The DOI matches its Crossref record; 31 of the 32 references it cites were found in a registry or an index.
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Open accessAbstract
In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the non-protein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C) and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist. We discover a series of discrete 200-kilobase to 1 Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains. TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Consistent with prior studies16, we found that genes in the same domain correlate across samples, but that genes separated by a boundary show lower correlation (Fig. 1e).”
From Insulator dysfunction and oncogene activation in IDH mutant gliomas (2016) · cites this paper as [16]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Consistent with prior studies16, we found that genes in the same domain correlate across samples, but that genes separated by a boundary show lower correlation (Fig. 1e).”
From Insulator dysfunction and oncogene activation in IDH mutant gliomas (2016) · cites this paper as [16]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“metazoan genomes are organised into megabase-scale segregated domains that are often invariant between cell types, termed topologically associating domains (TADs) [432–434].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [433]
The cited source says what the claim attributes to it.
In the citing paper
“Second, it was demonstrated that eukaryotic chromosomes are partitioned into so-called topologically associated domains (TADs) [35,36,37], which appear to restrict the areas of enhancer action [38,39,40,41].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [35]
In the citing paper
“Indeed, the genome is now known to be hierarchically organized in a series of 3D structures, starting from nucleosome clutches, to chromatin loops, to chromosomal domains called topologically associating domains (TADs), and finally to active or repressive compartments and chromosome territories 15,46,[48][49][50] .”
From Advances in epigenetics link genetics to the environment and disease (2019) · cites this paper as [48]
In the citing paper
“These changes enable proceeding through the 3C protocol in a single tube per sample, allow handling of over 20 samples in parallel, reduce the amount of cells needed by a factor 5 to 10 and cut down the time needed to complete the protocol from 8 days (Nora et al. 2012) to 4 days.”
From Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization (2017) · cites this paper as Nora et al. 2012
In the citing paper
“loop extrusion mediated by cohesin and CTCF mediates the formation of chromatin loops and self-interacting Topologically Associating Domains (TADs)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [85]
In the citing paper
“Mammalian genomes are organized into a hierarchy of Megabase (Mb)-scale topologically associating domains (TADs) (Dixon et al., 2012; Nora et al., 2012) and smaller, nested subTADs (Dixon et al., 2012; Nora et al., 2012; Phillips-Cremins et al., 2013; Rao et al., 2014).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Nora et al., 2012
In the citing paper
“Consistent with previous reports, we found enrichment for the architectural protein CCCTC-binding factor (CTCF) at human ES cell boundaries compared to loci internal to domains (Figure S6A-B) (Dixon et al., 2012; Nora et al., 2012; Phillips-Cremins et al., 2013).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Nora et al., 2012
In the citing paper
“The deposition of chromatin marks is thought to contribute to this process (Dixon et al., 2015, Nora et al., 2012)”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Nora et al., 2012
In the citing paper
“At intermediate scales (100 kb to 1 Mb), a major discovery is the existence of topologically associating domains (TADs) (Dixon et al., 2012, Nora et al., 2012, Sexton et al., 2012).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Nora et al., 2012
In the citing paper
“Recent chromosome conformation studies have revealed that mammalian chromosomes are structured into largely tissue-invariant TADs in which the DNA interactions are more frequent within a given domain than with regions in other domains4,5.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [5]
In the citing paper
“The disruption of domain boundaries can result in ectopic interactions between neighboring domains and affect the regulation of nearby genes5,9.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [5]
In the citing paper
“TADs were identified through Hi-C3,4 and their existence have since been confirmed by alternative methods such as intrinsic 3C (i3C),18 which avoids the cross-linking step and Genome Architecture Mapping (GAM),19 which avoids the ligation step.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“First, chromatin is organized into Topological Associating Domains (TADs) that are characterized by preferential contacts between loci inside the same TAD and insulation from loci in adjacent TADs.3,4”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“A large body of evidence suggests that TADs correspond to functional regulatory domains by primarily restricting contact between enhancers and promoters to occur within the same TAD3,21–25”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“Accordingly, deletion of a boundary between two TADs causes ectopic contacts between previously insulated loci3 and can cause aberrant gene expression through improper enhancer-promoter contact.27,28”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“suggesting an important functional role of CTCF and cohesin in TAD formation and maintenance (Fig. 2A).”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“Both DNA FISH3,9,36–39 and single-cell Hi-C40,41 studies show that genome organization is highly variable between cells and that even strong Hi-C loop anchors only contact in a small subset of cells”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“After TADs were discovered through Hi-C studies, it quickly became clear that TAD boundaries are near universally enriched in CTCF and cohesin ChIP-Seq peaks,3,4,16”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“The CTCF/cohesin anchored loop domain matching the Hi-C corner-peak actually only exists in a small subset of cells, which is also consistent with the high levels of cell-to-cell variability in contact probability observed in DNA FISH studies.3,9,36–39”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [3]
In the citing paper
“Furthermore, individual chromosomes are partitioned into megabase- sized topologically associating domains (TADs), regions with relatively high intradomain DNA interaction frequencies as measured by Hi-C chromosome conformation capture data (Dixon et al., 2012; Nora et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Nora et al., 2012
In the citing paper
“Nonetheless, the TADs identified by processing Hi-C data with the Hidden Markov algorithm (Dixon et al., 2012; Nora et al., 2012) can also be identified when this algorithm is used to process cohesin ChIA-PET data (Ji et al., 2016).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Nora et al., 2012
In the citing paper
“genome-wide, high-resolution understanding of chromosome cell-cycle dynamics11 is still limited by current technologies”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [4]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Self-citationTopological 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
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098
Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904715106 · Cited by 2,872
Three-dimensional folding and functional organization principles of the Drosophila genome
Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012) · Cell · doi:10.1016/j.cell.2012.01.010 · Cited by 1,983
Mediator and cohesin connect gene expression and chromatin architecture
Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939
Self-citationDostie, J., Richmond, T., Arnaout, R., Selzer, R. R., Lee, W. L., Honan, T., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., et al. (2006) · Genome Research · doi:10.1101/gr.5571506 · Cited by 1,237
Self-citationMolecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation
Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W. M., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.016 · Cited by 1,050
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.018 · Cited by 806
The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains
Caron, H. N., van Schaik, B. D. C., van der Mee, M., Baas, F., Riggins, G. J., Sluis, P. V., Hermus, M.-C., van Asperen, R., Boon, K., Voûte, P. A., et al. (2001) · Science · doi:10.1126/science.1056794 · Cited by 730
Flagged first, then by citations
1 of the 32 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 501–600 of 1,010
Role of the Epigenome in Heart Failure
Papait, R., Serio, S., & Condorelli, G. (2020) · Physiological Reviews · doi:10.1152/physrev.00037.2019 · Cited by 107
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
Liu, M., Lu, Y., Yang, B., Chen, Y., Radda, J. S. D., Hu, M., Katz, S. G., & Wang, S. (2020) · Nature Communications · doi:10.1038/s41467-020-16732-5 · Cited by 107
Austenaa, L. M. I., Barozzi, I., Simonatto, M., Masella, S., Chiara, G. D., Ghisletti, S., Curina, A., de Wit, E., Bouwman, B. A. M., de Pretis, S., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.018 · Cited by 111
The Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products.
Furlan, G., Hernandez, N. G., Huret, C., Galupa, R., van Bemmel, J. V., Romito, A., Heard, E., Morey, C., & Rougeulle, C. (2018) · Molecules and Cells · doi:10.1016/j.molcel.2018.03.024 · Cited by 106
The role of chromatin loop extrusion in antibody diversification
Zhang, Y., Zhang, X., Dai, H., Hu, H., & Alt, F. W. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00679-3 · Cited by 106
MOF-associated complexes ensure stem cell identity and Xist repression
Chełmicki, T., Dündar, F., Turley, M. J., Khanam, T., Aktaş, T., Ramírez, F., Gendrel, A.-V., Wright, P. R., Videm, P., Backofen, R., et al. (2014) · eLife · doi:10.7554/elife.02024 · Cited by 106
Large-scale chromatin organization: the good, the surprising, and the still perplexing
Belmont, A. S. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.10.002 · Cited by 104
Transcription-factor-mediated supervision of global genome architecture maintains B cell identity
Johanson, T. M., Lun, A. T. L., Coughlan, H. D., Tan, T., Smyth, G. K., Nutt, S. L., & Allan, R. S. (2018) · Nature Immunology · doi:10.1038/s41590-018-0234-8 · Cited by 109
Kaushal, A., Mohana, G., Dorier, J., Özdemir, İ., Omer, A., Cousin, P., Semenova, A. I., Taschner, M., Dergai, O., Marzetta, F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21366-2 · Cited by 99
Enabling functional genomics with genome engineeringPreprint
Hilton, I. B., & Gersbach, C. A. (2015) · Genome Research · doi:10.1101/gr.190124.115 · Cited by 106
Peeters, S. B., Cotton, A. M., & Brown, C. J. (2014) · BioEssays · doi:10.1002/bies.201400032 · Cited by 108
Surdez, D., Zaïdi, S., Grossetête, S., Laud-Duval, K., Ferre, A. S., Mous, L., Vourc’h, T., Tirode, F., Pierron, G., Raynal, V., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.04.001 · Cited by 106
Polycomb silencing: from linear chromatin domains to 3D chromosome folding
Cheutin, T., & Cavalli, G. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.11.016 · Cited by 102
Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques
Petrovic, J., Zhou, Y., Fasolino, M., Goldman, N., Schwartz, G. W., Mumbach, M. R., Nguyen, S. C., Rome, K., Sela, Y., Zapataro, Z., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.006 · Cited by 107
Fishman, V., Баттулин, Н. Р., Nuriddinov, M., Maslova, A., Zlotina, A. M., Strunov, A. A., Chervyakova, D. B., Korablev, A. N., Serov, O. L., & Krasikova, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1103 · Cited by 107
Transcription-mediated supercoiling regulates genome folding and loop formation
Neguembor, M. V., Martin, L., Castells-García, Á., Gómez-García, P. A., Vicario, C., Carnevali, D., Abed, J. A., Granados, A., Sebastián-Pérez, R., Sottile, F., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.06.009 · Cited by 106
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open QuestionsPreprint
Mirny, L. A., & Dekker, J. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040147 · Cited by 111
Self-citationBarrington, C., Georgopoulou, D., Pezic, D., Varsally, W., Herrero, J., & Hadjur, S. (2019) · Nature Communications · doi:10.1038/s41467-019-10725-9 · Cited by 102
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus
Barutcu, A. R., Maass, P. G., Lewandowski, J. P., Weiner, C. L., & Rinn, J. L. (2018) · Nature Communications · doi:10.1038/s41467-018-03614-0 · Cited by 101
CTCF: a Swiss-army knife for genome organization and transcription regulation
Braccioli, L., & de Wit, E. (2019) · Essays in Biochemistry · doi:10.1042/ebc20180069 · Cited by 106
Shinkai, S., Nozaki, T., Maeshima, K., & Togashi, Y. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005136 · Cited by 101
To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?
Cavalheiro, G. R., Pollex, T., & Furlong, E. E. M. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.015 · Cited by 108
Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis
Li, D., Ning, C., Zhang, J., Wang, Y., Tang, Q., Kui, H., Wang, T., He, M., Jin, L. G., Li, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27800-9 · Cited by 102
A collagen VI–dependent pathogenic mechanism for Hirschsprung’s disease
Soret, R., Mennetrey, M., Bergeron, K., Dariel, A., Neunlist, M., Righini‐Grunder, F., Faure, C. C., Silversides, D. W., Pilon, N., & for the Ente-Hirsch study group (2015) · Journal of Clinical Investigation · doi:10.1172/jci83178 · Cited by 107
Architectural proteins: regulators of 3D genome organization in cell fate
Gómez‐Díaz, E., & Corces, V. G. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.08.003 · Cited by 107
Co-regulation of paralog genes in the three-dimensional chromatin architecture
Ibn-Salem, J., Muro, E. M., & Andrade-Navarro, M. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw813 · Cited by 101
Higher order chromatin organization in cancer
Reddy, K. L., & Feinberg, A. P. (2012) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2012.12.001 · Cited by 102
Scc2/Nipbl hops between chromosomal cohesin rings after loading
Rhodes, J., Mazza, D., Nasmyth, K., & Uphoff, S. (2017) · eLife · doi:10.7554/elife.30000 · Cited by 102
HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
Wang, S., Lee, S., Chu, C., Jain, D., Kerpedjiev, P., Nelson, G. M., Walsh, J. M., Alver, B. H., & Park, P. J. (2020) · Genome Biology · doi:10.1186/s13059-020-01986-5 · Cited by 99
Lin, D., Hong, P., Zhang, S., Xu, W., Jamal, M., Yan, K., Lei, Y., Li, L., Ruan, Y., Fu, Z. F., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0111-2 · Cited by 100
Rosin, L. F., Nguyen, S. C., & Joyce, E. F. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007393 · Cited by 98
Cuadrado, A., Giménez-Llorente, D., Kojic, A., Rodríguez-Corsino, M., Cuartero, Y., Martín‐Serrano, G., Goméz-López, G., Martı́-Renom, M. A., & Losada, A. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.05.078 · Cited by 105
Chetverina, D., Aoki, T., Erokhin, M., Georgiev, P. G., & Schedl, P. D. (2013) · BioEssays · doi:10.1002/bies.201300125 · Cited by 97
3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering
Han, J., Zhang, Z., & Wang, K. (2018) · Molecular Cytogenetics · doi:10.1186/s13039-018-0368-2 · Cited by 104
Hi-C analysis: from data generation to integration
Pal, K., Forcato, M., & Ferrari, F. (2018) · Biophysical Reviews · doi:10.1007/s12551-018-0489-1 · Cited by 102
Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell
Maeshima, K., Tamura, S., Hansen, J. C., & Itoh, Y. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.02.016 · Cited by 101
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 98
Ruiz-Velasco, M., Kumar, M., Lai, M. C., Bhat, P., Solis-Pinson, A. B., Reyes, A., Kleinsorg, S., Noh, K., Gibson, T. J., & Zaugg, J. B. (2017) · Cell Systems · doi:10.1016/j.cels.2017.10.018 · Cited by 100
Epigenetics and epitranscriptomics in temporal patterning of cortical neural progenitor competence
Yoon, K., Vissers, C. B., Ming, G., & Song, H. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201802117 · Cited by 96
Michieletto, D., Orlandini, E., & Marenduzzo, D. (2016) · Physical Review X · doi:10.1103/physrevx.6.041047 · Cited by 100
DeepHiC: A generative adversarial network for enhancing Hi-C data resolution
Hong, H., Jiang, S., Li, H., Du, G., Sun, Y., Tao, H., Quan, C., Zhao, C., Li, R., Li, W., et al. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007287 · Cited by 97
Looping the Genome with SMC Complexes
Kim, E., Barth, R., & Dekker, C. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-032620-110506 · Cited by 96
Investigating the Transcriptional Control of Cardiovascular Development
Kathiriya, I. S., Nora, E. P., & Bruneau, B. G. (2015) · Circulation Research · doi:10.1161/circresaha.116.302832 · Cited by 100
Self-citationUnraveling the 3D Genome Architecture in Plants: Present and Future
Ouyang, W., Xiong, D., Li, G., & Li, X. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.10.002 · Cited by 96
Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles
Spitz, F. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.06.017 · Cited by 99
UMI-4C for quantitative and targeted chromosomal contact profiling
Schwartzman, O., Mukamel, Z., Elkayam, N. O., Olivares‐Chauvet, P., Lubling, Y., Landan, G., Izraeli, S., & Tanay, A. (2016) · Nature Methods · doi:10.1038/nmeth.3922 · Cited by 97
Miura, H., Takahashi, S., Poonperm, R., Tanigawa, A., Takebayashi, S., & Hiratani, I. (2019) · Nature Genetics · doi:10.1038/s41588-019-0474-z · Cited by 98
Identification of atrial fibrillation associated genes and functional non-coding variants
van Ouwerkerk, A. F., Bosada, F. M., van Duijvenboden, K., Hill, M. C., Montefiori, L. E., Scholman, K. T., Liu, J., de Vries, A. A. F., Boukens, B. J., Ellinor, P. T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12721-5 · Cited by 94
Density imaging of heterochromatin in live cells using orientation-independent-DIC microscopy
Imai, R., Nozaki, T., Tani, T., Kaizu, K., Hibino, K., Ide, S., Tamura, S., Takahashi, K., Shribak, M. I., & Maeshima, K. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e17-06-0359 · Cited by 94
Popay, T. M., & Dixon, J. R. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102117 · Cited by 94
Wang, X., Cui, W., & Peng, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx735 · Cited by 94
The physical size of transcription factors is key to transcriptional regulation in chromatin domains
Maeshima, K., Kaizu, K., Tamura, S., Nozaki, T., Kokubo, T., & Takahashi, K. (2015) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/27/6/064116 · Cited by 93
Chromatin loops, gene positioning, and gene expression
Holwerda, S. J. B., & de Laat, W. L. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00217 · Cited by 98
Stavreva, D. A., Coulon, A., Baek, S., Sung, M., John, S., Stixová, L., Tesikova, M., Hakim, O., Miranda, T. B., Hawkins, M. E., et al. (2015) · Genome Research · doi:10.1101/gr.184168.114 · Cited by 97
Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors
Meharena, H. S., Marco, A., Dileep, V., Lockshin, E. R., Akatsu, G. Y., Mullahoo, J., Watson, L. A., Ko, T., Guerin, L. N., Abdurrob, F., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2021.12.002 · Cited by 92
Nand, A., Zhan, Y., Salazar, O. R., Aranda, M., Voolstra, C. R., & Dekker, J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00841-y · Cited by 92
Self-citationShort-term memory of danger signals and environmental stimuli in immune cells
Monticelli, S., & Natoli, G. (2013) · Nature Immunology · doi:10.1038/ni.2636 · Cited by 92
TADtool: visual parameter identification for TAD-calling algorithms
Kruse, K., Hug, C. B., Hernández-Rodríguez, B., & Vaquerizas, J. M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw368 · Cited by 91
Form and function of topologically associating genomic domains in budding yeast
Eser, U., Chandler-Brown, D. B., Ay, F., Straight, A. F., Duan, Z., Noble, W. S., & Skotheim, J. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612256114 · Cited by 97
Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells
Faure, A. J., Schmiedel, J. M., & Lehner, B. (2017) · Cell Systems · doi:10.1016/j.cels.2017.10.003 · Cited by 92
Pulikkan, J. A., Hegde, M. B., Ahmad, H. M., Belaghzal, H., Illendula, A., Yu, J., O’Hagan, K., Ou, J., Müller‐Tidow, C., Wolfe, S. A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.048 · Cited by 92
Self-citationGhosh, S. K., & Jost, D. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006159 · Cited by 94
Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes
Yao, L., Berman, B. P., & Farnham, P. (2015) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2015.1087961 · Cited by 93
Casà, V., Gines, M. M., Gusmao, E. G., Slotman, J. A., Zirkel, A., Josipović, N., Oole, E., van IJcken, W. F. J., Houtsmuller, A. B., Papantonis, A., et al. (2020) · Genome Research · doi:10.1101/gr.253211.119 · Cited by 95
Genome-wide epigenomic profiling for biomarker discovery
Dirks, R. A. M., Stunnenberg, H. G., & Marks, H. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0284-4 · Cited by 94
Khoury, A., Achinger-Kawecka, J., Bert, S. A., Smith, G. C., French, H. J., Luu, P., Peters, T. J., Du, Q., Parry, A., Valdés‐Mora, F., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13753-7 · Cited by 94
Conte, M., Irani, E., Chiariello, A. M., Abraham, A., Bianco, S., Esposito, A., & Nicodemi, M. (2022) · Nature Communications · doi:10.1038/s41467-022-31856-6 · Cited by 98
Computational methods for analysing multiscale 3D genome organization
Zhang, Y., Boninsegna, L., Yang, M., Misteli, T., Alber, F., & Ma, J. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00638-1 · Cited by 97
Zhang, Y., Amaral, M. L., Zhu, C., Grieco, S. F., Hou, X., Lin, L., Buchanan, J., Tong, L., Preissl, S., Xu, X., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00719-6 · Cited by 89
Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments
Wijchers, P. J., Krijger, P. H. L., Geeven, G., Zhu, Y., Denker, A., Verstegen, M. J. A. M., Valdes‐Quezada, C., Vermeulen, C., Janssen, M., Teunissen, H., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.01.001 · Cited by 89
Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans
Fujioka, M., Mistry, H., Schedl, P. D., & Jaynes, J. B. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005889 · Cited by 89
Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations
Zhou, S., Treloar, A. E., & Lupien, M. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0745 · Cited by 89
Yu, W.-B., He, B., & Tan, K. (2017) · Nature Communications · doi:10.1038/s41467-017-00478-8 · Cited by 78
Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING)
Maass, P. G., Barutcu, A. R., Shechner, D. M., Weiner, C. L., Melé, M., & Rinn, J. L. (2017) · Nature Structural & Molecular Biology · doi:10.1038/s41594-017-0015-3 · Cited by 90
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
Raviram, R., Rocha, P. P., Müller, C. L., Miraldi, E. R., Badri, S., Fu, Y., Swanzey, E., Proudhon, C., Snetkova, V., Bonneau, R., et al. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004780 · Cited by 92
TADs and Their Borders: Free Movement or Building a Wall?
Chang, L., Ghosh, S., & Noordermeer, D. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.11.025 · Cited by 97
Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication
Yokoshi, M., Kazuma, S., & Fukaya, T. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.02.007 · Cited by 89
Paulson, J. R., Hudson, D. F., Cisneros-Soberanis, F., & Earnshaw, W. C. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.03.014 · Cited by 96
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 91
Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., & Hetzer, M. W. (2020) · Genes & Development · doi:10.1101/gad.335794.119 · Cited by 95
Integrating ChIP-seq with other functional genomics data
Jiang, S., & Mortazavi, A. (2018) · Briefings in Functional Genomics · doi:10.1093/bfgp/ely002 · Cited by 96
Oshidari, R., Strecker, J., Chung, D. K. C., Abraham, K. J., Chan, J. N. Y., Damaren, C. J., & Mekhail, K. (2018) · Nature Communications · doi:10.1038/s41467-018-05009-7 · Cited by 98
Dall’Agnese, A., Caputo, L., Nicoletti, C., di Iulio, J., Schmitt, A. D., Gatto, S., Diao, Y., Ye, Z., Forcato, M., Perera, R. J., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.036 · Cited by 93
Viggiano, E., Ergoli, M., Picillo, E., & Politano, L. (2016) · Human Genetics · doi:10.1007/s00439-016-1666-6 · Cited by 88
Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries
Nanni, L., Ceri, S., & Logie, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02108-x · Cited by 88
Modeling chromosomes: Beyond pretty pictures
Imakaev, M., Fudenberg, G., & Mirny, L. A. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.09.004 · Cited by 96
Lhoumaud, P., Badri, S., Rodriguez-Hernaez, J., Sakellaropoulos, T., Sethia, G., Kloetgen, A., Cornwell, M., Bhattacharyya, S., Ay, F., Bonneau, R., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12811-4 · Cited by 92
Local rewiring of genome–nuclear lamina interactions by transcription
Brueckner, L., Zhao, P. A., van Schaik, T., Leemans, C., Sima, J., Peric‐Hupkes, D., Gilbert, D. M., & van Steensel, B. (2020) · The EMBO Journal · doi:10.15252/embj.2019103159 · Cited by 87
Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment
Rosencrance, C. D., Ammouri, H., Yu, Q., Ge, T., Rendleman, E. J., Marshall, S. A., & Eagen, K. P. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.018 · Cited by 89
BRD4 orchestrates genome folding to promote neural crest differentiation
Linares-Saldana, R., Kim, W., Bolar, N. A., Zhang, H., Koch-Bojalad, B. A., Yoon, S., Shah, P. P., Karnay, A. M., Park, D. S., Luppino, J. M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00934-8 · Cited by 91
Architectural proteins, transcription, and the three‐dimensional organization of the genome
Cubeñas-Potts, C., & Corces, V. G. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.025 · Cited by 90
Transcriptional and epigenetic networks of helper T and innate lymphoid cells
Shih, H., Sciumè, G., Poholek, A. C., Vahedi, G., Hirahara, K., Villarino, A. V., Bonelli, M. M., Bosselut, R., Kanno, Y., Muljo, S. A., et al. (2014) · Immunological Reviews · doi:10.1111/imr.12208 · Cited by 91
Chromatin architecture transitions from zebrafish sperm through early embryogenesisPreprint
Wike, C. L., Guo, Y., Tan, M., Nakamura, R., Shaw, D. K., Díaz, N., Whittaker-Tademy, A. F., Durand, N. C., Aiden, E. L., Vaquerizas, J. M., et al. (2021) · Genome Research · doi:10.1101/gr.269860.120 · Cited by 87
Physical clustering of FLC alleles during Polycomb-mediated epigenetic silencing in vernalizationPreprint
Rosa, S., Lucia, F. D., Mylne, J. S., Zhu, D., Ohmido, N., Pendle, A. F., Kato, N., Shaw, P., & Dean, C. (2013) · Genes & Development · doi:10.1101/gad.221713.113 · Cited by 91
The Birth of the 3D Genome during Early Embryonic Development
Hug, C. B., & Vaquerizas, J. M. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.09.002 · Cited by 90
DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., et al. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0231-0 · Cited by 86
Self-citationLazaris, C., Kelly, S. M., Ntziachristos, P., Aifantis, I., & Tsirigos, A. (2016) · BMC Genomics · doi:10.1186/s12864-016-3387-6 · Cited by 83
Determinants of transcription factor regulatory range
Chen, C.-H., Zheng, R., Tokheim, C., Dong, X., Fan, J., Wan, C., Tang, Q., Brown, M., Liu, J. S., Meyer, C. A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16106-x · Cited by 85
Cooperativity, Specificity, and Evolutionary Stability of Polycomb Targeting in Drosophila
Schuettengruber, B., Elkayam, N. O., Sexton, T., Entrevan, M., Stern, S., Thomas, A., Yaffe, E., Parrinello, H., Tanay, A., & Cavalli, G. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.08.072 · Cited by 85
Trac-looping measures genome structure and chromatin accessibility
Lai, B., Tang, Q., Jin, W., Hu, G., Wangsa, D., Cui, K., Stanton, B. Z., Ren, G., Ding, Y., Zhao, M., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0107-y · Cited by 85
Metadata
- Authors
- 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., Gribnau, J., Barillot, E., Blüthgen, N., Dekker, J., & Heard, E.
- Affiliations
- Institut Curie (FR)
- University of Massachusetts Chan Medical School (US)
- Centre National de la Recherche Scientifique (FR)
- Inserm (FR)
- Humboldt-Universität zu Berlin (DE)
- University of California, San Francisco (US)
- Erasmus MC (NL)
- Corresponding author
- Dekker, Job
- ORCID
- Venue
- Nature
- Published
- 2012-04-11
- Volume
- 485
- Issue
- 7398
- Pages
- 381-385
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3555144
- OpenAlex
- W2161212572
- Cited by
- 2,895
- References
- 32
- Citations by year
- 2026: 145 · 2025: 168 · 2024: 181 · 2023: 213 · 2022: 241 · 2021: 276 · 2020: 255 · 2019: 300 · 2018: 247 · 2017: 241 · 2016: 201 · 2015: 173 · 2014: 112 · 2013: 103 · 2012: 34
- FWCI
- 50.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Digital Library (submittedVersion, other-oa)
- Funders
- W. M. Keck Foundation
- European Commission (257082, 242129)
- Agence Nationale de la Recherche (ANR-10-INBS-0009)
- Bundesministerium für Bildung und Forschung
- National Institutes of Health
- National Human Genome Research Institute (R01HG003143)
- FP7 Ideas: European Research Council (250367)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- X inactivation center, XIST, Tsix, topologically associating domains, 3D genome organization, long-range transcriptional regulation, X chromosome inactivation, chromatin interactions, embryonic stem cells, cell differentiation, lamina-associated domains, distal regulatory regions
- MeSH terms
- Animals, Cell Differentiation, Female, Fibroblasts, Gene Expression Regulation, Histones, Male, Methylation, Molecular Sequence Data, Promoter Regions, Genetic, X Chromosome, In Situ Hybridization, Fluorescence, DNA, Intergenic, RNA, Untranslated, Epigenesis, Genetic, X Chromosome Inactivation, Mice, Embryonic Stem Cells, Epigenomics, Transcriptome, RNA, Long Noncoding
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
