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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
.... Given the essential role of the centromere in chromatin segregation during mitosis, such integration events may disrupt centromere function and promote large-scale chromosomal rearrangements. Coincidentally, the human 8q24 region is also a common integration site for HPV (Akagi et al. 2023), indicating...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...from their target gene promoters and interact through long-range chromatin looping events as part of the three-dimensional (3D) structure (Heidari et al. 2014). Aberrant 3D interactions, particularly involving promoter–enhancer contacts, can lead to dysregulation of oncogenes and tumor suppressors...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...at sites of open chromatin, consistent with these elements being bound by transcription factors and functioning as regulatory elements (Fig. 1A; Supplemental Table S4; Tsompana and Buck 2014). Many of these are LTR elements of evolutionarily recent ERVs, including MER11D (28.46% overlap with ATAC-seq peaks...
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Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...and enhancer function in the , we examined epigenetic marks in HepG2 and K562 using ENCODE data (The ENCODE Project Consortium et al. 2020). We first profiled LTR18A elements overlapping ATAC peaks for open chromatin, which is a common epigenetic feature for active regulatory elements. In HepG2, LTR18A...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...and circularized by intramolecular 26 ligation in dilute conditions. These circularized chromatin contacts were amplified by HIV-1 specific primers 27 targeting HIV-1 core promoter and enhancer (HXB2 coordinates 249–728), where most transcription factors 1 bind. Of note, the two restriction enzymes NlaIII and Mlu...
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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
...identity. A better understanding of how enhancers work will improve the interpretation of noncoding variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...targets for PB and potentially other brain tumors.ResultsPan-transcriptomic and accessibility maps of PB progressionTo investigate gene expression and chromatin accessibility dynamics that occur during initiation and progression of PB, we extracted pineal glands from a well-characterized mouse model...
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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
...to identify and validate enhancers. During recent years, highthroughput sequencing efforts like ENCODE and the Epigenomics Roadmap have yielded an enormous wealth of regulatory data (Gerstein et al. 2012; Roadmap Epigenomics Consortium et al. 2015). Some of the most commonly used approaches are chromatin...
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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
...of MYC-driven cancers, we can potentially target MYC-associated chromatin interactions for cancer therapy.Dysregulation of the MYC oncogene, which encodes for the MYC transcription factor, is common in cancer. Elevated mRNA and protein expression of MYC is seen across most cancer types in The Cancer...
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Method: High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation
- Daniel Rico,
- Daniel Kent,
- Nefeli Karataraki,
- Aneta Mikulasova,
- Rolando Berlinguer-Palmini,
- Brian A. Walker,
- Biola M. Javierre,
- Lisa J. Russell,
- and Chris A. Brackley
Genome Res. July 2022 32: 1355-1366; Published in Advance July 21, 2022, doi:10.1101/gr.276028.121
...also observed extensive changes in enhancer-promoter interactions within the TAD, suggesting that it is the downstream chromatin remodeling which gives rise to the oncogene activation, rather than the presence of the inserted super-enhancer DNA sequence per se. Simulations of the IGH-CCND1 reciprocal...
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