Searching journal content for articles similar to Ing-Simmons et al. 25 (4): 504.

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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...the spatial and temporal dynamics of enhancer–promoter interactions. Understanding how enhancers interact with promoters will deepen our understanding of the regulation of gene expression and the molecular underpinnings of transcriptional control.Gene expression programs are encoded by cis-regulatory elements...
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Method: Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication
- Zihao Wang,
- Zhenquan Zhang,
- Songhao Luo,
- Tianshou Zhou,
- and Jiajun Zhang
Genome Res. January 2024 34: 106-118; Published in Advance January 3, 2024, doi:10.1101/gr.278631.123
...enhancer–promoter [E-P] spatial communication) in one-dimensional time shapes transcriptional bursting patterns still remains elusive.Hierarchic genomic structures captured by chromosome conformation capture and fluorescence in situ hybridization as well as other experimental technologies have provided...
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Method: Quantitative prediction of enhancer–promoter interactions
- Polina S. Belokopytova,
- Miroslav A. Nuriddinov,
- Evgeniy A. Mozheiko,
- Daniil Fishman,
- and Veniamin Fishman
Genome Res. January 2020 30: 72-84; Published in Advance December 2, 2019, doi:10.1101/gr.249367.119
...between, but also outside of, the promoter and enhancer should be considered. This makes sense in light of recently discovered mechanisms, underlying the spatial organization of chromatin. For example, according to the loop extrusion model (Fudenberg et al. 2017), binding of CTCFs in the converged...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...that at the sub-TAD scale, chromatin organizes into clutches of nucleosomes (Ricci et al. 2015; Ou et al. 2017) clustered into nanodomains (Szabo et al. 2020).Beyond the “static” picture of a layered spatial organization that contributes to regulation, more and more experiments on living cells highlighted...
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Research: Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters
- Vibhor Kumar,
- Nirmala Arul Rayan,
- Masafumi Muratani,
- Stefan Lim,
- Bavani Elanggovan,
- Lixia Xin,
- Tess Lu,
- Harshyaa Makhija,
- Jeremie Poschmann,
- Thomas Lufkin,
- Huck Hui Ng,
- and Shyam Prabhakar
Genome Res. May 2016 26: 612-623; Published in Advance March 8, 2016, doi:10.1101/gr.201038.115
...−4, which yielded an adequate number of such peaks (mE-Enh6 class) (Fig. 4A). We then categorized the genomic sequences tested in the Figure 4. Evaluating regulatory activity of different enhancer classes in reporter gene assays in mESCs and e11.5mouse forebrain. (A) Spatial heatmap of histone...
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Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
- Wendy A. Kellner,
- Joshua S.K. Bell,
- and Paula M. Vertino
Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
...that the TSS and 3′ CGI edge can be readily resolved, allowing us to determine the spatial relationship between enhancer contacts and the paused Pol II (Hah et al. 2011, 2013; Danko et al. 2013). A high-resolution 3C assay was used to finely map estrogen-induced enhancer interactions at these loci in MCF7...
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Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
- Federico Comoglio,
- Hyun Jung Park,
- Stefan Schoenfelder,
- Iros Barozzi,
- Daniel Bode,
- Peter Fraser,
- and Anthony R. Green
Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
...by rapid and extensive epi remodeling of cis-regulatory landscapes that is spatially coordinated within topologically associating domains (TADs). Moreover, TPO-responsive enhancers are spatially clustered and engage in preferential homotypic intra- and inter-TAD interactions that are largely refractory...
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