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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...in mice may allow for the discovery of pathways that inform therapeutic strategies in humans. In a preliminary dominant suppressor mutagenesis screen using the supermutagen N-ethyl-N-nitrosourea (ENU), we isolated five modifier loci, named suppressor of methyl CpG binding protein (Sum) 1–5, which suppress...
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Research: Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice
- Maha Alriyami,
- Luc Marchand,
- Quan Li,
- Xiaoyu Du,
- Martin Olivier,
- and Constantin Polychronakos
Genome Res. December 2019 29: 1951-1961; Published in Advance November 6, 2019, doi:10.1101/gr.247882.118
...cells by autoreactive CD4+ and CD8+ T cells in T1D (Polychronakos and Li 2011; Pearson et al. 2016). Similar to human T1D, diabetes in NOD mice is caused by a combination of polygenic inheritance and environmental factors (Polychronakos and Li 2011; Pearson et al. 2016). Female mice are predominantly...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...vulnerability code of 39 genes, including Atf4, Nupr1, Ddit3, and Penk, involved in apoptosis, as well as a proregenerative and antiapoptotic signature consisting of Atf3, Vgf, Ina, Sprr1a, Fgf21, Gap43, Adcyap1, and Mt1. Machine learning using genes upregulated in SOD1G93A spinal MN predicts disease in human...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...4-sensitive chromatin accessibility changes associated with common human SNPs. (A) Experimental layout. (B) Dot plot representing scaled single-cell mRNA expression per cell (color) and fraction of cells expressing (size) within each annotated cell population isolated from mice 3 days post...
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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
...Medical University (Naval Medical University), Shanghai 200433, China; 2Center for Translational Medicine, Second Military Medical University (Naval Medical University), Shanghai 200433, China; 3National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...was conducted with particular attention to biological plausibility. To this end, the human cerebral cortex data set was selected, as it follows a well-characterized linear developmental trajectory, in contrast to more structurally complex tissues such as breast cancer. Figure 1 depicts the comprehensive...
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Letter: Widespread and tissue specific age-related DNA methylation changes in mice
- Shinji Maegawa,
- George Hinkal,
- Hyun Soo Kim,
- Lanlan Shen,
- Li Zhang,
- Jiexin Zhang,
- Nianxiang Zhang,
- Shoudan Liang,
- Lawrence A. Donehower,
- and Jean-Pierre J. Issa
Genome Res. March 2010 20: 332-340; Published in Advance January 27, 2010, doi:10.1101/gr.096826.109
...of autosomal genes showing hypermethylation was 884 out of 8821 (10%), while 1% of genes showed age-related hypomethylation. Because of a generally poor sequence conservation between mice and humans at promoter CpG islands (Antequera and Bird 1993; Matsuo et al. 1993), only 2108 genes could be compared...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
.... 2021). Crp, a known 484 anti-apoptosis factor (Sopko et al. 2015; Atkins et al. 2016), could function to maintain the 485 hemocyte population upon infection, with motifs enriched in mid- and late-expressed immune 486 genes and among enhancers associated with effector and signaling genes. Both Hnf4...
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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
...to inhibit the clearance processes of cfDNA (Martin-Alonso et al. 2024). Administration of these priming agents prior to blood collection increased the recovery of circulating tumor DNA by more than 10-fold, as demonstrated in a preclinical model of mice with lung cancer (Martin-Alonso et al. 2024).It...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...of tissue sections in a cost-efficient manner, as illustrated by the setup of a three-dimensional molecular cartography of human cerebral organoids (Lozachmeur et al. 2023). Herein, we present the use of double-barcoded DNA arrays to perform spatial epigenomic landscaping. Specifically, this implies (1...
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