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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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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...electrophoresis. A total of three different replicates of double transfections with puromycin treatment conducted at different times was processed. Two milligrams of total RNA was used for generation of cDNA primed with oligo(dT) according to the manufacturer's instructions (AffinityScript cDNA synthesis kit...
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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 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...replication dynamics. 544 Chromosome Res 9: 1–19. 545 Hyrien O, Guilbaud G, Krude T. 2025. The double life of mammalian DNA replication origins. Genes 546 Dev 39: 304–324. 547 Johnson WE, Li C, Rabinovic A. 2007. Adjusting batch effects in microarray expression data using 548 Sadu Murari et al., Page 23...
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...of nucleosomes needed for wrapping newly synthesized DNA, progression of the replication fork requires nucleosomes to disassemble, at least transiently. Nucleosome disassembly is required at actively replicating locations, but nucleosome replacement could also extend to regions ahead of the fork, where...
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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
...-spread replication stress (Agrawal et al. 2014). 61 Although each damaging agent specifically induces known DNA damage repair pathways, a 62 broad and temporal DNA damage response occurs in cells. Thus, to evaluate this response 63 in a global manner, comprehensive DDR studies utilizing omics methods are essential...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the is replicated from early and late firing origins and is partitioned into domains...
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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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Research: Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork
- Mónica P. Gutiérrez,
- Heather K. MacAlpine,
- and David M. MacAlpine
Genome Res. July 2019 29: 1123-1133; Published in Advance June 19, 2019, doi:10.1101/gr.243386.118
..., including the histone variant H2AZ, which marked loci with rapid maturation kinetics. The chromatin maturation at origins of DNA replication was dependent on whether the origin underwent initiation or was passively replicated from distal-originating replication forks, suggesting distinct chromatin assembly...
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Method: Quantifying pathological progression from single-cell transcriptomic data with scPSS
- Samin Rahman Khan,
- M Saifur Rahman,
- M. Sohel Rahman,
- and Md Abul Hassan Samee
Genome Res. February 2026 36: 375-386; Published in Advance January 14, 2026, doi:10.1101/gr.280411.125
...rigorous. The key strength of scPSS is its applicability in a “semisupervised” setting, where only healthy reference cells are known and diseased-labeled data are not provided for model training. As existing methods do not support cell-level pathological progression measurement in this setting, we adapt...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...in double-stranded DNA and ∼200 years in single-stranded DNA (Frederico et al. 1990). In contrast, the rate of deamination is vastly accelerated for cytosine bases in CPDs, with a half-life of tens to hundreds of hours (Taylor 2022). Because even error-free replicative bypass of a deaminated CPD (d...
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