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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
..., and four origin recognition complex (ORC) components are all enriched in GSC-like cells compared with CySC-like cells (Table 1).View this table: In this window In a new window Table 1. Composition and function of select DNA replication and chromatin regulation complexesTo control for potential biases...
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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
...(Fig. 2A; Supplemental Fig. S1). Then, intact nuclei were isolated by detergent lysis (Fig. 2B; Supplemental Fig. S1) and DNA stained for cell cycle analysis (Fig. 2C) as previously described (Meyer-Nava et al. 2023). Purified nuclei were analyzed by flow cytometry, and the cell cycle was estimated...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...-value < 0.001, Student's t-test.To further confirm whether the strand-specific mismatch pattern originated from DNA modification, we investigated the difference between the raw WGS and WGA current signals at the possible modified sites. By checking the signal around a forward error-prone G site in E...
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Method: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...16802, USA ↵3 These authors contributed equally to this work. Corresponding author: mxs2589@psu.eduAbstractCircular RNA (circRNA) is a class of RNA molecules that forms a closed loop with their 5′ and 3′ ends covalently bonded. CircRNAs are known to be more stable than linear RNAs, have distinct...
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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...diversity, evolution, and carcinogenesis and are, as such, important for human health. However, it remains unclear how spatial proximity of double-strand breaks (DSBs) affects the formation of SVs. To investigate if spatial proximity between two DSBs affects DNA repair, we used data from 3C experiments (Hi...
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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
...cycles. In reality, some mobile elements are linear, and circular mobile elements can contain repeat elements that produce circuits, both of which would not be detected by our approach. Although linear extrachromosomal DNA is outside the scope of this work, the ongoing transition to long-read sequencing...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...on different DNA strands referred to as interstrand crosslinks (ICLs) (Huang et al. 1995). This damage is often repaired by NER; however, there is a cell cycle-dependent compilation of various repair pathways to address this damage, including HR, NER, translesion synthesis (TLS), and the Fanconi Anemia (FA...
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Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- Brian S. Roberts,
- E. Christopher Partridge,
- Bryan A. Moyers,
- Vikram Agarwal,
- Kimberly M. Newberry,
- Beth K. Martin,
- Jay Shendure,
- Richard M. Myers,
- and Gregory M. Cooper
Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
...to impact only a limited number of loci (Muerdter et al. 2015; Liu et al. 2017; Barakat et al. 2018; Schöne et al. 2018; Wang et al. 2018; Sun et al. 2019; Ramaker et al. 2020). However, the case for strand asymmetry of DNA function within MPRAs is, in general, strong. Indeed, gene transcription, perhaps...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...by the change in allelic ratios between the output library, including replicate1 (C) and replicate2 (D), and the input library. Statistical significance (false discovery rate [FDR] < 0.05) was evaluated using Fisher's exact test. (E) DNA-binding motif-breaking scores were assessed for regulatory SNPs...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...Science and Technology of China, Quzhou 324000, Zhejiang, China; 3College of Biomedical Engineering, Sichuan University, Chengdu 610041, Sichuan, China Corresponding author: luoximei@uestc.edu.cnAbstractDNA N4-methylcytosine (4mC), a key epigenetic modification regulating DNA repair and replication...
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