Searching journal content for articles similar to Giannopoulou and Elemento 23 (8): 1295.

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  1. Method: A universal framework for detecting cis-regulatory diversity in DNA regions
    • Anushua Biswas and
    • Leelavati Narlikar
    Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
    ...and multiple low-complexity DNA motifs are discovered (Supplemental Fig. S7), suggesting the diminishing influence of GR motifs over the regions away from the ChIP summit.Enhancers have a different structure based on the detection assayEnhancers play critical roles in activating gene transcription while often...
  2. Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
    • Deepani W. Poramba-Liyanage,
    • Tessy Korthout,
    • Christine E. Cucinotta,
    • Ila van Kruijsbergen,
    • Tibor van Welsem,
    • Dris El Atmioui,
    • Huib Ovaa,
    • Toshio Tsukiyama,
    • and Fred van Leeuwen
    Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
    ...interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here...
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  3. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...of cohesin complexes, peaks in chromatin proximity assays such as Hi-C or ChIA-PET), and the appearance of randomly, bidirectionally transcribed nonpolyadenylated cognate eRNA (Long et al. 2016). Most accessible repositories for the entry-level molecular geneticist with a limited number of GOIs are those...
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  4. Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
    • Stacey E.P. Joosten,
    • Sebastian Gregoricchio,
    • Suzan Stelloo,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Kerim Yavuz,
    • Maria Donaldson Collier,
    • Tunç Morova,
    • Umut Berkay Altintaş,
    • Yongsoo Kim,
    • Sander Canisius,
    • Cathy B. Moelans,
    • Paul J. van Diest,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • Michiel Vermeulen,
    • Sabine C. Linn,
    • and Wilbert Zwart
    Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
    ...of SHRs cannot be directly translated to genuine enhancer activity but rather that a relatively small fraction of SHR-chromatin bound sites is actively induced in activity following stimulation, as determined by massive parallel reporter assays. These findings, in combination with the observed enhancer...
  5. 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 TPO (Fig. 6G).We previously demonstrated that in the absence of TPO, chromatin-bound uSTAT5 restrains a megakaryocytic transcriptional program in hematopoietic stem/progenitor cells, and TPO-mediated phosphorylation of STAT5 triggers a -wide relocation of STAT5 to canonical GAS motifs (Park et al...
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  6. Method: A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
    • Christian Pflueger,
    • Dennis Tan,
    • Tessa Swain,
    • Trung Nguyen,
    • Jahnvi Pflueger,
    • Christian Nefzger,
    • Jose M. Polo,
    • Ethan Ford,
    • and Ryan Lister
    Genome Res. August 2018 28: 1193-1206; Published in Advance June 15, 2018, doi:10.1101/gr.233049.117
    ...Table S1). The reciprocal αGCN4-D3A ChIP-seq experiment using the C-terminal 3xTy1 epitope yielded only one significant peak at the on-target SHB site (Supplemental Table S1).View larger version: In this window In a new window Figure 3. Genome-wide off-target DNA methylation assessment. (A) Compilation...
  7. Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
    • Joseph D. Fleming,
    • Giulio Pavesi,
    • Paolo Benatti,
    • Carol Imbriano,
    • Roberto Mantovani,
    • and Kevin Struhl
    Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
    ...element. Genome-wide mapping reveals 5000–15,000 NF-Y binding sites depending on the cell type, with the NF-YA and NF-YB subunits binding asymmetrically with respect to the CCAAT motif. Despite being characterized as a proximal promoter TF, only 25% of NF-Y sites map to promoters. A comparable number...
  8. Research: HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter
    • Mijke Visser,
    • Manfred Kayser,
    • and Robert-Jan Palstra
    Genome Res. March 2012 22: 446-455; Published in Advance January 10, 2012, doi:10.1101/gr.128652.111
    .... This concept is highly relevant for future studies aiming to unveil the functional basis of genetically determined phenotypes, including diseases. [Supplemental material is available for this article.] Genome-wide association studies (GWAS) have successfully identified numerous genetic variants...
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