupiáñez, D. G. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz028 · Cited by 69 · see citing works
Yang, H., Zhang, H., Luan, Y., Liu, T., Yang, W., Roberts, K. G., Qian, M., Zhang, B., Yang, W., Pérez-Andreu, V., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00993-x · Cited by 75 · see citing works
Sungalee, S., Liu, Y., Lambuta, R. A., Katanayeva, N., Donaldson Collier, M., Tavernari, D., Roulland, S., Ciriello, G., & Oricchio, E. (2021) · Nature Genetics · doi:10.1038/s41588-021-00842-x · Cited by 70 · see citing works
Whole-genome doubling drives oncogenic loss of chromatin segregation
Lambuta, R. A., Nanni, L., Liu, Y., Díaz-Miyar, J., Iyer, A., Tavernari, D., Katanayeva, N., Ciriello, G., & Oricchio, E. (2023) · Nature · doi:10.1038/s41586-023-05794-2 · Cited by 68 · see citing works
Reprogramming: identifying the mechanisms that safeguard cell identity
Brumbaugh, J., Stefano, B. D., & Hochedlinger, K. (2019) · Development · doi:10.1242/dev.182170 · Cited by 64 · see citing works
Three-dimensional chromatin in disease: What holds us together and what drives us apart?
Ibrahim, D. M., & Mundlos, S. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.01.003 · Cited by 66 · see citing works
Global impact of somatic structural variation on the DNA methylome of human cancers
Zhang, Y., Yang, L., Kucherlapati, M. H., Hadjipanayis, A. G., Pantazi, A., Bristow, C. A., Lee, E. A., Mahadeshwar, H. S., Tang, J., Zhang, J., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1818-9 · Cited by 67 · see citing works
Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X
Liu, Y., Li, C., Shen, S., Chen, X., Szlachta, K., Edmonson, M. N., Shao, Y., Ma, X., Hyle, J., Wright, S., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0659-5 · Cited by 64 · see citing works
Harbers, L., Agostini, F., Nicoś, M., Poddighe, D., Bienko, M., & Crosetto, N. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.700568 · Cited by 64 · see citing works
When TADs go bad: Chromatin structure and nuclear organisation in human disease
Kaiser, V. B., & Semple, C. A. (2017) · F1000Research · doi:10.12688/f1000research.10792.1 · Cited by 64 · see citing works
The Emerging Role of Super-enhancers as Therapeutic Targets in The Digestive System Tumors
Li, X., Qu, J., Teng, X.-Q., Zhuang, H.-H., Dai, Y.-H., Yang, Z. G., & Qu, Q. (2023) · International Journal of Biological Sciences · doi:10.7150/ijbs.78535 · Cited by 63 · see citing works
Targeting Super-Enhancers as a Therapeutic Strategy for Cancer Treatment
He, Y., Long, W., & Liu, Q. (2019) · Frontiers in Pharmacology · doi:10.3389/fphar.2019.00361 · Cited by 63 · see citing works
Kycia, I., Wolford, B. N., Huyghe, J. R., Fuchsberger, C., Vadlamudi, S., Kursawe, R., Welch, R., Albanus, R. D., Uyar, A., Khetan, S., et al. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.02.020 · Cited by 57 · see citing works
Defining Functionally Relevant Spatial Chromatin Domains: It is a TAD Complicated
Sikorska, N., & Sexton, T. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.12.006 · Cited by 56 · see citing works
The multifaceted roles of cohesin in cancer
Nardo, M. D., Pallotta, M. M., & Musio, A. (2022) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-022-02321-5 · Cited by 58 · see citing works
Kaiser, V., & Semple, C. (2017) · Genome Biology · doi:10.1186/s13059-018-1483-4 · Cited by 52 · see citing works
Chromatin Conformation in Development and Disease
Boltsis, I., Grosveld, F. G., Giraud, G., & Kolovos, P. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.723859 · Cited by 56 · see citing works
The whole-genome panorama of cancer driversPreprint
Sabarinathan, R., Pich, O., Martincorena, I., Rubio-Pérez, C., Juul, M., Wala, J. A., Schumacher, S. E., Shapira, O., Sidiropoulos, N., Waszak, S. M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/190330 · Cited by 55 · see citing works
Self-citationGene regulation on extrachromosomal DNA
Hung, K. L., Mischel, P. S., & Chang, H. Y. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00806-7 · Cited by 53 · see citing works
3D genome and its disorganization in diseases
Li, R., Liu, Y., Hou, Y., Gan, J., Wu, P., & Cheng, L. (2018) · Cell Biology and Toxicology · doi:10.1007/s10565-018-9430-4 · Cited by 56 · see citing works
Yang, L., Chen, F., Zhu, H., Chen, Y., Dong, B., Shi, M., Wang, W., Jiang, Q., Zhang, L., Huang, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24044-5 · Cited by 55 · see citing works
Self-citationNanopore sequencing of DNA concatemers reveals higher-order features of chromatin structurePreprint
Ulahannan, N., Pendleton, M., Deshpande, A. S., Schwenk, S., Behr, J. M., Dai, X., Tyer, C., Rughani, P., Kudman, S., Adney, E. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/833590 · Cited by 49 · see citing works
Franke, M., Daly, A., Palmeira, L., Tirosh, A., Stigliano, A., Trifan, E., Faucz, F. R., Abboud, D., Pétrossians, P., Tena, J. J., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.02.002 · Cited by 49 · see citing works
Schöpflin, R., Melo, U. S., Moeinzadeh, H., Heller, D., Laupert, V., Hertzberg, J., Holtgrewe, M., Alavi, N., Klever, M.-K., Jungnitsch, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34053-7 · Cited by 51 · see citing works
Ren, J., Du, Y., Li, S., Ma, S., Jiang, Y., & Wu, C. (2019) · Genetic Epidemiology · doi:10.1002/gepi.22194 · Cited by 50 · see citing works
Sadowski, M., Kraft, A., Szałaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., & Plewczyński, D. (2019) · Genome biology · doi:10.1186/s13059-019-1728-x · Cited by 50 · see citing works
Ooi, W. F., Nargund, A. M., Lim, K. J., Zhang, S., Xing, M., Mandoli, A., Lim, J. Q., Ho, S. W. T., Guo, Y. A., Yao, X., et al. (2019) · Gut · doi:10.1136/gutjnl-2018-317612 · Cited by 48 · see citing works
3D genome evolution and reorganization in the Drosophila melanogaster species group
Torosin, N. S., Anand, A., Golla, T. R., Cao, W., & Ellison, C. E. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009229 · Cited by 49 · see citing works
Androgen Receptor-Mediated Transcription in Prostate Cancer
Özturan, D., Morova, T., & Lack, N. A. (2022) · Cells · doi:10.3390/cells11050898 · Cited by 50 · see citing works
Super-enhancers complexes zoom in transcription in cancer
Wang, M., Chen, Q., Wang, S., Xie, H., Liu, J., Huang, R., Xiang, Y., Jiang, Y., Tian, D., & Bian, E. (2023) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-023-02763-5 · Cited by 49 · see citing works
Chromatin topology in development and disease.
Bompadre, O., & Andrey, G. (2019) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2019.04.007 · Cited by 36 · see citing works
Naqvi, S., Bellott, D. W., Lin, K. S., & Page, D. C. (2018) · Genome Research · doi:10.1101/gr.230433.117 · Cited by 48 · see citing works
Copy number alterations unmasked as enhancer hijackers
Beroukhim, R., Zhang, X., & Meyerson, M. (2017) · Nature Genetics · doi:10.1038/ng.3754 · Cited by 46 · see citing works
Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies
Yang, J., Zhou, F., Luo, X., Fang, Y., Wang, X., Liu, X., Xiao, R., Jiang, D., Tang, Y., Yang, G., et al. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02366-3 · Cited by 50 · see citing works
A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement
Zhang, Y., Chen, F., Donehower, L. A., Scheurer, M. E., & Creighton, C. J. (2021) · Nature Communications · doi:10.1038/s41467-021-21081-y · Cited by 46 · see citing works
The Application of Long-Read Sequencing to Cancer
Ermini, L., & Driguez, P. (2024) · Cancers · doi:10.3390/cancers16071275 · Cited by 48 · see citing works
Enhancer dysfunction in leukemia
Bhagwat, A. S., Lu, B., & Vakoc, C. R. (2018) · Blood · doi:10.1182/blood-2017-11-737379 · Cited by 44 · see citing works
Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis
Wang, W., Li, L., & Cui, J. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-020-00371-7 · Cited by 44 · see citing works
Beyes, S., Bediaga, N. G., & Zippo, A. (2021) · Cancers · doi:10.3390/cancers13194969 · Cited by 42 · see citing works
Rausch, T., Snajder, R., Léger, A., Simovic-Lorenz, M., Giurgiu, M., Villacorta, L., Henssen, A. G., Fröhling, S., Stegle, O., Birney, E., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100281 · Cited by 37 · see citing works
Self-citationGlobal impact of somatic structural variation on the cancer proteome
Chen, F., Zhang, Y., Chandrashekar, D. S., Varambally, S., & Creighton, C. J. (2023) · Nature Communications · doi:10.1038/s41467-023-41374-8 · Cited by 42 · see citing works
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome
Kim, K., Jang, I., Kim, M., Choi, J., Kim, M.-S., Lee, B.-W., & Jung, I. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1078 · Cited by 39 · see citing works
- Authors
- 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., Efthymiopoulos, T., Erkek, S., Siegl, C., Brenner, H., Brustugun, O. T., Dieter, S. M., Northcott, P. A., Petersen, I., Pfister, S. M., Schneider, M., Solberg, S. K., Thunissen, E., Weichert, W., Zichner, T., Thomas, R., Peifer, M., Helland, A., Ball, C. R., Jechlinger, M., Sotillo, R., Glimm, H., & Korbel, J. O.
- Affiliations
- University of Copenhagen (DK)
- German Cancer Research Center (DE)
- European Molecular Biology Laboratory (DE)
- University of Cologne (DE)
- Oslo University Hospital (NO)
- St. Jude Children's Research Hospital (US)
- Jena University Hospital (DE)
- Heidelberg University (DE)
- Amsterdam UMC Location Vrije Universiteit Amsterdam (NL)
- European Bioinformatics Institute (GB)
- Corresponding author
- Glimm, Hanno
- Korbel, Jan O
- ORCID
- Weischenfeldt, Joachim
- Drainas, Alexandros P
- Mardin, Balca R
- Chen, Yuanyuan
- Stütz, Adrian M
- Waszak, Sebastian M
- Bosco, Graziella
- Halvorsen, Ann Rita
- Raeder, Benjamin
- Erkek, Serap
- Brenner, Hermann
- Brustugun, Odd Terje
- Dieter, Sebastian M
- Northcott, Paul A
- Petersen, Iver
- Pfister, Stefan M
- Schneider, Martin
- Solberg, Steinar K
- Weichert, Wilko
- Zichner, Thomas
- Thomas, Roman
- Peifer, Martin
- Ball, Claudia R
- Jechlinger, Martin
- Glimm, Hanno
- Korbel, Jan O
- Venue
- Nature Genetics
- Published
- 2016-11-21
- Volume
- 49
- Issue
- 1
- Pages
- 65-74
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5791882
- OpenAlex
- W2555451680
- Cited by
- 404
- References
- 92
- Citations by year
- 2026: 24 · 2025: 23 · 2024: 46 · 2023: 47 · 2022: 41 · 2021: 53 · 2020: 54 · 2019: 51 · 2018: 34 · 2017: 28 · 2016: 1
- FWCI
- 15.85
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- Funders
- Baden-Württemberg Stiftung (P-LS-ASII/33)
- Sundhed og Sygdom, Det Frie Forskningsråd
- Deutsches Krebsforschungszentrum
- European Commission (336045, 260791)
- Deutsche Forschungsgemeinschaft (KFO 227/BA 4806/1-2, KFO 227)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (155365)
- Bundesministerium für Bildung und Forschung (01ZX1303A, 01ZX1406)
- Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- somatic copy number alterations, enhancer hijacking, cis-regulatory elements, IRS4, insulin-like growth factor II, SMARCA1, telomerase reverse transcriptase, topologically associating domains, super-enhancers, 3D genome organization, gene overexpression, lung cancer, colorectal cancer, pan-cancer analysis, tandem duplication
- MeSH terms
- Enhancer Elements, Genetic, Humans, Insulin-Like Growth Factor II, Neoplasms, Promoter Regions, Genetic, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Insulin Receptor Substrate Proteins, Genetic Association Studies, DNA Copy Number Variations
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