Searching journal content for articles similar to Bashford-Rogers et al. 23 (11): 1874.

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  1. 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
    ...with deep sequencing (ChIP-seq) with DHT-only treatment or AR ChIP-seq with Dex-only treatment. ChIP-seq analyses indicated that DexDHT treatment substantially increased GR chromatin occupancy, whereas AR binding remained unchanged (Fig. 1A,B; Supplemental Table S1). Because AR-binding sites (ARBs) in VCa...
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  2. Research: Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
    • Stephen N. Sansom,
    • Noriko Shikama-Dorn,
    • Saule Zhanybekova,
    • Gretel Nusspaumer,
    • Iain C. Macaulay,
    • Mary E. Deadman,
    • Andreas Heger,
    • Chris P. Ponting,
    • and Georg A. Holländer
    Genome Res. December 2014 24: 1918-1931; Published in Advance September 15, 2014, doi:10.1101/gr.171645.113
    ...(TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing...
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  3. Research: Individualized VDJ recombination predisposes the available Ig sequence space
    • Andrei Slabodkin,
    • Maria Chernigovskaya,
    • Ivana Mikocziova,
    • Rahmad Akbar,
    • Lonneke Scheffer,
    • Milena Pavlović,
    • Habib Bashour,
    • Igor Snapkov,
    • Brij Bhushan Mehta,
    • Cédric R. Weber,
    • Jose Gutierrez-Marcos,
    • Ludvig M. Sollid,
    • Ingrid Hobæk Haff,
    • Geir Kjetil Sandve,
    • Philippe A. Robert,
    • and Victor Greiff
    Genome Res. December 2021 31: 2209-2224; Published in Advance November 23, 2021, doi:10.1101/gr.275373.121
    ...in human individuals (in naive B cell repertoires), we computed the normalized JSD on a cohort of 99 unrelated individuals from the HUMAN3 data set (see Methods, “Experimental immunoglobulin sequencing data”) (Fig. 3A; Gidoni et al. 2019). Analogously to the HUMAN1 and the HUMAN2 data sets (Fig. 2), we...
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  4. Perspective: Challenges and considerations for reproducibility of STARR-seq assays
    • Maitreya Das,
    • Ayaan Hossain,
    • Deepro Banerjee,
    • Craig Alan Praul,
    • and Santhosh Girirajan
    Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
    ...-specific manner makes them critical components of gene regulatory networks (Shlyueva et al. 2014). Although enhancer–reporter assays (Banerji et al. 1981) and comparative genomics (Pennacchio et al. 2006) enabled initial discoveries, enhancers are usually mapped within nucleosome-free open chromatin regions...
  5. Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
    • Akanksha Bafna,
    • Gareth Banks,
    • Michael H. Hastings,
    • and Patrick M. Nolan
    Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
    ...is generated by a genetic network of cell-autonomous transcription–translation feedback loops (TTFLs) driven by the activators circadian locomotor output cycles kaput (CLOCK) and basic helix-loop-helix ARNT like 1 (BMAL1) and the repressors period (PER) and cryptochrome (CRY) (Takahashi et al. 2008...
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  6. Method: A general calculus of fitness landscapes finds genes under selection in cancers
    • Teng-Kuei Hsu,
    • Jennifer Asmussen,
    • Amanda Koire,
    • Byung-Kwon Choi,
    • Mayur A. Gadhikar,
    • Eunna Huh,
    • Chih-Hsu Lin,
    • Daniel M. Konecki,
    • Young Won Kim,
    • Curtis R. Pickering,
    • Marek Kimmel,
    • Lawrence A. Donehower,
    • Mitchell J. Frederick,
    • Jeffrey N. Myers,
    • Panagiotis Katsonis,
    • and Olivier Lichtarge
    Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
    ...patients remains hidden for lack of a population-wide role (Garraway and Lander 2013; Chang et al. 2016). The sequencing of diverse types of somatic tumor tissue from a large number of patients by The Cancer Genome Atlas (TCGA) (The Cancer Genome Atlas Research Network 2008; The Cancer Genome Atlas...
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  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
    ...by deep DNA sequencing. Antibodies (Dolfini et al. 2009)were validated by Western blot and IP-WB, showing that NF-YA and NF-YB are specifically recognized (Supplemental Fig. 1A,B). Immunoprecipitated DNA was validated on known NF-Y targets (Supplemental Fig. 1C,D) and the reproducibility between...
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