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Research: Extensive protein dosage compensation in aneuploid human cancers
- Klaske M. Schukken and
- Jason M. Sheltzer
Genome Res. July 2022 32: 1254-1270; Published in Advance June 14, 2022, doi:10.1101/gr.276378.121
.... 2021). Similarly, studies of subchromosomal amplifications in cancers suggest that up to ∼30% of DNA copy number changes do not result in corresponding changes in protein abundance (Zhang et al. 2014, 2016; Mertins et al. 2016; Gonçalves et al. 2017; Sousa et al. 2019). Although proportional synthesis...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
..., the transcriptome data 207 shows specific transcriptional regulation kinetics of the DNA damage response dependent on 208 the genotoxic stressor. 209 Protein expression over time reveals specific trends involved in DDR 210 As for the transcriptome, we used self-organizing maps clustering 2,582 dynamically 211...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...EV clones. Bottom: Plots showing the log2 fold change in expression levels of Jpx, Ftx, Rlim in D1 ΔXp versus WT clone and WT EV clones as quantified through RNA-seq. (F) RNA-FISH using double-stranded DNA probe for Xist/Tsix-Cy3 (red) in wild-type empty-vector transfected (WT EV) and heterozygous...
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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
...remain underexplored. One study stratified pancreatic ductal adenocarcinoma into two distinct subgroups based on specific DNA elements, such as transposable elements (TEs), although it was limited by the use of labor-intensive FACS sorting with small sample sizes (Espinet et al. 2021). TEs exhibit...
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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
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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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
...; Shadrach et al. 2021) has revealed a response to DNA damage and cell injury as well as activation of compensatory regeneration.So far no comprehensive analysis has been conducted to dissect how vulnerable versus resilient neurons respond to ALS over time. We reasoned that an analysis of how differentially...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
...that most transcriptional alterations in tumor samples were DNA methylation–independent. Instead, altered histone H3 trimethylation at lysine 27 (H3K27me3) was the predominant molecular defect at deregulated genes. Our results also suggest that the presence of a bivalent chromatin signature at CpG island...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...located within the duplicated region. (F) Copy numbers of CSMD1 and MICU3 after passaging proband cells for 12, 22, 33, 40, and 50 passages. Mean ± SEM; data from representative trials are shown (n ≥ 3 total trials). Genomic DNA from the near-diploid MCF10A cell line was used as a control...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...feature analysis modules to explore RTE dynamics in a user-defined condition. To our knowledge, scARE represents the first systematic investigation of RTE dynamics at the single-cell level within the context of neurodegenerative diseases.Transposable elements (TEs) are DNA elements that are capable...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...networks(Lee and Young 2013; Levine 66 et al. 2014; Long et al. 2016). Understanding these regulatory mechanisms beyond transcription 67 may reveal critical aspects of how cellular changes during aging contribute to PD pathology. 68 A pivotal study employing the multiome technique in human aging and PD...
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