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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...&Tag to map a variety of histone PTMs, including the euchromatin marks H3K9ac, H3K14ac, and H3K27ac, facultative heterochromatin mark H3K27me3, and constitutive heterochromatin marks H3K9me2 and H3K9me3. We also used ChIP-seq to profile the H3K9 methylation binding protein CBX1.Scaling all LADs to a uniform...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...similar to the histone dimer of B. bacteriovorus (Supplemental Fig. 1).ATAC-seq reveals the accessible chromatin landscape in BacteriovoraxTo map the chromatin accessibility landscape in Bacteriovorax, we adapted the previously described bacterial ATAC (bac-ATAC) protocol (Melfi et al. 2021), which...
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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
...-axis, and fragment length is plotted on the y-axis, indicating nucleosome or TF-sized DNA. (C) Genome-wide map of chromatin changes in response to genetic perturbations. Loci with significant chromatin changes in response to a deletion are highlighted in purple (those reflecting the mutant deletion itself...
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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
....Transcriptional regulation in eukaryotes is profoundly influenced by chromatin status, integrating diverse cellular signals to control gene expression (Berger 2007). Chromatin dynamics are modulated by multiple mechanisms, including histone modifications, DNA methylation, and chromatin remodeling complexes (Shilatifard 2006...
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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
...of regulatory elements and chromatin states in the human , as well as to estimate the absolute abundance of transcribed and accessible/single-stranded structures. In addition, we map nucleosomal and subnucleosomal structures associated with active transcription and comprehensively measure TF footprints...
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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
...to analyze the transcriptome, histone modification patterns, and replication timing of germline stem cell (GSC)–like and somatic cyst stem cell (CySC)–like cells. Single-cell RNA sequencing validates previous findings on GSC–CySC intercellular communication and reveals a high expression of chromatin...
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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
...nucleosomes (Cannistraro and Taylor 2010; Song et al. 2011, 2014). Nucleosomes are the fundamental packaging unit of eukaryotic chromatin and are composed of an octamer of histone proteins and ∼147 bp of DNA (Luger et al. 1997). As the nucleosomal DNA wraps around the histone octamer, the minor groove...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
.... High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22: 2990–2997. doi:10.1093/nar/22.15.2990 ↵Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. 2008. Shotgun bisulphite sequencing of the Arabidopsis reveals DNA methylation...
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Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...3457–E3465. doi:10.1073/pnas.1424804112 ↵Jiang C, Pugh BF. 2009. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae . Genome Biol 10: R109. doi:10.1186/gb-2009-10-10-r109 ↵Jin C, Felsenfeld G. 2007. Nucleosome stability mediated by histone variants H3...
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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
...of genomic architectural stripes from Hi-C or Micro-C chromatin contact maps, that relies on robust image processing techniques and rigorous statistical tests for enrichment. Quagga outperforms other stripe detection methods in accuracy and is highly versatile, working with Hi-C, Micro-C, and other chromatin...
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