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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
...talk between GR and ESR1, as well as ESR1 and AR, has been well characterized in breast cancer (Swinstead et al. 2018; Hickey et al. 2021; Paakinaho and Palvimo 2021; Prekovic et al. 2023). Notably, direct cross talk is not limited to steroid receptors alone; other TFs like FOXA1, NF-kB, and CREB have...
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Research: Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
- Sarah K. Sasse,
- Margaret Gruca,
- Mary A. Allen,
- Vineela Kadiyala,
- Tengyao Song,
- Fabienne Gally,
- Arnav Gupta,
- Miles A. Pufall,
- Robin D. Dowell,
- and Anthony N. Gerber
Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
...(also known as A20). However, our studies lacked sufficient temporal resolution to determine whether GR-mediated repression is affected solely as a secondary consequence of inductive gene regulation, including targets of GR-RELA cooperation such as TNFAIP3, or whether primary repression of NF-kB...
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Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...high pool mostly contained cell types from the neuronal lineage (Fig. 4B, left), confirming previous findings on the essential role of RFX in sensory neuron differentiation (Swoboda et al. 2000). Despite the fact that the NF-kB and NFAT motifs are associated to two related families of Rel Homology...
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Research: Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers
- Søren Fisker Schmidt,
- Bjørk Ditlev Larsen,
- Anne Loft,
- Ronni Nielsen,
- Jesper Grud Skat Madsen,
- and Susanne Mandrup
Genome Res. September 2015 25: 1281-1294; Published in Advance June 25, 2015, doi:10.1101/gr.188300.114
.... 2002). The major transactivating subunit of NFκB is v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA; also known as p65), which, following inflammatory activation, translocates to the nucleus and binds DNA as a heterodimer with the mature product of NFKB1 (p50) to GGGRNYYYCC response...
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Research: Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation
- Ofir Hakim,
- Myong-Hee Sung,
- Shingo Nakayamada,
- Ty C. Voss,
- Songjoon Baek,
- and Gordon L. Hager
Genome Res. March 2013 23: 462-472; Published in Advance December 3, 2012, doi:10.1101/gr.147652.112
...transcription factors such as NFKB, AP-1, and NFAT respond to T-cell receptor (TCR) signaling that occurs universally during differentiation for all Th lineages (Isakov and Altman 2002). These transcription factors 3Present address: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University...
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Research: Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation
- Hélène Neyret-Kahn,
- Moussa Benhamed,
- Tao Ye,
- Stéphanie Le Gras,
- Jack-Christophe Cossec,
- Pierre Lapaquette,
- Oliver Bischof,
- Maia Ouspenskaia,
- Mary Dasso,
- Jacob Seeler,
- Irwin Davidson,
- and Anne Dejean
Genome Res. October 2013 23: 1563-1579; Published in Advance July 26, 2013, doi:10.1101/gr.154872.113
...TP53, CDKN2A (also known as P16), or CDKN1A (also known as P21) was observed (Fig. 6F). Similarly, no increase in phosphorylation of RELA, the subunit of NFKB normally associated with activation of the secretome genes, was observed, whereas HMGA1 expression was increased as reported previously (Fig...
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Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- Lesley T. MacNeil and
- Albertha J.M. Walhout
Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
...in multicellular organisms (e.g., Odomet al. 2004; Carroll et al. 2005; Cao et al. 2010). The second, gene-centered (DNA-to-protein) methods for the identification of TF–target gene interactions start with a regulatory genomic DNA sequence and identify the repertoire of TFs with which this sequence can interact...

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