The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Chromatin architecture reorganization during stem cell differentiation
Open accessAbstract
Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages. An analysis of genome-wide chromatin interactions during human embryonic stem cell differentiation reveals changes in chromatic organization and simultaneously identifies allele-resolved chromatin structure and differences in gene expression during differentiation. Higher-order chromatin structures are among the factors influencing gene expression, although how these structures evolve during differentiation and lineage specification in mammalian systems is still unclear. Bing Ren and colleagues have mapped the differences in genome-wide chromatin interactions between human embryonic stem cells and their differentiated progeny. They delineate biases in allelic gene expression that correlate with allele-biased chromatin interactions between distal enhancers and proximal promoters.
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
“While standard Hi-C cannot discriminate whether an interacting fragment originated from the same or the other allele, allele-specific interaction maps can separate cis-allele from trans-allele interactions, thereby greatly improving the analysis of chromatin dynamics and gene regulation 20, 21.”
From SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes (2016) · cites this paper as [20]
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
“The classic model is that enhancers recruit cell- and condition-specific TFs and then loop in 3D space to interact with their target promoter90.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [90]
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
“In mammalian differentiation models, in contrast, extensive remodelling of enhancer–promoter contacts is typically observed consistently with enhancer activation [141, 394–397].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [397]
Experimental — accuracy not yet measuredIn the citing paper
“These methods have been used to decipher pathological evolution in tumors11,15,195–197 and somatic mosaicism198 in healthy tissues and in non-cancerous disease199–203.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [195]
In the citing paper
“Fundamentally different chromosome topologies have so far primarily been observed when comparing different developmental lineages (Dixon et al., 2015, Krijger et al., 2016).”
From The cohesin release factor WAPL restricts chromatin loop extension (2017) · cites this paper as Dixon et al., 2015
In the citing paper
“which are functionally related to gene expression and can switch extensively during differentiation (Dixon et al., 2015).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Dixon et al., 2015
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 Dixon et al., 2015
In the citing paper
“we observed a similar increase in insulation around SOX11 (Figure S3M).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Dixon et al., 2015
In the citing paper
“These TADs, which have similar boundaries in all human cell types examined, have been proposed to constrain enhancer-gene interactions because most DNA contacts occur within the TADs (Dixon et al., 2015; Dixon et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2015
In the citing paper
“These TADs, which have similar boundaries in all human cell types examined, have been proposed to constrain enhancer-gene interactions because most DNA contacts occur within the TADs (Dixon et al., 2015; Dixon et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2015
In the citing paper
“the striking similarity of TAD boundaries across cell types (Dixon et al., 2015; Dixon et al., 2012)”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2015
In the citing paper
“Studies on TADs have estimated that most TAD boundaries are shared by any two cell types (Dixon et al., 2015; Dixon et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Dixon et al., 2015
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
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457
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
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
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
Self-citationSystematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398
Self-citationSpatial 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
The accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533
Self-citationThree-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
Flagged first, then by citations
Cited by
Sorted by citations
Items 201–300 of 999
Exploiting sequence-based features for predicting enhancer–promoter interactions
Yang, Y., Zhang, R., Singh, S. K., & Ma, J. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx257 · Cited by 113
Emerging themes in cohesin cancer biology
Waldman, T. A. (2020) · Nature reviews. Cancer · doi:10.1038/s41568-020-0270-1 · Cited by 117
Liu, Y., Nanni, L., Sungalee, S., Zufferey, M., Tavernari, D., Mina, M., Ceri, S., Oricchio, E., & Ciriello, G. (2021) · Nature Communications · doi:10.1038/s41467-021-22666-3 · Cited by 112
Getting the genome in shape: the formation of loops, domains and compartments
Bouwman, B. A. M., & de Laat, W. L. (2015) · Genome biology · doi:10.1186/s13059-015-0730-1 · Cited by 115
Bovijn, J., Jackson, L. M., Censin, J. C., Chen, C., Laisk, T., Laber, S., Ferreira, T. C., Pulit, S. L., Glastonbury, C. A., Smoller, J. W., et al. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.11.004 · Cited by 114
Barrington, C., Georgopoulou, D., Pezic, D., Varsally, W., Herrero, J., & Hadjur, S. (2019) · Nature Communications · doi:10.1038/s41467-019-10725-9 · Cited by 102
Laugsch, 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
Inoue, F., Kreimer, A., Ashuach, T., Ahituv, N., & Yosef, N. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.09.010 · Cited by 109
The genetic architecture of sporadic and multiple consecutive miscarriage
Laisk, T., Soares, A. G., Ferreira, T. C., Painter, J. N., Censin, J. C., Laber, S., Bačelis, J., Chen, C., Lepamets, M., Lin, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19742-5 · Cited by 117
Robson, M. I., de las Heras, J. I., Czapiewski, R., Sivakumar, A., Kerr, A. R. W., & Schirmer, E. C. (2017) · Genome Research · doi:10.1101/gr.212308.116 · Cited by 107
Conserved non-coding elements: developmental gene regulation meets genome organization
Polychronopoulos, D., King, J. W. D., Nash, A. J., Tan, G., & Lenhard, B. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1074 · Cited by 111
Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency
Schlesinger, S., & Meshorer, E. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.01.003 · Cited by 109
Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence
Swygert, S. G., Kim, S., Wu, X., Fu, T., Hsieh, T.-H. S., Rando, O. J., Eisenman, R. N., Shendure, J., McKnight, J. N., & Tsukiyama, T. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.11.020 · Cited by 113
Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging
Liu, Z., Ji, Q., Ren, J., Yan, P., Wu, Z., Wang, S., Sun, L., Wang, Z., Li, J., Sun, G., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.05.004 · Cited by 109
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock
Ray, J., Munn, P. R., Vihervaara, A., Lewis, J. J., Ozer, A., Danko, C. G., & Lis, J. T. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1901244116 · Cited by 109
Predicting chromatin organization using histone marks
Huang, J., Marco, E., Pinello, L., & Yuan, G. (2015) · Genome biology · doi:10.1186/s13059-015-0740-z · Cited by 116
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
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
Decaesteker, B., Denecker, G., Neste, C. V., Dolman, M. E. M., Loocke, W. V., Gartlgruber, M., Nunes, C., Vloed, F. D., Depuydt, P., Verboom, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06699-9 · Cited by 102
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
Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Lazar, N. H., Nevonen, K. A., O'Connell, B., McCann, C., O'Neill, R. J., Green, R. E., Meyer, T. J., Okhovat, M., & Carbone, L. (2018) · Genome Research · doi:10.1101/gr.233874.117 · Cited by 107
Functional organization of the human 4D Nucleome
Chen, H., Chen, J., Muir, L. A., Ronquist, S., Meixner, W., Ljungman, M. E., Ried, T., Smale, S. T., & Rajapakse, I. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505822112 · Cited by 105
The Tug1 lncRNA locus is essential for male fertility
Lewandowski, J. P., Dumbović, G., Watson, A. R., Hwang, T., Jacobs-Palmer, E., Chang, N. P., Much, C., Turner, K. M., Kirby, C., Schulz, J. F., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02081-5 · Cited by 114
Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01089-w · Cited by 101
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
Spatial reorganization of telomeres in long-lived quiescent cells
Guidi, M., Ruault, M., Marbouty, M., Loïodice, I., Cournac, A., Billaudeau, C., Hocher, A., Mozziconacci, J., Koszul, R., & Taddei, A. (2015) · Genome biology · doi:10.1186/s13059-015-0766-2 · Cited by 114
Takayama, N., Murison, A., Takayanagi, S., Arlidge, C., Zhou, S., García‐Prat, L., Chan‐Seng‐Yue, M., Zandi, S., Gan, O. I., Boutzen, H., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.11.001 · Cited by 101
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
Sheikh, B. N., Guhathakurta, S., & Akhtar, A. (2019) · EMBO Reports · doi:10.15252/embr.201847630 · Cited by 103
YAP/TAZ drives cell proliferation and tumour growth via a polyamine–eIF5A hypusination–LSD1 axis
Li, H., Wu, B.-K., Kanchwala, M., Cai, J., Wang, L., Xing, C., Zheng, Y., & Pan, D. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00848-5 · Cited by 106
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression
Quigley, I. K., & Kintner, C. R. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006538 · Cited by 103
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
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
Self-citationUMI-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
Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids
D’Ippolito, A. M., McDowell, I. C., Barrera, A., Hong, L. K., Leichter, S. M., Bartelt, L. C., Vockley, C. M., Majoros, W. H., Safi, A., Song, L., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.06.007 · Cited by 106
Zhang, X., Liu, X., Du, Z., Wei, L., Fang, H., Dong, Q., Niu, J., Li, Y., Gao, J. T., Zhang, M. Q., et al. (2021) · Genome Research · doi:10.1101/gr.275235.121 · Cited by 103
Self-citation3C 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
Principles of 3D compartmentalization of the human genome
Nichols, M. H., & Corces, V. G. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109330 · Cited by 91
Control of plant cell differentiation by histone modification and DNA methylation
Ikeuchi, M., Iwase, A., & Sugimoto, K. (2015) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2015.09.004 · Cited by 97
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
Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity
Zhang, X., Jeong, M., Huang, X., Wang, X. Q. D., Wang, X., Zhou, W., Shamim, M. S., Gore, H., Himadewi, P., Liu, Y., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.018 · Cited by 95
Kubo, N., Chen, P. B., Hu, R., Ye, Z., Sasaki, H., & Ren, B. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.030 · Cited by 99
Self-citationOnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
An, L., Yang, T., Yang, J., Nuebler, J., Xiang, G., Hardison, R. C., Li, Q., & Zhang, Y. (2019) · Genome biology · doi:10.1186/s13059-019-1893-y · Cited by 91
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
Okabe, A., Huang, K., Matsusaka, K., Masaki, F., Xing, M., Ong, X., Hoshii, T., Usui, G., Seki, M., Mano, Y., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0665-7 · Cited by 88
CRISPR/Cas System and Factors Affecting Its Precision and Efficiency
Javaid, N., & Choi, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.761709 · Cited by 106
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
Wang, X., Cui, W., & Peng, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx735 · Cited by 94
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
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
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
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
Statistical methods for SNP heritability estimation and partition: A review
Zhu, H., & Zhou, X. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.06.011 · Cited by 103
Nucleome Dynamics during Retinal Development
Norrie, J. L., Lupo, M. S., Xu, B., Aldiri, I., Valentine, M. B., Putnam, D. K., Griffiths, L. M., Zhang, J., Johnson, D. A., Easton, J. B., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.08.002 · Cited by 87
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
Self-citationThe 3D architecture of the pepper genome and its relationship to function and evolution
Liao, Y., Wang, J., Zhu, Z., Liu, Y., Chen, J., Zhou, Y., Liu, F., Lei, J., Gaut, B. S., Cao, B., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31112-x · Cited by 88
Domestic dog lineages reveal genetic drivers of behavioral diversification
Dutrow, E. V., Serpell, J. A., & Ostrander, E. A. (2022) · Cell · doi:10.1016/j.cell.2022.11.003 · Cited by 100
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
Augsornworawat, P., Hogrebe, N. J., Ishahak, M., Schmidt, M. D., Marquez, E., Maestas, M. M., Veronese-Paniagua, D., Gale, S. E., Miller, J. R., Velazco-Cruz, L., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01150-8 · Cited by 91
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
Chromatin organisation and cancer prognosis: a pan-cancer study
Kleppe, A., Albregtsen, F., Vlatkovic, L., Pradhan, M., Nielsen, B., Hveem, T. S., Askautrud, H. A., Kristensen, G. B., Nesbakken, A., Trovik, J., et al. (2018) · The Lancet Oncology · doi:10.1016/s1470-2045(17)30899-9 · Cited by 87
Chromatin state changes during neural development revealed by in vivo cell-type specific profiling
Marshall, O. J., & Brand, A. H. (2017) · Nature Communications · doi:10.1038/s41467-017-02385-4 · Cited by 89
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
Fadason, T., Ekblad, C., Ingram, J. R., Schierding, W. S., & O'Sullivan, J. M. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00150 · Cited by 90
Lazaris, C., Kelly, S. M., Ntziachristos, P., Aifantis, I., & Tsirigos, A. (2016) · BMC Genomics · doi:10.1186/s12864-016-3387-6 · Cited by 83
Restraint‐based three‐dimensional modeling of genomes and genomic domains
Serra, F., Stefano, M. D., Spill, Y. G., Cuartero, Y., Goodstadt, M. N., Baù, D., & Martı́-Renom, M. A. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.012 · Cited by 86
TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains
Cresswell, K. G., & Dozmorov, M. G. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00158 · Cited by 81
DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift
Franzen, J., Georgomanolis, T., Selich, A., Kuo, C., Stöger, R. J., Brant, L., Mulabdić, M. S., Fernández‐Rebollo, E., Grezella, C., Ostrowska, A., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02116-y · Cited by 90
Caputo, L., Witzel, H. R., Kolovos, P., Cheedipudi, S. M., Looso, M., Mylona, A., van IJcken, W. F. J., Laugwitz, K., Evans, S. Μ., Braun, T. W., et al. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.08.007 · Cited by 88
Common DNA sequence variation influences 3-dimensional conformation of the human genome
Gorkin, D. U., Qiu, Y., Hu, M., Fletez‐Brant, K., Liu, T., Schmitt, A. D., Noor, A., Chiou, J., Gaulton, K. J., Sebat, J. L., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1855-4 · Cited by 82
Self-citationChromatin 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
Genomes in Focus: Development and Applications of CRISPR‐Cas9 Imaging Technologies
Knight, S. C., Tjian, R., & Doudna, J. A. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201709201 · Cited by 86
DNA Methylation and Psychiatric Disorders
Liu, C., Jiao, C., Wang, K., & Yuan, N. (2018) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2018.01.006 · Cited by 86
multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments
Stansfield, J. C., Cresswell, K. G., & Dozmorov, M. G. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz048 · Cited by 81
Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos
Chen, M., Zhu, Q., Li, C., Kou, X., Zhao, Y., Li, Y., Xu, R., Yang, L., Yang, L., Gu, L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15607-z · Cited by 85
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
Epigenetic Regulators as the Gatekeepers of Hematopoiesis
Rodrigues, C. P., Shvedunova, M., & Akhtar, A. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.09.015 · Cited by 99
Rhee, H. S., Closser, M., Guo, Y., Bashkirova, E., Tan, G. C., Gifford, D. K., & Wichterle, H. (2016) · Neuron · doi:10.1016/j.neuron.2016.11.037 · Cited by 86
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 87
Chromatin Architectural Changes during Cellular Senescence and Aging
Sun, L., Yu, R., & Dang, W. (2018) · Genes · doi:10.3390/genes9040211 · Cited by 90
Liu, Y., Reynolds, L. M., Ding, J., Hou, L., Lohman, K., Young, T., Cui, W., Huang, Z., Grenier, C., Wan, M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00517-4 · Cited by 83
Chen, H., Zhang, Z., Jiang, S., Li, R., Li, W., Zhao, C., Hong, H., Huang, X., Li, H., & Bo, X. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz072 · Cited by 82
Forces driving the three‐dimensional folding of eukaryotic genomes
Rada-Iglesias, Á., Grosveld, F. G., & Papantonis, A. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188214 · Cited by 84
Differential contribution of steady‐state RNA and active transcription in chromatin organization
Barutcu, A. R., Blencowe, B., & Rinn, J. (2019) · EMBO Reports · doi:10.15252/embr.201948068 · Cited by 71
Transcriptional reprogramming at the intersection of the heat shock response and proteostasis
Pessa, J. C., Joutsen, J., & Sistonen, L. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.11.024 · Cited by 85
RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells
Barutcu, A. R., Hong, D., Lajoie, B. R., McCord, R. P., van Wijnen, A. J., Lian, J. B., Stein, J. L., Dekker, J., Imbalzano, A. N., & Stein, G. S. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.08.003 · Cited by 80
IC-Finder: inferring robustly the hierarchical organization of chromatin folding
Haddad, N., Vaillant, C., & Jost, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx036 · Cited by 81
Transcriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81
Ito, H., Tanaka, S., Akiyama, Y., Shimada, S., Adikrisna, R., Matsumura, S., Aihara, A., Mitsunori, Y., Ban, D., Ochiai, T., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0146564 · Cited by 82
Dong, P., Tu, X., Li, H., Zhang, J., Grierson, D. S., Li, P., & Zhong, S. (2019) · Journal of Integrative Plant Biology · doi:10.1111/jipb.12809 · Cited by 83
Chromosome-level organization of the regulatory genome in the Drosophila nervous system
Mohana, G., Dorier, J., Li, X., Mouginot, M., Smith, R. C., Malek, H., Leleu, M., Rodríguez, D., Khadka, J., Rosa, P., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.008 · Cited by 81
Acemel, R. D., Maeso, I., & Gómez-Skármeta, J. L. (2017) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.265 · Cited by 82
Pouikli, A., Parekh, S., Maleszewska, M., Nikopoulou, C., Baghdadi, M., Tripodi, I. J., Folz‐Donahue, K., Hinze, Y., Mesaros, A., Hoey, D. A., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00105-8 · Cited by 84
3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk
Su, C., Gao, L., May, C. L., Pippin, J. A., Boehm, K. D., Lee, M., Liu, C., Pahl, M. C., Golson, M. L., Naji, A., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.08.014 · Cited by 78
Deciphering Hi-C: from 3D genome to function
Kong, S., & Zhang, Y. (2019) · Cell Biology and Toxicology · doi:10.1007/s10565-018-09456-2 · Cited by 85
The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders
Zepeda‐Mendoza, C. J., & Morton, C. C. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.02.024 · Cited by 83
Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells
Chen, C., Yu, W., Tober, J. M., Gao, P., He, B., Lee, K., Trieu, T., Blobel, G. A., Speck, N. A., & Tan, K. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.065 · Cited by 79
dcHiC detects differential compartments across multiple Hi-C datasets
Chakraborty, A., Wang, J., & Ay, F. (2022) · Nature Communications · doi:10.1038/s41467-022-34626-6 · Cited by 76
Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C
Maass, P. G., Barutcu, A. R., Weiner, C. L., & Rinn, J. L. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.02.007 · Cited by 73
Metadata
- Authors
- Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V. V., Ecker, J. R., Thomson, J. A., & Ren, B.
- Affiliations
- Ludwig Cancer Research (BE)
- Peking University (CN)
- University of Illinois Urbana-Champaign (US)
- National Institutes of Health (US)
- Salk Institute for Biological Studies (US)
- University of Wisconsin–Madison (US)
- University of California San Diego (US)
- Corresponding author
- Ren, Bing
- ORCID
- Venue
- Nature
- Published
- 2015-02-18
- Volume
- 518
- Issue
- 7539
- Pages
- 331-336
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4515363
- OpenAlex
- W2080477348
- Cited by
- 1,646
- References
- 45
- Citations by year
- 2026: 76 · 2025: 101 · 2024: 112 · 2023: 132 · 2022: 141 · 2021: 202 · 2020: 181 · 2019: 186 · 2018: 186 · 2017: 133 · 2016: 130 · 2015: 63
- FWCI
- 74.52
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-sa)
- Funders
- Howard Hughes Medical Institute
- California Institute of Regenerative Medicine (RN2-00905)
- Ludwig Institute for Cancer Research
- National Institutes of Health
- National Institute of General Medical Sciences (T32GM007198)
- National Institute of Environmental Health Sciences (U01ES017166, R01ES024984)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromatin structure, chromatin interactions, human embryonic stem cells, stem cell differentiation, lineage specification, chromatin domains, distal enhancers, enhancer-promoter interactions, long-range gene regulation, epigenome, transcriptome
- MeSH terms
- Alleles, Cell Differentiation, Chromatin, Enhancer Elements, Genetic, Humans, Promoter Regions, Genetic, Reproducibility of Results, Cell Lineage, Allelic Imbalance, Chromatin Assembly and Disassembly, Epigenesis, Genetic, Gene Regulatory Networks, Embryonic Stem Cells, Epigenomics
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
