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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...the gene regulatory network of the cancer .One of the most important and well-studied guardians of genomic integrity, TP53 (protein product of TP53, also known as p53), leverages regulatory opportunities provided by TEs for its function. One group of TE families, human endogenous retroviruses (ERVs...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...events lead to chromatin opening and potential enhancer activation, suggesting TP53 pioneer-factor activity (Younger and Rinn 2017). For the majority of these binding events, though, TP53 is not required for chromatin accessibility (Karsli Uzunbas et al. 2019). TP63, on the other hand, plays an extensive...
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Method: Defining TP53 pioneering capabilities with competitive nucleosome binding assays
- Xinyang Yu and
- Michael J. Buck
Genome Res. January 2019 29: 107-115; Published in Advance November 8, 2018, doi:10.1101/gr.234104.117
...RE, Appella E, Hager GL, Nagaich AK. 2010. p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element. J Biol Chem 285: 1321–1332. doi:10.1074/jbc.M109.081182 ↵Sammons MA, Zhu J, Drake AM, Berger SL. 2015. TP53 engagement with the occurs in distinct local chromatin...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
....aerts@med.kuleuven.be Abstract Transcription factors regulate their target genes by binding to regulatory regions in the genome. Although the binding preferences of TP53 are known, it remains unclear what distinguishes functional enhancers from nonfunctional binding. In addition, the genome is scattered with recognition...
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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
...novo sites), showing context-dependent pioneer activity of this receptor (John et al. 2011; Johnson et al. 2018). To assess the chromatin environment of GRtetra binding sites, we measured (1) chromatin accessibility by the assay for transposase-accessible chromatin (ATAC)-seq and (2) the binding...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...development and progression. ESR1 genomic action is thought to operate under tight epigenetic control, with its chromatin binding and subsequent transcriptional output heavily reliant on the pioneer transcription factor FOXA1, which renders chromatin accessible for ESR1 binding. However, the exact...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...type, as well as understanding how the specificity of such a network is encoded in the DNA sequence of genomic enhancers. Profiling accessible chromatin via DNase I hypersensitive sequencing (DNase-seq) or via the assay for transposase-accessible chromatin using sequencing (ATAC-seq) represents...
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Research: Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state
- Connor Rogerson,
- Edward Britton,
- Sarah Withey,
- Neil Hanley,
- Yeng S. Ang,
- and Andrew D. Sharrocks
Genome Res. May 2019 29: 723-736; Published in Advance April 8, 2019, doi:10.1101/gr.243345.118
..., the TP53 motif showed evidence of reduced footprinting depth and local chromatin accessibility (Supplemental Fig. S2). Given the enrichment of these TF motifs, we next determined whether any of the transcription factors which recognize these motifs are up-regulated in EAC. Again, we used RNA-seq data...
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Method: Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers
- Aleksander Jankowski,
- Ewa Szczurek,
- Ralf Jauch,
- Jerzy Tiuryn,
- and Shyam Prabhakar
Genome Res. August 2013 23: 1307-1318; Published in Advance April 3, 2013, doi:10.1101/gr.154922.113
...correspond to overlapping motifs. Predicted and known dimers are compact, i.e., tightly spaced. Rigid and compact transcription factor dimers Genome Research 1313 www..org limited ability of chromatin openness to confer binding specificity upon pioneer TFs. Our results suggest that multiple homodimeric...
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