Searching journal content for articles similar to Blanchard et al. 29 (9): 1429.

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  1. Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V. Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...indel calling from TCGARNA-seq increases the TCGAdriver indel repertoire by∼14%, especially in samples with purity less than 0.4, including actionable EGFR indels in lung adenocarcinoma and FLT3 in acute myeloid leukemia. Our study not only reveals confounders in somatic mutant ASE analysis but also...
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  2. Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
    • Hosiana Abewe,
    • Alexandra Richey,
    • Jeffery M. Vahrenkamp,
    • Matthew Ginley-Hidinger,
    • Craig M. Rush,
    • Noel Kitchen,
    • Xiaoyang Zhang,
    • and Jason Gertz
    Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
    ...active regulatory regions of endometrial cancer cells in response to estrogen treatment and uncovered significant differential long-range interactions strongly enriched for estrogen receptor alpha (ER, also known as ESR1)–bound sites (ERBSs). The ERBSs anchoring differential chromatin loops with either...
  3. Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
    • Johannes Hiltunen,
    • Laura Helminen,
    • Niina Aaltonen,
    • Kaisa-Mari Launonen,
    • Hanna Laakso,
    • Marjo Malinen,
    • Einari A. Niskanen,
    • Jorma J. Palvimo,
    • and Ville Paakinaho
    Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
    ...is particularly prevalent among steroid receptors, a subclass of the nuclear receptor superfamily, including glucocorticoid (NR3C1, also known as GR), estrogen (ESR1), and androgen (AR) receptors, which can exert either oncogenic or tumor-suppressive effects depending on the context of their enhancer interactions...
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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
    ...-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.The Estrogen Receptor 1 (ESR1; also known as ERα, encoded by the ESR1 gene) is the driving force in most breast cancers diagnosed in women—as well as men...
  5. Research: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
    • Angela Jimeno-Martín,
    • Erick Sousa,
    • Rebeca Brocal-Ruiz,
    • Noemi Daroqui,
    • Miren Maicas,
    • and Nuria Flames
    Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
    ...helix loop helix (bHLH), zinc finger (ZF), basic leucine zipper domain (bZIP), and nuclear hormone receptors (NHR). HD TF members are overrepresented, supporting a key role for this family in the establishment of neuronal identities. These five TF families are also prevalent when considering mutant...
  6. Research: Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
    • Edward S. Rice,
    • Satomi Kohno,
    • John St. John,
    • Son Pham,
    • Jonathan Howard,
    • Liana F. Lareau,
    • Brendan L. O'Connell,
    • Glenn Hickey,
    • Joel Armstrong,
    • Alden Deran,
    • Ian Fiddes,
    • Roy N. Platt II,
    • Cathy Gresham,
    • Fiona McCarthy,
    • Colin Kern,
    • David Haan,
    • Tan Phan,
    • Carl Schmidt,
    • Jeremy R. Sanford,
    • David A. Ray,
    • Benedict Paten,
    • Louis J. Guillette, Jr.,
    • and Richard E. Green
    Genome Res. May 2017 27: 686-696; Published in Advance January 30, 2017, doi:10.1101/gr.213595.116
    ...to exogenous estrogen while incubated at a male-producing temperature (MPT) causes it to develop ovaries instead of testes. Estrogen, whose presence is detected and transduced via the transcription factor estrogen receptor alpha (Bull et al. 1988; Milnes et al. 2005; Kohno et al. 2015), is an early effector...
  7. Research: Enhancer transcripts mark active estrogen receptor binding sites
    • Nasun Hah,
    • Shino Murakami,
    • Anusha Nagari,
    • Charles G. Danko,
    • and W. Lee Kraus
    Genome Res. August 2013 23: 1210-1223; Published in Advance May 1, 2013, doi:10.1101/gr.152306.112
    ...Enhancer transcripts mark active estrogen receptor binding sites Nasun Hah 1 , 2 , 6 , Shino Murakami 3 , 4 , Anusha Nagari 3 , Charles G. Danko 1 , 5 and W. Lee Kraus 1 , 2 , 3 , 4 , 7 1 Department...
  8. Research: Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
    • Jason Gertz,
    • Timothy E. Reddy,
    • Katherine E. Varley,
    • Michael J. Garabedian,
    • and Richard M. Myers
    Genome Res. November 2012 22: 2153-2162; Published in Advance September 26, 2012, doi:10.1101/gr.135681.111
    ...estrogen receptor α ) binding sites, and RNA-seq in endometrial cancer cells exposed to bisphenol A (BPA; found in plastics), genistein (GEN; found in soybean), or 17 β -estradiol (E2; an endogenous estrogen). GEN and BPA treatment induces thousands of ESR1 binding sites and >50 gene expression changes...
  9. Research: Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome
    • Ville Paakinaho,
    • Thomas A. Johnson,
    • Diego M. Presman,
    • and Gordon L. Hager
    Genome Res. August 2019 29: 1223-1234; Published in Advance July 23, 2019, doi:10.1101/gr.244814.118
    ...using the A465T mutation within DBDs of the mouse glucocorticoid receptor NR3C1 (also known as GR), known as the GRdim mutant (Heck et al. 1994; Reichardt et al. 1998), and led to the development of the dissociated model of glucocorticoid action (Clark and Belvisi 2012). This model describes two modes...
  10. Research: Hormone-control regions mediate steroid receptor–dependent genome organization
    • François Le Dily,
    • Enrique Vidal,
    • Yasmina Cuartero,
    • Javier Quilez,
    • A. Silvina Nacht,
    • Guillermo P. Vicent,
    • José Carbonell-Caballero,
    • Priyanka Sharma,
    • José Luis Villanueva-Cañas,
    • Roberto Ferrari,
    • Lara Isabel De Llobet,
    • Gaetano Verde,
    • Roni H.G. Wright,
    • and Miguel Beato
    Genome Res. January 2019 29: 29-39; Published in Advance December 14, 2018, doi:10.1101/gr.243824.118
    ...is coordinately regulated in response to steroid hormones. Here we further describe that responsive TADs contain 20- to 100-kb-long clusters of intermingled estrogen receptor (ESR1) and progesterone receptor (PGR) binding sites, hereafter called hormone-control regions (HCRs). In T47D cells, we identified more...
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