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Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
..., Illinois 60628, USA ↵3 These authors contributed equally to this work. Corresponding author: zhe.ji@northwestern.eduAbstractWe describe a low-input RNase footprinting approach for the rapid quantification of ribosome-protected fragments with as few as 1000 cultured cells. The assay uses a simplified...
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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
...was sequenced as “input,” whereas the remaining chromatin was prepared for low input chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) using antibodies against H3K4me3, H3K27me3, or H3K9me3 (Fig. 3A). We chose these histone modifications because they represent distinct chromatin domains: H3K4me3...
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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
...for Biotechnology, Huntsville, Alabama 35806, USA; 6Department of Medicine, Division of Endocrinology & Metabolism, University of California San Diego, La Jolla, California 92093, USA Corresponding author: agoren@ucsd.eduAbstractChromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study...
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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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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
...) Heat map showing sensitivity of PH-1 and mutants to various abiotic stresses. Growth inhibition of PH-1 under each condition was normalized to 1.0. Data are mean ± standard deviation (n = 3). For panels C, D, F, and H, data are presented as mean ± standard deviation (s.d.) from three independent...
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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
...definition, a transcriptomic analysis can only identify readouts of expressed genes, but it cannot distinguish between genes being repressed or kept in a prone transcriptional state, because both are transcriptionally inactive.In bulk assays, the use of chromatin immunoprecipitation strategies...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...clusters can be challenging, restricting the import of sensitive data. Furthermore, importing large data sets (e.g., hundreds of thousands of individuals) and managing genomic annotations are also difficult. Commercial platforms, such as DNAnexus (https://www.dnanexus.com) and the suite of Qiagen products...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...sequence features, including transcription factor motifs that are central to cell type–specific chromatin accessibility.Evaluating model sensitivity to genetic point variantsExperimentally profiling chromatin accessibility for every genetic variant is prohibitively resource-intensive, highlighting the need...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...DNA (Supplemental Fig. S1D).Sperm ATAC-seq profiles are sensitive to cell-free chromatin contaminationOur initial efforts to probe sperm chromatin architecture were performed using the same “untreated” ATAC-seq conditions reported by Jung et al. (2017). Under these conditions, we robustly reproduce...
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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
...indicating the standard deviation. (C) Histogram comparing the frequencies of log(TPM) values for confident (r ≥ 0.9) and nonconfident (r < 0.9) annotations of the transcribed chromatin state in the running example. The x-axis represents ranges of log(TPM) with each pair of bars corresponding to confident...
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