Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
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In mammalian differentiation models, extensive remodelling of enhancer-promoter contacts is typically observed consistently with enhancer activation.
“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 [395]
The Results and Discussion report extensive promoter–enhancer loop rewiring coupled to enhancer activation during 3T3-L1 adipocyte differentiation. But the paper studies one differentiation model and says previous studies had not reached a clear consensus on loop plasticity; it does not establish that this is typically observed across mammalian differentiation models. Page numbers are unavailable in our copy. (LLM, conf=0.86)
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“[15-60] Solyc08g062437 Solyc08g062437 Mo f Mo f family P-value”
BackgroundTranscriptional control of energy metabolism by nuclear receptors
Scholtes, C., & Giguère, V. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00486-7 · Cited by 129 · see citing works
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 · see citing works
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
Schoenfelder, S., Javierre, B. M., Furlan-Magaril, M., Wingett, S., & Fraser, P. (2018) · Journal of Visualized Experiments · doi:10.3791/57320 · Cited by 114 · see citing works
Self-citationp53 Functions in Adipose Tissue Metabolism and Homeostasis
Krstić, J., Reinisch, I., Schupp, M., Schulz, T. J., & Prokesch, A. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092622 · Cited by 106 · see citing works
Adipose PD-L1 Modulates PD-1/PD-L1 Checkpoint Blockade Immunotherapy Efficacy in Breast Cancer
Wu, B., Sun, X., Gupta, H. B., Yuan, B., Li, J., Ge, F., Chiang, H.-C., Zhang, X., Zhang, C., Zhang, D., et al. (2018) · OncoImmunology · doi:10.1080/2162402x.2018.1500107 · Cited by 98 · see citing works
“tion mediator protein frequently associated with transcriptional enhancers.(63) Two clusters of MED1 ChIP-seq are observed around the Cd274/Pd-l1 locus after, but not before, differentiation (Clusters 1 and 2; Supplementary Figure 6).”
BackgroundMadsen, J. G. S., Madsen, M. S., Rauch, A., Traynor, S., Hauwaert, E. L. V., Haakonsson, A. K., Javierre, B. M., Hyldahl, M., Fraser, P., & Mandrup, S. (2020) · Nature Genetics · doi:10.1038/s41588-020-0709-z · Cited by 94 · see citing works
Self-citationDall’Agnese, A., Caputo, L., Nicoletti, C., di Iulio, J., Schmitt, A., Gatto, S., Diao, Y., Ye, Z., Forcato, M., Perera, R. J., et al. (2019) · Molecules and Cells · doi:10.1016/j.molcel.2019.07.036 · Cited by 82 · see citing works
“While higher genomic structures appear to be generally conserved, chromatin interactions within TADs, subTADs and INs, could rather be cell-type specific and dynamic (Bonev et al., 2017; Dixon et al., 2015; Hnisz et al., 2013; Hnisz et al., 2016a; Javierre et al., 2016; Ji et al., 2016; Phanstiel et al., 2017; Remesei…”
BackgroundResultTRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells
Elster, D., Tollot, M., Schlegelmilch, K., Ori, A., Rosenwald, A., Sahai, E. A., & von Eyß, B. (2018) · Nature Communications · doi:10.1038/s41467-018-05370-7 · Cited by 85 · see citing works
Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates
Eres, I. E., Luo, K., Hsiao, C. J., Blake, L. E., & Gilad, Y. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008278 · Cited by 85 · see citing works
“Nevertheless, independent evidence strongly suggests that changes in 3D genomic structure can affect interactions between regulatory elements and promoters [45, 63-66], which may ultimately drive differences in gene expression levels [33, 63-68].”
BackgroundIncreased enhancer–promoter interactions during developmental enhancer activation in mammals
Chen, Z., Snetkova, V., Bower, G., Jacinto, S. H., Clock, B., Dizehchi, A., Barozzi, I., Mannion, B. J., Alcaina‐Caro, A., López-Rı́os, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01681-2 · Cited by 84 · see citing works
Pollex, T., Rabinowitz, A. H., Gambetta, M. C., Marco-Ferreres, R., Viales, R. R., Jankowski, A., Schaub, C., & Furlong, E. E. M. (2024) · Nature Genetics · doi:10.1038/s41588-024-01678-x · Cited by 82 · see citing works
“Many studies started with a chromatin conformation capture experiment and then used chromatin signatures (for example, H3K27ac and p300) 6,9,12,13 or promoter proximity itself (from Capture-C) 5,10,14 to define putative enhancers, which may bias findings to enhancers in an active state or already…”
BackgroundMethodForces 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 81 · see citing works
“Interactions involving gene promoters and cognate enhancers can either be pre-established (“pre-looped”; Ghavi-Helm et al , 2014; Cruz-Molina et al , 2017), fully static, or dynamic in response to TNF a signaling (mediated by NF-j B; Kolovos et al , 2016), during macrophage development (mediated by AP-1; Phanstiel et…”
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 82 · see citing works
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 · see citing works
Self-citationIntegrated analysis of motif activity and gene expression changes of transcription factorsPreprint
Madsen, J. G. S., Rauch, A., Hauwaert, E. L. V., Schmidt, S. F., Winnefeld, M., & Mandrup, S. (2017) · Genome Research · doi:10.1101/gr.227231.117 · Cited by 72 · see citing works
Self-citationQin, Y., Grimm, S. A., Roberts, J. D., Chrysovergis, K., & Wade, P. A. (2020) · Nature Communications · doi:10.1038/s41467-020-14796-x · Cited by 67 · see citing works
Briand, N., & Collas, P. (2018) · Nucleus · doi:10.1080/19491034.2018.1449498 · Cited by 64 · see citing works
“These genome-related functions of lamin A are consistent with a rewiring of chromatin loops (promoterenhancer contacts) inside TADs upon adipose differentiation [55].”
BackgroundHolmes, A. G., Parker, J. B., Sagar, V., Truica, M. I., Soni, P. N., Han, H., Schiltz, G. E., Abdulkadir, S. A., & Chakravarti, D. (2022) · Science Advances · doi:10.1126/sciadv.abh3635 · Cited by 61 · see citing works
“Further investigation into the differential enhancer-promoter contacts induced by MYCi975 using promoter capture Hi-C ( 46 , 47 ) may reveal the role of enhancer-bound MYC/ MAX heterodimers in MYCi975-sensitive gene regulation.”
Genome-Wide Estrogen Receptor Activity in Breast Cancer
Farcas, A. M., Nagarajan, S., Cosulich, S. C., & Carroll, J. S. (2020) · Endocrinology · doi:10.1210/endocr/bqaa224 · Cited by 58 · see citing works
“While the role of coactivators is better understood, increasing evidence suggests that transcriptional corepressors such as the nucleosome remodeling and deacetylase (NuRD) complex, nuclear receptor corepressor (NCoR), or silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) (75, 76) also occupy acti…”
BackgroundTranscriptional networks controlling stromal cell differentiation
Rauch, A., & Mandrup, S. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00357-7 · Cited by 57 · see citing works
Self-citationChromatin Conformation in Development and Disease
Boltsis, I., Grosveld, F. G., Giraud, G., & Kolovos, P. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.723859 · Cited by 56 · see citing works
Nuclear-localized human respiratory syncytial virus NS1 protein modulates host gene transcription
Pei, J., Beri, N. R., Zou, A. J., Hubel, P., Dorando, H. K., Bergant, V., Andrews, R., Pan, J., Andrews, J. M., Sheehan, K. C. F., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109803 · Cited by 54 · see citing works
“bridge between enhancers and promoters, forming chromatin loops that are essential for transcriptional regulation (Park et al., 2005; Siersbæk et al., 2017; Soutourina, 2018), including many immune response genes.”
BackgroundHigashijima, Y., Matsui, Y., Shimamura, T., Nakaki, R., Nagai, N., Tsutsumi, S., Abe, Y., Link, V. M., Osaka, M., Yoshida, M., et al. (2018) · bioRxiv · doi:10.15252/embj.2019103949 · Cited by 54 · see citing works
Moyo, M., Parker, J. B., & Chakravarti, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14701-6 · Cited by 51 · see citing works
Raviram, R., Rocha, P. P., Luo, V. M., Swanzey, E., Miraldi, E. R., Chuong, E. B., Feschotte, C., Bonneau, R., & Skok, J. A. (2018) · Genome biology · doi:10.1186/s13059-018-1598-7 · Cited by 51 · see citing works
Bian, E., Chen, X., Cheng, L., Cheng, M., Chen, Z., Yue, X., Zhang, Z., Chen, J., Sun, L., Huang, K., et al. (2021) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-021-02129-9 · Cited by 51 · see citing works
“A recent study showed that MED1 mainly binds to the enhancer and promoter regions of target genes to promote transcriptional activation of the gene [50].”
BackgroundFoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expressionPreprint
Ramírez, R. N., Chowdhary, K., Léon, J., Mathis, D. J., & Benoist, C. O. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.12.468430 · Cited by 49 · see citing works
Huang, Z., Liang, N., Goñi, S., Damdimopoulos, A. E., Wang, C., Ballaire, R., Jager, J., Niskanen, H., Han, H., Jakobsson, T., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.040 · Cited by 49 · see citing works
Laurette, P., Coassolo, S., Davidson, G., Michel, I., Gambi, G., Yao, W., Sohier, P., Li, M., Mengus, G., Larue, L., et al. (2019) · Cell Death and Differentiation · doi:10.1038/s41418-019-0333-6 · Cited by 47 · see citing works
Zhang, N., Mendieta-Esteban, J., Magli, A., Lilja, K. C., Perlingeiro, R., Martí-Renom, M., Tsirigos, A., & Dynlacht, B. (2020) · Nature Communications · doi:10.1038/s41467-020-19999-w · Cited by 38 · see citing works
Pahl, M. C., Doege, C. A., Hodge, K. M., Littleton, S. H., Leonard, M. E., Lu, S., Rausch, R., Pippin, J. A., Rosa, M. C. D., Basak, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27001-4 · Cited by 46 · see citing works
MED1 Regulates BMP/TGF-β in Endothelium: Implication for Pulmonary Hypertension
Wang, C., Xing, Y., Zhang, J., He, M., Dong, J., Chen, S., Wu, H., Huang, H., Chou, C., Bai, L., et al. (2022) · Circulation Research · doi:10.1161/circresaha.122.321532 · Cited by 46 · see citing works
Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes
McAllan, L., Baranas̆ić, D., Villicaña, S., Brown, S., Zhang, W., Lehne, B. C., Adamo, M., Jenkinson, A. D., Elkalaawy, M., Mohammadi, B., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38439-z · Cited by 45 · see citing works
Park, Y. J., Lee, S., Lim, S., Nahmgoong, H., Ji, Y., Huh, J. Y., Alfadda, A. A., Kim, S., & Kim, J. B. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021073118 · Cited by 42 · see citing works
“However, recent findings have highlighted that, in addition to proximal regulatory regions, the regulatory circuit mediated by long-range genomic interactions contributes to adipocyte gene expression (8, 17) and that disruption of chromosomal looping in adipocytes is closely associated with obesity-related metabolic t…”
BackgroundPanigrahi, A. K., Foulds, C. E., Lanz, R. B., Hamilton, R. A., Yi, P., Lonard, D. M., Tsai, M., Tsai, S. Y., & O’Malley, B. W. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.04.014 · Cited by 40 · see citing works
“Genome-wide ChIA-PET and Hi-C experiments have defined promoter-gene body interactions (Jin et al., 2013; Li et al., 2012; Siersbæk et al., 2017).”
Chromatin interactome mapping at 139 independent breast cancer risk signals
Beesley, J., Sivakumaran, H., Marjaneh, M. M., Lima, L. G., Hillman, K. M., Kaufmann, S., Tuano, N., Hussein, N., Ham, S., Mukhopadhyay, P., et al. (2020) · Genome biology · doi:10.1186/s13059-019-1877-y · Cited by 43 · see citing works
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Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters
Oruba, A., Saccani, S., & van Essen, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14950-5 · Cited by 41 · see citing works
Broekema, M. F., Savage, D. B., Monajemi, H., & Kalkhoven, E. (2019) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2019.02.002 · Cited by 41 · see citing works
Joslin, A. C., Sobreira, D. R., Hansen, G. T., Sakabe, N. J., Aneas, I., Montefiori, L. E., Farris, K. M., Gu, J., Lehman, D. M., Ober, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25614-3 · Cited by 37 · see citing works
Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism
Williams, K., Ingerslev, L. R., Bork‐Jensen, J., Wohlwend, M., Hansen, A. N., Small, L., Ribel‐Madsen, R., Astrup, A. V., Pedersen, O. B., Auwerx, J. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16537-6 · Cited by 39 · see citing works
Role of A‐ and B‐type lamins in nuclear structure–function relationships
Patil, S., & Sengupta, K. (2021) · Biology of the Cell · doi:10.1111/boc.202000160 · Cited by 38 · see citing works
“For example, during adipogenic differentiation, a large number of lamin-genome associations are remodelled globally that alters associated transcription outputs (Siersbæk et al., 2017).”
BackgroundChromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits
Shi, C., Ray-Jones, H., Ding, J., Duffus, K., Fu, Y., Gaddi, V. P., Gough, O., Hankinson, J., Martin, P., McGovern, A., et al. (2021) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2021.01.015 · Cited by 32 · see citing works
“Although these techniques are very promising, there has been a lack of studies in disease-relevant cell types, and as recently evidenced, both chromatin interactions and gene regulation are cell type and stimulation specific (Burren et al., 2017; Dixon et al., 2012; Hansen et al., 2018; Mumbach et al., 2017; Rao et al…”
BackgroundPPARα and NCOR/SMRT corepressor network in liver metabolic regulation
Kang, Z., & Fan, R. (2020) · The FASEB Journal · doi:10.1096/fj.202000055rr · Cited by 37 · see citing works
Chen, W., Schwalie, P. C., Pankevich, E. V., Gubelmann, C., Raghav, S. K., Dainese, R., Cassano, M., Imbeault, M., Jang, S. M., Russeil, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09803-9 · Cited by 36 · see citing works
Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools
Freire-Pritchett, P., Ray-Jones, H., Rosa, M. D., Eijsbouts, C., Orchard, W. R., Wingett, S., Wallace, C., Cairns, J. M., Spivakov, M., & Malysheva, V. (2021) · Nature Protocols · doi:10.1038/s41596-021-00567-5 · Cited by 34 · see citing works
“…high-throughput sequencing (ATAC-seq) and RNA-seq has provided insights, for example, into the rewiring of promoter – enhancer contacts upon the differentiation of embryonic stem (ES) cells 23 – 25 , adipocytes 26 and keratinocytes 27 , as well as upon cohesin depletion in a human cell line 28 .”
BackgroundSelf-citationTreuter, E., Fan, R., Huang, Z., Jakobsson, T., & Venteclef, N. (2017) · FEBS Letters · doi:10.1002/1873-3468.12850 · Cited by 34 · see citing works
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
Schoenfelder, S., Javierre, B. M., Furlan-Magaril, M., Wingett, S., & Fraser, P. (2018) · Journal of Visualized Experiments · doi:10.3791/57320-v · Cited by 34 · see citing works
Self-citationLeung, K. L., Sanchita, S., Pham, C. T., Davis, B. A., Okhovat, M., Ding, X., Dumesic, P., Grogan, T. R., Williams, K. J., Morselli, M., et al. (2020) · Clinical Epigenetics · doi:10.1186/s13148-020-00970-x · Cited by 33 · see citing works
“, exposure to adipogenic media) like that seen in 3T3-L1 cells [31] to promote adipocyte function.”
BackgroundGenome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis
He, M., Li, Y., Tang, Q., Li, D., Jin, L. G., Tian, S., Che, T., Shen, H., Deng, L., Gao, G., et al. (2018) · International Journal of Biological Sciences · doi:10.7150/ijbs.25328 · Cited by 33 · see citing works
“32 Mb), and fibroblasts (2,590 TADs with median length of 680 kb) [16, 25, 26].”
BackgroundResultInfluentialReduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer
Long, M. D., Jacobi, J. J., Singh, P. K., Llimos, G., Wani, S. A., Rowsam, A. M., Rosario, S. R., Hoogstraat, M., Linder, S., Kirk, J. S., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110109 · Cited by 33 · see citing works
“Consequently, NCOR2 and other co-repressor complexes (Hnisz et al., 2013) may offer a safeguard to overactivation of SEs and aid in their complete shutdown during cell differentiation processes (Siersbæk et al., 2017, Zhuang et al., 2018).”
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation
Karpińska, M. A., Zhu, Y., Ghazvini, Z. F., Ramasamy, S., Barbieri, M., Cao, T. B. N., Varahram, N., Aljahani, A., Lidschreiber, M., Papantonis, A., et al. (2025) · bioRxiv · doi:10.1038/s41594-025-01555-z · Cited by 28 · see citing works
“It has been suggested that these interactions form in the context of nuclear condensates, which Article https://doi.org/10.1038/s41594-025-01555-z”
InfluentialZc3h10 regulates adipogenesis by controlling translation and F-actin/mitochondria interaction
Audano, M., Pedretti, S., Ligorio, S., Gualdrini, F., Polletti, S., Russo, M., Ghisletti, S., Bean, C., Crestani, M., Caruso, D., et al. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202003173 · Cited by 29 · see citing works
Emerging roles of epigenetic regulation in obesity and metabolic disease
Park, Y. J., Han, S. M., Huh, J. Y., & Kim, J. B. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101296 · Cited by 32 · see citing works
“(29) revealed that the transition from preadipocytes to mature adipocytes is accompanied by the rapid rewiring of chromosome loops linking promoters and enhancers, whereas higher-order chromatin organization at the level of TADs remains relatively constant during adipocyte differentiation.”
BackgroundTargeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation
Park, J., Lee, D. H., Ham, S., Oh, J., Noh, J., Lee, Y. K., Park, Y. J., Lee, G., Han, S. M., Han, J. S., et al. (2022) · Nature Metabolism · doi:10.1038/s42255-022-00597-7 · Cited by 31 · see citing works
Laverré, A., Tannier, É., & Necşulea, A. (2021) · Genome Research · doi:10.1101/gr.275901.121 · Cited by 30 · see citing works
Epigenetic Regulation of Adipogenesis by Histone-Modifying Enzymes
Macchia, P. E., Nettore, I. C., Franchini, F., Santana-Viera, L., & Ungaro, P. (2021) · Epigenomics · doi:10.2217/epi-2020-0304 · Cited by 30 · see citing works
Hao, R.-H., Guo, Y., Wang, C., Chen, F., Di, C., Dong, S., Cao, Q.-L., Guo, J., Rong, Y., Yao, S., et al. (2022) · Cell Death and Differentiation · doi:10.1038/s41418-022-01035-7 · Cited by 30 · see citing works
自閉症関連タンパク質CHD8はC/EBPβと協調して脂肪分化を制御する
喜多, 泰. (2018) · Kyushu University Institutional Repository (QIR) (Kyushu University) · Cited by 30 · see citing works
Zouari, Y. B., Molitor, A., Sikorska, N., Pancaldi, V., & Sexton, T. (2018) · Genome Biology · doi:10.1186/s13059-019-1706-3 · Cited by 27 · see citing works
Dumesic, D. A., Tulberg, A., Leung, K. L., Fisch, S. C., Grogan, T., Abbott, D. H., Naik, R., & Chazenbalk, G. D. (2020) · Fertility and Sterility · doi:10.1016/j.fertnstert.2020.10.003 · Cited by 28 · see citing works
KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin
Campbell, M., Chantarasrivong, C., Yanagihashi, Y., Inagaki, T., Davis, R., Nakano, K., Kumar, A., Tepper, C., & Izumiya, Y. (2022) · bioRxiv · doi:10.1128/jvi.00565-22 · Cited by 21 · see citing works
“age commitment (37), reprogramming (60), differentiation (61, 62), senescence (63), and possibly heat shock (64, 65).”
BackgroundLing, X., Liu, X., Jiang, S., Fan, L., & Ding, J. (2022) · Cell Regeneration · doi:10.1186/s13619-022-00145-4 · Cited by 29 · see citing works
3D genome organization links non-coding disease-associated variants to genes
Orozco, G., Schoenfelder, S., Walker, N. J., Eyre, S., & Fraser, P. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.995388 · Cited by 25 · see citing works
“Furthermore, although cell differentiation is often characterized by dynamic rewiring of promoter-enhancer loops (Freire-Pritchett et al., 2017; Siersbæk et al., 2017), some speci fi c interactions do not contemporaneously drive gene expression.”
BackgroundSelf-citationTolkachov, A., Fischer, C., Ambrosi, T. H., Bothe, M., Han, T., Muenzner, M., Mathia, S., Salminen, M., Seifert, G., Thiele, M., et al. (2018) · Molecular and Cellular Biology · doi:10.1128/mcb.00599-17 · Cited by 25 · see citing works
Chromatin Landscape During Skeletal Muscle Differentiation
Hernández‐Hernández, Ó., Ávila‐Avilés, R. D., & Hernández‐Hernández, J. M. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.578712 · Cited by 24 · see citing works
Waves of sumoylation support transcription dynamics during adipocyte differentiation
Zhao, X., Hendriks, I. A., Gras, S. L., Ye, T., Ramos-Alonso, L., Aurélie Nguéa, P., Lien, G. F., Ghasemi, F., Klungland, A., Jost, B., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac027 · Cited by 24 · see citing works
“Given that the presence of RXR at the chromatin matches gene expression and genome architecture dynamics during adipogenesis (41,42), sumoylation of RXR and other chromatin-bound SUMO targets could support these critical aspects of adipogenesis.”
BackgroundA PPARγ/long noncoding RNA axis regulates adipose thermoneutral remodeling in mice
Zhang, Z., Cui, Y., Su, V., Wang, D., Tol, M. J. P. M., Cheng, L., Wu, X., Kim, J., Rajbhandari, P., Zhang, S., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci170072 · Cited by 24 · see citing works
“Intriguingly the Lexis binding site is near H3K27ac, H3K4me1, and H3K4me2 histone marks, which are associated with the higher activation of transcription of nearby genes (Supplemental Figure 5G) (55, 56).”
Gérard, D., Schmidt, F., Ginolhac, A., Schmitz, M., Halder, R., Ebert, P., Schulz, M. H., Sauter, T., & Sinkkonen, L. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1240 · Cited by 23 · see citing works
Ito, R., Xie, S., Tumenjargal, M., Sugahara, Y., Yang, C., Takahashi, H., Arai, M., Inoue, S.-I., Uchida, A., Nakano, K., et al. (2024) · iScience · doi:10.1016/j.isci.2024.109398 · Cited by 23 · see citing works
“314kb of Pgc1a ) physically interacted with the TSS in 3T3-L1 adipocytes 31 (Figure S7B).”
BackgroundRepair of DNA double-strand breaks leaves heritable impairment to genome function
Bantele, S. C. S., Mordini, I., Biran, A., Alcaraz, N., Zonderland, G., Wenger, A., Krietenstein, N., Groth, A., & Lukas, J. (2025) · Science · doi:10.1126/science.adk6662 · Cited by 30 · see citing works
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Challenges for visualizing three‐dimensional data in genomic browsers
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“35,115 Using the 4C-seq technique, we studied the genome-wide chromatin interaction of Cebpa during adipogenic differentiation.”
BackgroundMethodUnraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation
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“Although altered K27ac levels and the enzymes that catalyze its deposition and removal are functionally associated with Mediator at enhancers (4, 44), we are unaware of Mediator-dependent coordination of both activities in the same system or at gene loci.”
BackgroundInhibition of class I HDACs imprints adipogenesis toward oxidative and brown-like phenotype
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“Siersbæk and colleagues [26], in fact, demonstrated that when differentiation is induced with an adipogenic cocktail these regions loop together with promoters and recruit co-regulators.”
BackgroundApplication of Hi-C and other omics data analysis in human cancer and cell differentiation research
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Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution
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“For the raw data of GSE50934, GSE95533, and GSE50612, reads were mapped to the mouse genome (GRCm38) using HiSat2 [41], and annotated genes were quantified with featureCounts [42].”
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- Authors
- Siersbæk, R., Madsen, J. G. S., Javierre, B. M., Nielsen, R., Bagge, E. K., Cairns, J., Wingett, S. W., Traynor, S., Spivakov, M., Fraser, P., & Mandrup, S.
- Affiliations
- University of Southern Denmark (DK)
- Babraham Institute (GB)
- Florida State University (US)
- Corresponding author
- Fraser, Peter
- Mandrup, Susanne
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2017-05
- Volume
- 66
- Issue
- 3
- Pages
- 420-435.e5
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2610197120
- Cited by
- 243
- References
- 65
- Citations by year
- 2026: 9 · 2025: 20 · 2024: 18 · 2023: 28 · 2022: 41 · 2021: 44 · 2020: 27 · 2019: 24 · 2018: 26 · 2017: 6
- FWCI
- 9.28
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- University of Southern Denmark Research Portal (University of Southern Denmark) (publishedVersion)
- Funders
- Villum Fonden
- Danmarks Frie Forskningsfond
- Danish Diabetes Academy
- Augustinus Fonden (NNF15OC0014136)
- Medical Research Council (MR/L007150/1)
- Novo Nordisk Fonden
- Biotechnology and Biological Sciences Research Council (BB/J004480/1)
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences (12-125524)
- Shanxi Datong University
- Lundbeckfonden (R118-A11639)
- 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
- adipogenesis, 3T3-L1 preadipocytes, poised enhancers, histone H3 lysine 27 acetylation, MED1, SMC1A, P300, corepressors, NCoR, histone deacetylase, transcriptional regulation, enhancer activation
- MeSH terms
- Structural Maintenance of Chromosome Protein 1, Animals, Chromatin, Chromosomal Proteins, Non-Histone, Enhancer Elements, Genetic, Nucleic Acid Conformation, Promoter Regions, Genetic, RNA, Messenger, Time Factors, Transcription, Genetic, Transcriptional Activation, Sequence Analysis, RNA, Adipocytes, Cell Cycle Proteins, 3T3-L1 Cells, Chromatin Assembly and Disassembly, Chromatin Immunoprecipitation, Adipogenesis, E1A-Associated p300 Protein, Mice, Mediator Complex Subunit 1
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