Searching journal content for articles similar to Theodorou et al. 23 (1): 12.

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  1. Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
    • Yueqiang Song,
    • Fuyuan Li,
    • Shangzi Wang,
    • Yuntong Wang,
    • Cong Lai,
    • Lian Chen,
    • Ning Jiang,
    • Jin Li,
    • Xingdong Chen,
    • Swneke D. Bailey,
    • and Xiaoyang Zhang
    Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
    ...-specific. We develop a HiChIP-based methodology that navigates enhancer–promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63...
  2. Research: Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
    • Cui Du,
    • Jing Jiang,
    • Yuzhuo Li,
    • Miao Yu,
    • Jian Jin,
    • Shuai Chen,
    • Hairui Fan,
    • Todd S. Macfarlan,
    • Bin Cao,
    • and Ming-an Sun
    Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122
    ...of the MER41-enhancers to MER41 elements lacking the H3K27ac mark showed significant enrichment of the motif for GATA3 (Supplemental Fig. S12), but not MSX2, which demonstrates a role in transcriptional repression (Hornbachner et al. 2021). Of note, the motif of GRHL2 is enriched in MER41-enhancers 1.6-fold...
  3. Research: Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
    • Yujia Sun,
    • Chung-Yi Nien,
    • Kai Chen,
    • Hsiao-Yun Liu,
    • Jeff Johnston,
    • Julia Zeitlinger,
    • and Christine Rushlow
    Genome Res. November 2015 25: 1703-1714; Published in Advance September 2, 2015, doi:10.1101/gr.192542.115
    ...-favoring sequences promote high nucleosome occupancy at these regions, closing enhancers and reducing transcriptional output. Thus, Zld acts as a timer of ZGA in that it controls the engagement and decommission of TFs at target enhancers by transiently reducing the nucleosome barrier. Since the Zld-mediated...
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  4. Method: Models of human core transcriptional regulatory circuitries
    • Violaine Saint-André,
    • Alexander J. Federation,
    • Charles Y. Lin,
    • Brian J. Abraham,
    • Jessica Reddy,
    • Tong Ihn Lee,
    • James E. Bradner,
    • and Richard A. Young
    Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115
    ...et al. 2003; Ferri 2004; Sisodiya et al. 2006; Lujan et al. 2012). They also contain well-characterized proto-oncogenes of cancer subtypes represented by cancer cell lines, such as ESR1 and GATA3 in MCF-7 breast cancer cells (Usary et al. 2004; Holst et al. 2007) and TCF7L2 and SMAD3 in HCT-116 colon...
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