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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
...regulators in GSC-like cells. To characterize chromatin landscapes, we develop a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3-enriched regions, corresponding to the euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively...
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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
...the anchor position across all stripes in the designated area. We examine H3K4me2 (strongly associated with promoters and enhancers), H3K4me3 (strong correlation to promoters), and H3K27ac (active enhancer mark) (Calo and Wysocka 2013). We compare CTCF-stripes to EP-stripes to emphasize the difference...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...of Sciences, Beijing 100101, China; 4University of the Chinese Academy of Sciences, Beijing 100049, China ↵5 These authors contributed equally to this work. Corresponding author: shandong@mail.hzau.edu.cnAbstractCentromeres, characterized by their unique chromatin attributes, are indispensable...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...of development and neurobiology (Brenner 1974; Corsi et al. 2015). For any organism, a key element of modern biological understanding is to sequence and characterize its . C. elegans was the first animal to have its sequenced in 1998 (The C. elegans Sequencing Consortium 1998); by 2005, its was considered...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
..., Kellis M. 2012. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9: 215–216. doi:10.1038/nmeth.1906 ↵Feng J, Liu T, Qin B, Zhang Y, Liu XS. 2012. Identifying ChIP-seq enrichment using MACS. Nat Protoc 7: 1728–1740. doi:10.1038/nprot.2012.101 ↵Fu Y, Sinha M, Peterson CL...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...diameters of strains in A. Data are mean ± standard deviation (s.d.) (n = 3). Different letters indicate statistically significant differences (ANOVA, Tukey's multiple comparisons test, P < 0.05). (C) Western blot analysis of PH-1 and deletion mutants using antibodies against H3K4me3, H3K9me3, H3K27me3, H3K...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...factors bind directly to the DNA to activate or repress transcription (Marr et al. 2021; Minnoye et al. 2021). Recent advances in sequencing technology have enabled the characterization of chromatin remodelers, nucleosome positioning, and chromatin accessibility using high-throughput assays like Ch...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
..., the absence of broad H3K4me3 domain at these loci is often associated with repressive chromatin enriched with Polycomb-associated states. As described before for cell lines and primary tissues, here we showed that broad H3K4me3 domains dynamically associate with cell identity genes throughout T cell...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...features such as topoisomerase-II, H3K27ac, H3K4me3, Pol II, GRO-seq, and ATAC-seq (top). Zoom-in near a fountain origin is shown at the bottom. (C) Average profile of GRO-seq data from Kruesi et al. (2013) split into plus (red) and minus (blue) strands is plotted with respect to the fountain origins...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 47: 810–822. doi:10.1016/j.molcel.2012.07.030 ↵Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ. 2014. Fully automated high-throughput chromatin...

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