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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...@wi.mit.eduAbstractRates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem...
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Research: Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus
- William R. Thomas,
- Cecilia Baldoni,
- Yuanyuan Zeng,
- David Carlson,
- Julie Holm-Jacobsen,
- Marion Muturi,
- Dominik von Elverfeldt,
- Tue B. Bennike,
- Dina K.N. Dechmann,
- John Nieland,
- Angelique P. Corthals,
- and Liliana M. Dávalos
Genome Res. January 2026 36: 61-70; Published in Advance November 4, 2025, doi:10.1101/gr.280639.125
...), including those associated with increased fatty acid oxidation (Villanueva-Cañas et al. 2014), as hibernators rely on gradual fat utilization over winter. Research on shrew physiology indicates they also rely extensively on lipid metabolism in winter (Keicher et al. 2017) and may share some molecular...
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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
..., as it alleviates lipid toxicity, mitigates ER stress, provides energy, and supports cell survival (Zadoorian et al. 2023). These findings suggest that TEs contribute to the diversity of the PLAAT4 gene products and function, thereby contributing to cancer metabolism remodeling (Fig. 6H).View larger version...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...coexpression modules with differential responses to environmental microbiota. Third, we link the microbial and host transcriptome data by predicting a global map of more than 2800 metabolic interactions. These interactions represent statistical associations between variation in bacterial metabolic potential...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...metabolitesGiven the significant influence of epigenetic mechanisms on lipid metabolism (Gomez-Alonso et al. 2021) and the observation that calorie restriction can modulate both epigenetic drift and metabolic pathways (Hahn et al. 2017; Maegawa et al. 2017), we further explored the impact of our EDS on serum...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
..., becoming less constrained in lineages evolving more herbivorous diets. We further consider the biological functions associated with diet evolution and observe that pathways related to amino acid and lipid metabolism, biological oxidation, and small molecule transport experienced reduced purifying selection...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...has deficiency in lipid and 314 protein catabolism that influences phenotypic responses to diets (Gillette et al. 2020). As 315 validated by Sanger sequencing, honey bee spen has a p.322 Tyr>Cys recoding site with 316 significantly higher editing level in CV than in GF (Figure 6B). 317 Ly-6 protein XM...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...(Long and Holtzman 2019). The accumulation of amyloid-β (Aβ) plaques and tau protein tangles are a hallmark of AD pathology. However, it is increasingly recognized that additional neuropathological processes, such as neuroinflammation, lipid metabolism dysfunction, mitochondrial impairment, axonal...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
..., and metabolic responses to exercise, including glucose metabolism, lipid metabolism, and lactate production (Hultman et al. 1991; Romijn et al. 1993, 2000; Greenhaff et al. 1994; Bottinelli et al. 1999; Trappe et al. 2003, 2006; Kosek et al. 2006; Luden et al. 2008; Raue et al. 2009; Dickinson et al. 2010...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...the galactolipids in food, which is important for the lipid metabolism of herbivores.We recognized that although a number of complementary models were used in the present study, they may not adequately represent the general genetic basis of feeding habits in fish, as there are more than 32,000 species of fish...
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