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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
...author: twang@wustl.eduAbstractThe relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling of TE expression dynamics under the regulation of TP53 provides valuable resources for more clarity in TP53's roles...
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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
...of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14203, USA Corresponding author: mjbuck@buffalo.eduAbstractThe TP53 family of transcription factors plays key roles in driving development and combating cancer by regulating gene expression. TP53, TP63, and TP73...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...-luciferase miRNA target expression vectors (Promega E1330) harboring sequences corresponding to targets of Ago2 binding at Ak7, Spag17, or Tdrd9 mRNA. The inserted sequences are centered on the eCLIP peak (12–30 bp) and extended in both directions for a final insert length of 400 bp (Supplemental Table S10...
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Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
...; Mirza 2003). Previous research showed that the TP53 regulatory network mainly includes protein-coding and noncoding genes, such as lncRNAs and miRNAs (Riley et al. 2008; Hermeking 2012; Zhang et al. 2014). However, in our study, we first systematically identified a group of novel regulators, peptides...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...across development from 0 h post egg-synchronization (embryos) to 72 h (young adults) (Fig. 1C). We extracted and sequenced mRNA to a minimum depth of 3 million reads and with a minimum quality score of 30, ultimately resulting in more than 3.5 billion high-quality reads that we anticipate...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...-dependent and that this regulation modulates the transcription of genes involved in cell adhesion and mRNA translation in colorectal cancer cells. Proteomic analyses reveal that ACTB and SETD3 interact with multiple large protein complexes, including complexes associated with transcriptional regulation...
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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
...data sets. Table 1 presents the data sets and the mRNA properties. As can be seen, these included a diverse set of downstream tasks related to mRNA translation, stability, and regulation. In addition, these data sets represent a range of molecules, including newly published data sets for recombinant...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...was used as the initial material for the RNA sample preparation. Briefly, mRNA was purified from total RNA using poly(T) oligo-attached magnetic beads. Then, the RNA was fragmented into short strands in NEBNext first-strand synthesis reaction buffer under an elevated temperature. Subsequently, the first c...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...for destabilization and translational inhibition (Chekulaeva and Filipowicz 2009). Our cell type–specific mRNA half-life measurements also allowed us to examine the decay of known miRNA targets. C. elegans genes encoding subunits of the vacuolar adenosine triphosphatase (V-ATPase) complex, which controls...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
.... 2015). These smRNAs can, in turn, cause transcripts to enter into the RNA interference (RNAi) pathway (Baulcombe 2004; Li et al. 2012; Cuerda-Gil and Slotkin 2016; Hung and Slotkin 2021). These observations suggest that sufficiently structured mRNAs, like miRNAs, form secondary structures that act...
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