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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
...(Kulik et al. 2021). This suggests that in the same cellular environment, differential coregulator recruitment may influence each receptor's ability to access closed chromatin sites. Future chromatin proteomic studies on GR- and AR-associated partners will clarify whether this preference also occurs...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...Dynamic evolution of satellite DNAs drastically differentiates the s of Tribolium sibling species Damira Veseljak, Evelin Despot-Slade, Marin Volarić, Lucija Horvat, Tanja Vojvoda Zeljko, Nevenka Meštrović and Brankica Mravinac Ruđer Bošković Institute, Division of Molecular Biology, HR-10000...
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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...in metazoans and show that it learns a highly effective recognition code that can predict de novo DNA-binding specificities for TFs. Furthermore, we show that the inferred amino acid–nucleotide contacts reveal whether and how nucleotide preferences at individual binding site positions are altered by mutations...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...-TF competition scenarios. If paralogous TFs have identical DNA-binding preferences, then their binding is determined by the levels of the TFs in the nucleus (top panels). However, most paralogs have diverged in specificity, binding differently at different sites even in the absence of other proteins (Berger et...
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Research: ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors
- Stephan R. Starick,
- Jonas Ibn-Salem,
- Marcel Jurk,
- Céline Hernandez,
- Michael I. Love,
- Ho-Ryun Chung,
- Martin Vingron,
- Morgane Thomas-Chollier,
- and Sebastiaan H. Meijsing
Genome Res. June 2015 25: 825-835; Published in Advance February 26, 2015, doi:10.1101/gr.185157.114
...ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors Stephan R. Starick 1 , 3 , Jonas Ibn-Salem 1 , 2 , 3 , Marcel Jurk 1 , 3 , Céline...
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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
...recruitment sites, the receptor clearly binds to a pre-existing nucleosome.The findings presented herein support the concept of DNA as an allosteric effector of GR action (Meijsing et al. 2009; Watson et al. 2013). However, a primary effect of DNA binding is to convert the receptor to a tetrameric state...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...et al. 2016; Kasumyan 2019). The sense of taste is important in the differentiation of feeding preferences and feeding habits (Kasumyan 2019; Jiao et al. 2021). Taste is perceived via the taste receptor signaling pathway (including genes such as tas1rs) in the taste buds (Bruch et al. 1988; Bachmanov...
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Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
- Ian C. McDowell,
- Alejandro Barrera,
- Anthony M. D'Ippolito,
- Christopher M. Vockley,
- Linda K. Hong,
- Sarah M. Leichter,
- Luke C. Bartelt,
- William H. Majoros,
- Lingyun Song,
- Alexias Safi,
- D. Dewran Koçak,
- Charles A. Gersbach,
- Alexander J. Hartemink,
- Gregory E. Crawford,
- Barbara E. Engelhardt,
- and Timothy E. Reddy
Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
...(GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibility predetermine GR binding and activity. However, there are vast excesses of both features relative to the number of GR binding sites. Thus, these features alone are unlikely to account for the specificity...
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Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
- Bradford H. Casey,
- Rahul K. Kollipara,
- Karine Pozo,
- and Jane E. Johnson
Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
...to different sites throughout the (Cao et al. 2010; Castro et al. 2011; Fong et al. 2012, 2015; Meredith et al. 2013; Borromeo et al. 2014; Schuijers et al. 2015), thereby activating distinct transcriptional targets for expression. Factor-specific preference in DNA binding motifs can account for some...
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Research: Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. April 2018 28: 497-508; Published in Advance March 21, 2018, doi:10.1101/gr.229518.117
...binding proteins. How selectivity is achieved, particularly in the context of an entire , is not fully understood. Recent work has suggested that some proteins recognize both the sequence and shape of a DNA binding site, with shape not uniquely specified by sequence (Rohs et al. 2009; Slattery et al. 2014...
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