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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
..., Guelph, ON N1G 2W1, Canada Corresponding author: michael.wilson@sickkids.caAbstractTransposable elements (TEs) provide a source of transcription factor (TF) binding sites that can rewire gene regulatory networks. NF-kB is an evolutionarily conserved TF complex primarily involved in innate immunity...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
..., these elements could still act on gene regulation if they carry cis-elements as transcription factor binding site (TFBS).TEs located near genes can modulate gene expression by donating TFBSs or poly(A) signals to the ancestral regulatory motifs. To investigate the potential functional role of the observed...
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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
...-derived promoters in isogenic cancer cell lines and provide a high-confidence TE expression atlas of TE promoters that are direct and indirect targets of TP53.About half of the human is made up of transposable elements (TEs) (Burns 2017; Deniz et al. 2019). Throughout evolution, TEs have been exapted as cis-regulatory...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...@smmu.edu.cn, ljing@smmu.edu.cnAbstractEukaryotic s contain numerous transposable elements (TEs), whose dysregulation threatens stability and may contribute to cancer. Pancreatic adenocarcinoma (PAAD) is among the deadliest cancers, marked by abundant stroma that obscures tumor-specific molecular signals...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...includes a new, comprehensive analysis of transposable element (TE) composition, location, and diversity. SVs and TEs are frequently close to coding sequences and many SVs are heterozygous, suggesting that SVs might impact gene and allele-specific expression. Most SVs are uniquely present in only one...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...as beta-catenin) drives the expression of target genes from regulatory regions bound by TCF/LEF transcription factors. Gene regulation, however, entails the interplay between sequence information and 3D structure, yet the impact of Wnt signaling on structure has been poorly explored. Here, we investigate...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...PGE accurately discovers some crucial TF motifs within prioritized cCREs and reveals the different regulatory types of these cCREs.Cell type–specific gene expression patterns are primarily determined through complex interactions between cis-regulatory elements (CREs) and transcriptional factors, playing...
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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
...of transposable elements (HTT) is an important driver of evolution, yet the factors conditioning this phenomenon remain poorly characterized. Here, we screen 247 animal s from four phyla (annelids, arthropods, mollusks, chordates), spanning 19 independent transitions between aquatic and terrestrial lifestyles...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that, in tetrapods, the targeting and repression of lineage-specific transposable elements (TEs) plays a critical role in the evolution of the Krüppel...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...Lake Malawi cichlid pan graph reveals extensive structural variation driven by transposable elements Fu Xiang Quah1,2, Miguel Vasconcelos Almeida1, Moritz Blumer2, Chengwei Ulrika Yuan1,2, Bettina Fischer2, Kirsten See1, Ben Jackson2, Richard Zatha3, Bosco Rusuwa3, George F. Turner4, M. Emília...
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