The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
Open accessAbstract
Recent epigenomic studies have predicted thousands of potential enhancers in the human genome. However, there has not been systematic characterization of target promoters for these potential enhancers. Using H3K4me2 as a mark for active enhancers, we identified genome-wide EP interactions in human CD4(+) T cells. Among the 6 520 long-distance chromatin interactions, we identify 2 067 enhancers that interact with 1 619 promoters and enhance their expression. These enhancers exist in accessible chromatin regions and are associated with various histone modifications and polymerase II binding. The promoters with interacting enhancers are expressed at higher levels than those without interacting enhancers, and their expression levels are positively correlated with the number of interacting enhancers. Interestingly, interacting promoters are co-expressed in a tissue-specific manner. We also find that chromosomes are organized into multiple levels of interacting domains. Our results define a global view of EP interactions and provide a data set to further understand mechanisms of enhancer targeting and long-range chromatin organization. The Gene Expression Omnibus accession number for the raw and analyzed chromatin interaction data is GSE32677.
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?
In the citing paper
“Enhancer-bound proteins are constrained such that they tend to interact only with genes within these CTCF-CTCF loops.”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Chepelev et al., 2012
In the citing paper
“In the models that emerge from these data, each chromosome contains thousands of DNA loops, formed by the interaction of two CTCF molecules bound to different sites, and reinforced by a cohesin molecule (Figure 2A).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Chepelev et al., 2012
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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
(1996) · Cited by 20,179
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
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
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
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
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
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
Flagged first, then by citations
Research works printed but not linked: 1
- Wang Z, Zang C, Rosenfeld JA, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 2008; 40:897–903. · DOI · Paper page
Cited by
Sorted by citations
Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers
Lovén, J., Hoke, H. A., Lin, C. Y., Lau, A., Orlando, D. A., Vakoc, C. R., Bradner, J. E., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.036 · Cited by 2,961
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550
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
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
Dowen, J. M., Fan, Z. P., Hnisz, D., Ren, G., Abraham, B. J., Zhang, L. N., Weintraub, A. S., Schuijers, J., Lee, T. I., Zhao, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.030 · Cited by 884
Beyond GWASs: Illuminating the Dark Road from Association to Function
Edwards, S. L., Beesley, J., French, J. D., & Dunning, A. M. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.012 · Cited by 784
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 742
Enhancers: five essential questions
Pennacchio, L. A., Bickmore, W. A., Dean, A., Nóbrega, M. A., & Bejerano, G. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3458 · Cited by 625
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
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
Hnisz, D., Day, D. S., & Young, R. A. (2016) · Cell · doi:10.1016/j.cell.2016.10.024 · Cited by 420
dbSUPER: a database of super-enhancers in mouse and human genome
Khan, A., & Zhang, X. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1002 · Cited by 392
Different Neuronal Activity Patterns Induce Different Gene Expression Programs
Tyssowski, K. M., DeStefino, N. R., Cho, J.-H., Dunn, C. J., Poston, R. G., Carty, C. E., Jones, R. D., Chang, S. M., Romeo, P., Wurzelmann, M. K., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.04.001 · Cited by 390
Enhancer RNAs are an important regulatory layer of the epigenome
Sartorelli, V., & Lauberth, S. M. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0446-0 · Cited by 380
Mechanisms of enhancer action: the known and the unknown
Panigrahi, A., & O’Malley, B. W. (2021) · Genome biology · doi:10.1186/s13059-021-02322-1 · Cited by 376
Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors
Crotti, A., Benner, C., Kerman, B. E., Gosselin, D., Lagier-Tourenne, C., Zuccato, C., Cattaneo, E., Gage, F. H., Cleveland, D. W., & Glass, C. K. (2014) · Nature Neuroscience · doi:10.1038/nn.3668 · Cited by 333
Nakayama, R. T., Pulice, J. L., Valencia, A. M., McBride, M. J., McKenzie, Z. M., Gillespie, M. A. K., Ku, W. L., Teng, M., Cui, K., Williams, R. T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3958 · Cited by 300
Genome-wide map of regulatory interactions in the human genome
Heidari, N., Phanstiel, D. H., He, C., Grubert, F., Jahanbani, F., Kasowski, M., Zhang, M. Q., & Snyder, M. P. (2014) · Genome Research · doi:10.1101/gr.176586.114 · Cited by 278
Global view of enhancer–promoter interactome in human cells
He, B., Chen, C., Teng, L., & Tan, K. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320308111 · Cited by 263
Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex
Liu, Z., Merkurjev, D., Yang, F., Li, W., Oh, S., Friedman, M. J., Song, X., Zhang, F., Ma, Q., Ohgi, K. A., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.027 · Cited by 221
Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells
Hu, G., Cui, K., Fang, D., Hirose, S., Wang, X., Wangsa, D., Jin, W., Ried, T., Liu, P., Zhu, J., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.01.013 · Cited by 199
Self-citationRNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation
Rahnamoun, H., Lee, J. H., Sun, Z., Lu, H., Ramsey, K. M., Komives, E. A., & Lauberth, S. M. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0102-0 · Cited by 184
Zrimec, J., Börlin, C. S., Buric, F., Muhammad, A. S., Chen, R., Siewers, V., Verendel, V., Nielsen, J., Töpel, M., & Zelezniak, A. (2020) · Nature Communications · doi:10.1038/s41467-020-19921-4 · Cited by 174
Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Zrimec, J., Buric, F., Muhammad, A. S., Chen, R., Verendel, V., Töpel, M., & Zelezniak, A. (2019) · doi:10.1101/792531 · Cited by 173
Genome organization and long-range regulation of gene expression by enhancers
Smallwood, A., & Ren, B. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.02.005 · Cited by 155
Bunting, K. L., Soong, T. D., Singh, R., Jiang, Y., Béguelin, W., Poloway, D. W., Swed, B. L., Hatzi, K., Reisacher, W., Teater, M., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.08.012 · Cited by 141
Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions
Li, X., Luo, O. J., Wang, P., Zheng, M., Wang, D., Piecuch, E., Zhu, J. J., Tian, S. Z., Tang, Z., Li, G., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2017.012 · Cited by 129
Long-range interactions between proximal and distal regulatory regions in maize
Li, E., Liu, H., Huang, L., Zhang, X., Dong, X., Song, W., Zhao, H., & Lai, J. (2019) · Nature Communications · doi:10.1038/s41467-019-10603-4 · Cited by 134
MIR retrotransposon sequences provide insulators to the human genome
Wang, J., Vicente‐García, C., Seruggia, D., Moltó, E., Fernández‐Miñán, A., Neto, A., Lee, E., Gómez-Skármeta, J. L., Montoliu, L., Lunyak, V. V., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1507253112 · Cited by 128
Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application
Li, G., Cai, L., Chang, H., Hong, P., Zhou, Q., Kulakova, E. V., Kolchanov, N. A., & Ruan, Y. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s12-s11 · Cited by 131
DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements
Mercer, T. R., Edwards, S. L., Clark, M. B., Neph, S. J., Wang, H., Stergachis, A. B., John, S., Sandstrom, R. S., Li, G., Sandhu, K. S., et al. (2013) · Nature Genetics · doi:10.1038/ng.2677 · Cited by 130
Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae
Ngan, C. Y., Wong, C., Choi, C., Yoshinaga, Y., Louie, K., Jia, J., Chen, C., Bowen, B. P., Cheng, H., Leonelli, L., et al. (2015) · Nature Plants · doi:10.1038/nplants.2015.107 · Cited by 119
HACER: an atlas of human active enhancers to interpret regulatory variants
Wang, J., Dai, X., Berry, L. D., Cogan, J. D., Liu, Q., & Shyr, Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky864 · Cited by 110
Chromatin-Driven Behavior of Topologically Associating Domains
Ciabrelli, F., & Cavalli, G. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.09.013 · Cited by 123
In the loop: promoter–enhancer interactions and bioinformatics
Mora, A., Sandve, G. K., Gabrielsen, O. S., & Eskeland, R. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv097 · Cited by 126
Chromatin and epigenetic features of long-range gene regulation
Harmston, N., & Lenhard, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt499 · Cited by 113
Decker, K. F., Zheng, D., He, Y., Bowman, T. A., Edwards, J. R., & Li, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks888 · Cited by 106
Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling
Rahnamoun, H., Lu, H., Duttke, S. H. C., Benner, C. W., Glass, C. K., & Lauberth, S. M. (2017) · Nature Communications · doi:10.1038/s41467-017-01117-y · Cited by 103
Rosin, L. F., Nguyen, S. C., & Joyce, E. F. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007393 · Cited by 98
H3K4me2 reliably defines transcription factor binding regions in different cells
Wang, Y., Li, X., & Hu, H. (2014) · Genomics · doi:10.1016/j.ygeno.2014.02.002 · Cited by 97
Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes
Choudhary, M. N. K., Quaid, K., Xing, X., Schmidt, H. K., & Wang, T. (2023) · Nature Communications · doi:10.1038/s41467-023-36364-9 · Cited by 102
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
ChIA-PET analysis of transcriptional chromatin interactions
Zhang, J., Poh, H. M., Peh, S. Q., Sia, Y. Y., Li, G., Mulawadi, F. H., Goh, Y., Fullwood, M. J., Sung, W.-K. K., Ruan, X., et al. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.009 · Cited by 96
Long distance relationships: Enhancer–promoter communication and dynamic gene transcription
Marsman, J., & Horsfield, J. A. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.10.008 · Cited by 91
Kim, K.-D., Tanizawa, H., Iwasaki, O., & Noma, K.-I. (2016) · Nature Genetics · doi:10.1038/ng.3647 · Cited by 86
Thévenin, A., Ein-Dor, L., Ozery-Flato, M., & Shamir, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku667 · Cited by 84
Harmston, N., Ing‐Simmons, E., Perry, M., Barešić, A., & Lenhard, B. (2015) · BMC Genomics · doi:10.1186/s12864-015-2140-x · Cited by 83
Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Burren, O. S., Rubio García, A., Javierre, B.-M., Rainbow, D. B., Cairns, J., Cooper, N. J., Lambourne, J. J., Schofield, E., Castro Dopico, X., Ferreira, R. C., et al. (2017) · Genome Biology · doi:10.1186/s13059-017-1285-0 · Cited by 80
Arnesen, S., Blanchard, Z., Williams, M. M., Berrett, K. C., Li, Z., Oesterreich, S., Richer, J. K., & Gertz, J. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-1171 · Cited by 85
Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer
Ding, P., Ge, G., Gong, Y., Zhan, Y., He, S., Guan, B., Li, Y., Xu, Z., Hao, H., He, Z., et al. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0527-7 · Cited by 78
Understanding the regulatory and transcriptional complexity of the genome through structurePreprint
Mercer, T. R., & Mattick, J. S. (2013) · Genome Research · doi:10.1101/gr.156612.113 · Cited by 77
Guan, Y., Zhang, C., Lyu, G., Zhang, X., Zhuang, T., Zhuang, T., Jia, L., Zhang, C., Zhang, C., Li, C., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa858 · Cited by 81
Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
Wang, J., Zhao, Y., Zhou, X., Hiebert, S. W., Liu, Q., & Shyr, Y. (2018) · BMC Genomics · doi:10.1186/s12864-018-5016-z · Cited by 77
Dynamic evolution of regulatory element ensembles in primate CD4+ T cells
Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Wojno, E. D. T., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0447-5 · Cited by 75
Gorkin, D. U., Lee, D., Reed, X., Fletez-Brant, C., Bessling, S. L., Loftus, S. K., Beer, M., Pavan, W. J., & McCallion, A. S. (2012) · Genome Research · doi:10.1101/gr.139360.112 · Cited by 72
Accurate loop calling for 3D genomic data with cLoops
Cao, Y., Chen, Z., Chen, X., Ai, D., Chen, G., McDermott, J., Huang, Y., Guo, X., & Han, J. J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz651 · Cited by 69
Alcina, A., Fedetz, M., Fernández, Ó., Saiz, A., Izquierdo, G., Lucas, M., Leyva, L., García-León, J.-A., Abad-Grau, M. D. M., Alloza, I., et al. (2013) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2012-101085 · Cited by 69
The role of MyoD1 and histone modifications in the activation of muscle enhancers
Blum, R., & Dynlacht, B. D. (2013) · Epigenetics · doi:10.4161/epi.25441 · Cited by 63
Russ, B. E., Olshansky, M., Li, J., Nguyen, M. L. T., Gearing, L. J., Nguyen, T. H. O., Olson, M. R., McQuilton, H. A., Nüssing, S., Khoury, G., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.11.097 · Cited by 65
Visser, M., Palstra, R.-J., & Kayser, M. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv029 · Cited by 57
A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
Paulsen, J., Rødland, E. A., Holden, L., Holden, M., & Hovig, E. J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku738 · Cited by 61
Babu, D., & Fullwood, M. J. (2015) · Nucleus · doi:10.1080/19491034.2015.1106676 · Cited by 59
Epigenomics and the Regulation of Aging
Boyd-Kirkup, J. D., Green, C. D., Wu, G., Wang, D., & Han, J. J. (2013) · Epigenomics · doi:10.2217/epi.13.5 · Cited by 57
Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers
Khan, A., Mathelier, A., & Zhang, X. (2018) · Epigenetics · doi:10.1080/15592294.2018.1514231 · Cited by 58
Rennie, S., Dalby, M., Lloret-Llinares, M., Bakoulis, S., Vaagensø, C. D., Jensen, T. H., & Andersson, R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky244 · Cited by 59
Li, J., Xiang, Y., Zhang, L., Qi, X., Zheng, Z., Zhou, P., Tang, Z., Jin, Y., Zhao, Q., Fu, Y., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01322-2 · Cited by 51
Eukaryotic enhancers: common features, regulation, and participation in diseases
Erokhin, M., Vassetzky, Y. S., Georgiev, P. G., & Chetverina, D. (2015) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-015-1871-9 · Cited by 54
Xu, H., Zhang, S., Yi, X., Plewczyński, D., & Li, M. J. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.02.013 · Cited by 48
Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux
Palstra, R.-J. T. S., & Grosveld, F. G. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00195 · Cited by 55
Rhie, S. K., Hazelett, D. J., Coetzee, S. G., Yan, C., Noushmehr, H., & Coetzee, G. A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-331 · Cited by 47
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies
Xiao, X., Chang, H., & Li, M. (2017) · Molecular Psychiatry · doi:10.1038/mp.2016.241 · Cited by 51
siVAE: interpretable deep generative models for single-cell transcriptomes
Choi, Y., Li, R., & Quon, G. (2023) · Genome biology · doi:10.1186/s13059-023-02850-y · Cited by 51
Cooperation of Genomic and Rapid Nongenomic Actions of Estrogens in Synaptic Plasticity
Lai, Y., Yu, D. S., Zhang, J. H., & Chen, G. (2016) · Molecular Neurobiology · doi:10.1007/s12035-016-9979-y · Cited by 47
Winata, C. L., Kondrychyn, I., Kumar, V., Srinivasan, K. G., Orlov, Y. L., Ravishankar, A., Prabhakar, S., Stanton, L. W., Korzh, V. P., & Mathavan, S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003852 · Cited by 44
Gene Positioning Effects on Expression in Eukaryotes
Nguyen, H. Q., & Bosco, G. (2015) · Annual Review of Genetics · doi:10.1146/annurev-genet-112414-055008 · Cited by 43
Tallury, S. S., Spontak, R. J., & Pasquinelli, M. A. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4904388 · Cited by 43
EnhancerDB: a resource of transcriptional regulation in the context of enhancers
Kang, R., Zhang, Y., Huang, Q., Meng, J., Ding, R., Chang, Y., Xiong, L., & Guo, Z. (2018) · Database · doi:10.1093/database/bay141 · Cited by 40
Chen, Y., Wang, Y., Xuan, Z., Chen, M., & Zhang, M. Q. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw225 · Cited by 41
O’Brien, S. A., Lee, K., Fu, H., Lee, Z., Le, T. S., Stach, C. S., McCann, M. G., Zhang, A. Q., Smanski, M. J., Somia, N. V., et al. (2018) · Biotechnology Journal · doi:10.1002/biot.201800226 · Cited by 41
Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops
Liu, S., Cao, Y., Cui, K., Tang, Q., & Zhao, K. (2022) · Nature Communications · doi:10.1038/s41467-022-34276-8 · Cited by 42
Ma, Q., Yang, F., Mackintosh, C., Jayani, R. S., Oh, S., Jin, C., Nair, S. J., Merkurjev, D., Ma, W., Allen, S., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2020.107532 · Cited by 37
Estrogen receptor-mediated long-range chromatin interactions and transcription in breast cancer
Liu, M. H., & Cheung, E. C. W. (2013) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2013.09.019 · Cited by 40
Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome
Naville, M., Ishibashi, M., Ferg, M., Bengani, H., Rinkwitz, S., Krecsmarik, M., Hawkins, T. A., Wilson, S. W., Manning, E., Chilamakuri, C. S. R., et al. (2015) · Nature Communications · doi:10.1038/ncomms7904 · Cited by 38
Gene functioning and storage within a folded genome
Razin, S. V., & Ulianov, S. V. (2017) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-017-0050-4 · Cited by 37
Lopes, R., Sprouffske, K., Sheng, C., Uijttewaal, E., Wesdorp, A. E., Dahinden, J., Wengert, S., Díaz-Miyar, J., Yildiz, U., Bleu, M., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf5733 · Cited by 31
Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication
Ulianov, S. V., Gavrilov, A. A., & Razin, S. V. (2015) · International review of cytology · doi:10.1016/bs.ircmb.2014.11.004 · Cited by 37
Lu, M., McComish, B. J., Burdon, K. P., Taylor, B. V., & Körner, H. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.00488 · Cited by 37
Chromatin remodeling effects on enhancer activity
García-González, E. G., Escamilla-Del-Arenal, M., Arzate‐Mejía, R. G., & Targa, F. R. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2184-3 · Cited by 41
Rahnamoun, H., Hong, J., Sun, Z., Lee, J. H., Lu, H., & Lauberth, S. M. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.003387 · Cited by 35
INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues ofArabidopsis
Yadav, V. K., Santos‐González, J., & Köhler, C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab191 · Cited by 35
NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Merelli, I., Lió, P., & Milanesi, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075146 · Cited by 32
Nuclear architecture as an epigenetic regulator of neural development and function
Alexander, J. M., & Lomvardas, S. (2014) · Neuroscience · doi:10.1016/j.neuroscience.2014.01.044 · Cited by 32
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers
Khan, A., & Zhang, X. (2019) · Scientific Reports · doi:10.1038/s41598-019-38979-9 · Cited by 33
Rozenwald, M., Galitsyna, A. A., Sapunov, G. V., Khrameeva, E. E., & Gelfand, M. S. (2020) · PeerJ Computer Science · doi:10.7717/peerj-cs.307 · Cited by 32
Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment
Boya, R., Yadavalli, A. D., Nikhat, S., Kurukuti, S., Palakodeti, D., & Pongubala, J. M. R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx722 · Cited by 30
Lee, B. H., Wu, Z., & Rhie, S. (2022) · Epigenetics & Chromatin · doi:10.1186/s13072-022-00473-4 · Cited by 24
Transcription factor and chromatin features predict genes associated with eQTLs
Wang, D. Y. Q., Rendon, A., & Wernisch, L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1339 · Cited by 32
Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
Feigin, C. Y., Newton, A. H., & Pask, A. J. (2019) · Genome Research · doi:10.1101/gr.244251.118 · Cited by 33
Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer
Ropri, A. S., DeVaux, R. S., Eng, J., Chittur, S. V., & Herschkowitz, J. I. (2021) · Breast Cancer Research · doi:10.1186/s13058-021-01479-8 · Cited by 30
Comprehensive characterization of the epigenetic landscape in Multiple Myeloma
Alaterre, E., Ovejero, S., Herviou, L., de Boussac, H., Papadopoulos, G. L., Kulis, M., Boireau, S., Robert, N., Requirand, G., Bruyer, A., et al. (2022) · Theranostics · doi:10.7150/thno.54453 · Cited by 30
Functional characterization of human genomic variation linked to polygenic diseases
Fabo, T., & Khavari, P. A. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.02.014 · Cited by 32
Hijacked enhancer–promoter and silencer–promoter loops in cancer
Wang, X., & Yue, F. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102199 · Cited by 32
Metadata
- Authors
- Chepelev, I., Wei, G., Wangsa, D., Tang, Q., & Zhao, K.
- Affiliations
- National Heart, Lung, and Blood Institute (US)
- National Institutes of Health (US)
- Corresponding author
- Zhao, Keji
- Venue
- Cell Research
- Published
- 2012-01-24
- Volume
- 22
- Issue
- 3
- Pages
- 490-503
- ISSN
- 1001-0602 (ISSN-L)
- 1748-7838
- PMC
- PMC3292289
- OpenAlex
- W2154077612
- Cited by
- 253
- References
- 48
- Citations by year
- 2026: 6 · 2025: 11 · 2024: 6 · 2023: 14 · 2022: 23 · 2021: 27 · 2020: 14 · 2019: 21 · 2018: 23 · 2017: 18 · 2016: 20 · 2015: 19 · 2014: 23 · 2013: 19 · 2012: 9
- FWCI
- 8.99
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Cell Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute
- NHLBI Division of Intramural Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- enhancer-promoter interactions, long-range chromatin interactions, H3K4me2, CD4+ T cells, chromatin organization, chromosome domains, histone modifications, chromatin accessibility, gene expression regulation
- MeSH terms
- Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Histone-Lysine N-Methyltransferase, Genome, Human
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