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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...Global 3′ UTR shortening, exhibiting cell type–specific patterns, has been reported in some model organisms, such as mice and Drosophila (Shulman and Elkon 2019; Lee et al. 2022). However, in pigs, the dynamics of these patterns, particularly at single-cell resolution, remain largely unexplored. Given...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS Qunlun Shen1,2, Shuqin Zhang1,3 and Shihua Zhang2,4,5 1School of Mathematical Sciences, Fudan University, Shanghai 200433, China; 2State Key Laboratory of Mathematical Sciences, Academy...
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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
...–specific cis-regulatory DNA elements (CREs), we pinpoint 141 ADNC-associated genes. Using gene set enrichment analysis (GSEA) and network proximity analysis, we further identify nine candidate repurposable drugs that were associated with these ADNC-related genes. In summary, this cell type–specific multiomic...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...phosphorylation that abolishes their DNA binding capacity (Dovat et al. 2002; Dephoure et al. 2008; Rizkallah and Hurt 2009). Indeed, previous observations showed CTCF is phosphorylated during mitosis (Sekiya et al. 2017). We note that, although the different cell lines in this study warrant different...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. Stripes are thought to play an important role in gene regulation and have been implicated in regulating a cell's lineage...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...DNA loss and A B C D E Figure 5. Cell cycle regulation of DNA replication and gene expression. (A) Exemplary genomic locus from Chromosome 4 showing enrichment of gene expression at the early replicating regions. Collapsed E/L ratios from PARTAGE Repli-seq data, PARTAGE multifraction signals...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...cells to re-enter the cell cycle partially restores a youthful H3K27me3 landscape, suggesting that DNA replication may rejuvenate chromatin structure (Yang et al. 2023). However, even mitotically active somatic stem cells display age-related increases in Polycomb repression: Aged Drosophila intestinal...
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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
...Figure 4. Inferring chromatin-state transitions across the mouse embryo by integrating consecutive spatial epigenomic landscapes. (A, left) Scan of a DNA array (TRITC filter) hosting a cryosection of a mouse embryo (E11.5) and immunostained with an antibody targeting the histone modification H3K27...
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Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
- Iris Zhu and
- David Landsman
Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
...view that housekeeping genes use common enhancers, which is based mainly on a study conducted in Drosophila cell lines with STARR-seq, in which DNA sequences do not function in their natural contexts (Zabidi et al. 2015). We further examined all the commonly expressed genes in mouse ESCs and MEF cells...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...-switching method to generate full-length cDNA libraries (see Methods). Because single-cell protocols can be biased toward retaining certain cell types (Mereu et al. 2020), hence changing the cell type proportions, this special approach maximizes our chance that the matched sequencing data share approximately...
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