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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
...% specific to cells expressing WT TP53 and ∼22% specific to cells without WT TP53 (Fig. 1F). We found more TE-derived transcripts exclusive to KO TP53 cells than in WT TP53 cells, which supported TP53's suppressive role over TEs and was consistent with our previous study showing higher levels of TE...
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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
...changes involved in development and tumor suppression.The TP53 family of transcription factors induces the expression of genes that determine the survival, proliferation, and differentiation of cells. In this family are three members: TP53, TP63, and TP73. TP53 has a well-known role in tumor suppression...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...associated with S5P RNA Pol II in irradiated samples (Fig. 1E). Pathway enrichment analyses of these up-regulated genes (Supplemental Fig. S2B) showed enrichment for TP53 signaling and cell cycle regulation, which are crucial for transcription of DDR genes and cell cycle arrest (Liu and Kulesz-Martin 2001...
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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: Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation
- Christopher Buccitelli,
- Lorena Salgueiro,
- Konstantina Rowald,
- Rocio Sotillo,
- Balca R. Mardin,
- and Jan O. Korbel
Genome Res. April 2017 27: 501-511; Published in Advance March 20, 2017, doi:10.1101/gr.212225.116
...that commonly deleted and amplified genes (e.g., TP53 and MYC) leave some transcriptional footprint unique to SCNA-, but not PM-, high tumors (Fig. 4). A recent study performed with fibroblasts suggests that these aberrations alone are insufficient to rescue the growthdefect experienced by aneuploid cells...
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Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
- Jean Fan,
- Hae-Ock Lee,
- Soohyun Lee,
- Da-eun Ryu,
- Semin Lee,
- Catherine Xue,
- Seok Jin Kim,
- Kihyun Kim,
- Nikolaos Barkas,
- Peter J. Park,
- Woong-Yang Park,
- and Peter V. Kharchenko
Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
...to drive tumor development typically relies on specific expression dysregulation of tumor cells. While some of the alterations have been tied to perturbations of known oncogenes and tumor suppressors, such as MYC and TP53 (Sekiguchi et al. 2014; Glitza et al. 2015), the process by which many genetic...
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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
...genes are associated with cell cycle control and the key regulatory factors RB1, E2F, and TP53 (Fig. 2I). Thus, in apparent contrast with the notion that the prominent effect of sumoylation on transcription is repression, we found here a positive correlation with promoter activity as well...
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Methods: Identification of rare cancer driver mutations by network reconstruction
- Ali Torkamani and
- Nicholas J. Schork
Genome Res. September 2009 19: 1570-1578; Published in Advance July 2, 2009, doi:10.1101/gr.092833.109
...once within a module, despite the number of mutations identified in it. Thus, modules containing a single frequently mutated gene (for example, TP53) would not be considered further because of the presence of a single highly mutated gene. Our goal was to identify networks containing multiple, though...
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Methods: Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)
- Zhenyi Liu,
- Anna C. Obenauf,
- Michael R. Speicher,
- and Raphael Kopan
Genome Res. November 2009 19: 2081-2089; Published in Advance October 1, 2009, doi:10.1101/gr.093856.109
...Chr. 9:tel-24136507/Chr.13: 19558594–36717548 RFX3; GLIS3; JAK2; PSIP1; MTAP; BRCA2; SMAD9; SACS; TNFRSF19 SMAD9 3 3 6 Chr. 17:7122558–7868524 TP53; TNK1; NLGN2; ATP1B2; FGF11; SOX15 FGF11 1 1 7 Chr. 18:957962–12021803 RAB12; ARHGAP28; RALBP1; NAPG RALBP1 1 1 For each sample, an RQPS probe, consisting...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...correlate with the gene expression profiles of GC (Tan et al. 2011), as well as the activity and mutation status of frequently mutated genes such as CDH1 (previously known as E-cadherin), TP53, and ARID1A (Park et al. 2016; Luo et al. 2018; Xu et al. 2023). Among such classifications are the mesenchymal...

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