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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
...and position within nucleosomesWe next examined whether the binding patterns observed in vitro were consistent in a cellular context. To extend our findings, we examined TP53 and TP63 ChIP-seq with MNase-seq to examine nucleosome occupancy at sites bound by these factors. The site of binding was defined...
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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
...regions with high DNA-encoded nucleosome occupancy. Genome Res 20: 1361–1368. doi:10.1101/gr.103945.109 ↵Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19–42. doi:10.1006/jmbi.1997.1494 ↵Luger K...
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Letter: A novel strategy of transcription regulation by intragenic nucleosome ordering
- Cédric Vaillant,
- Leonor Palmeira,
- Guillaume Chevereau,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Claude Thermes,
- and Alain Arneodo
Genome Res. January 2010 20: 59-67; Published in Advance October 26, 2009, doi:10.1101/gr.096644.109
...) Theoretical nucleosome energy gain [#2;E(s)] landscape predicted by the model II (Vaillant et al. 2007). Vaillant et al. 62 Genome Research www..org r =#2;0.23, P = 53 10#2;3. Hence, themore compact the nucleosomal array, the shorter the linker size, the higher the transcription rate. Consistently...
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Research: Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription
- Mukund Patel,
- Jeremy M. Simon,
- Michael D. Iglesia,
- Sam B. Wu,
- Andrew W. McFadden,
- Jason D. Lieb,
- and Ian J. Davis
Genome Res. February 2012 22: 259-270; Published in Advance November 15, 2011, doi:10.1101/gr.125666.111
...system to address questions regarding the genomic mechanisms by which chimeric transcription factors cause cancer. We found that in tumor cells, EWS–FLI targets regions of the distinct from FLI1, despite identical DNA-binding domains. In primary endothelial cells, however, EWS–FLI and FLI1 demonstrate...
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Method: Quantitative evaluation of all hexamers as exonic splicing elements
- Shengdong Ke,
- Shulian Shang,
- Sergey M. Kalachikov,
- Irina Morozova,
- Lin Yu,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. August 2011 21: 1360-1374; Published in Advance June 9, 2011, doi:10.1101/gr.119628.110
...of all 6-mers in splicing Genome Research 1367 www..org positioning at the test exon and vice versa. The data from all five locations consistently showed a good correspondence between LEIsc values and predicted nucleosome occupancy scores as described by Kaplan et al. (2009), leaving open the possibility...
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Research: TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
- Morgan A. Sammons,
- Jiajun Zhu,
- Adam M. Drake,
- and Shelley L. Berger
Genome Res. February 2015 25: 179-188; Published in Advance November 12, 2014, doi:10.1101/gr.181883.114
...) Average MNase-seq tag density (6750 bp from TP53 peak center) from all nutlin-induced TP53 binding sites and CTCF binding sites. TP53 binds to distinct chromatin environments Genome Research 183 www..org all TP53 binding sites (Fig. 4E). Conversely, we observe a large nucleosome-depleted region over...
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Research: High-throughput functional testing of ENCODE segmentation predictions
- Jamie C. Kwasnieski,
- Christopher Fiore,
- Hemangi G. Chaudhari,
- and Barak A. Cohen
Genome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014, doi:10.1101/gr.173518.114
.... 2010. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 38: 2522–2540. Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M, Segal E. 2010. p53 binds preferentially to genomic regions with high DNA-encoded nucleosome...
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Research: Local sequence features that influence AP-1 cis-regulatory activity
- Hemangi G. Chaudhari and
- Barak A. Cohen
Genome Res. February 2018 28: 171-181; Published in Advance January 5, 2018, doi:10.1101/gr.226530.117
...genomic regions occupied by multiple AP-1 binding proteins supports the former hypothesis. These results are not unique to the AP-1 family of proteins. Regions bound by multiple members of the FOX family are more often functional than regions bound by a single member (Chen et al. 2016). Different members...
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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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