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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
...their epigenomic profiles including chromatin accessibility and DNA methylation. We showed that LINEs and LTRs, especially ERV1s, served as active promoters for TE-derived transcripts and identified instances of TP53-mediated transcriptional initiation or repression over TE-derived promoters.TP53 activation has...
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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
...binding. Once bound, the nucleosome can then rewrap, thus kicking off the TF (Luo et al. 2014). Our results for TP53 suggest that TP53 can access the partially unwrapped nucleosome and remain stably bound. Binding by TP53 to nucleosomes differs when compared to FOXA, which can target its binding sites...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...(Saccharomyces cerevisiae) nucleosome (White et al. 2001). Although C4 atoms in most cytosine bases had zero SASA, a subset had a non-zero SASAC4 (Supplemental Fig. S10A), indicating that there are significant differences in C4 solvent accessibility depending upon the location of the cytosine base within...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., 8092 Zurich, Switzerland; 4Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Cité, 75014 Paris, France Corresponding authors: ekaterina.krymova@sdsc.ethz.ch, valentina.boeva@inf.ethz.chAbstractFine-grained prediction of chromatin accessibility from DNA sequence is a foundational step...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...and a repressor of the ARF/TP53 pathway. miR-34a has been linked to chemotherapy resistance in CLL, and its low expression is associated with TP53 aberrations and Richter transformation (Balatti et al. 2018); (3) TFs with different shapes of nucleosome occupancy profiles between CLL and NBCs, such as a depletion...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...of Michigan, Ann Arbor, Michigan 48109, USA; 9Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: mohlke@med.unc.eduAbstractChromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...and two H2A–H2B dimers) to form a nucleosome, and groups of nucleosomes are further folded into higher-order chromatin structures (Luger et al. 1997; McGinty and Tan 2015). Although chromatin packaging can protect the DNA from damage (Takata et al. 2013), it also inhibits the accessibility of DNA repair...
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Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...on their chromatin accessibility. Short-fragment nucleosomes in accessible regions exhibit high MNase sensitivity and are enriched at transcription start sites (TSSs) and CTCF peaks, similar to previously reported “fragile nucleosomes.” These SEM-defined accessible short-fragment nucleosomes are found not just...
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...blocks of chromatin (Luger et al. 1997). Nucleosomes limit access to the DNA, thus protecting the and providing a unified platform for regulating DNA-based processes (Kristjuhan and Svejstrup 2004; Schwabish and Struhl 2004; Bondarenko et al. 2006; Fleming et al. 2008; Lai and Pugh 2017). Regulatory...

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