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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
....fischer@sorbonne-universite.fr, zhou.xu@sorbonne-universite.frAbstractTelomeres gradually shorten at each cell division, and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a steady-state telomere length (TL) distribution. Here, we develop...
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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
...02139, USA; 3Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA; 4Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts 02139, USA; 5Department of Biochemistry and Molecular Biology, University of Texas Health Science Center Houston...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...Toward telomere-to-telomere cat s for precision medicine and conservation biology William J. Murphy1,2,3 and Andrew J. Harris1,3 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA; 2Department of Biology, Texas A&M University, College...
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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
...improved reproducibility, most existing efforts have automated only a subset of the workflow, and extending automation to efficiently map nonhistone proteins, such as chromatin regulators, remains challenging. Here, we present a fully automated implementation of our previously developed single-pot Ch...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...and low ESRRG (n = 123) expression. (H) Model of AR assisting the loading of GR to chromatin through modulation of chromatin accessibility and enhancer activation (top), and expansion of AR-regulated transcriptome by GR that leads to restriction of cell proliferation and PCa progression (bottom...
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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
...NeXt-based architectures, we performed feature attribution using integrated gradients (Sundararajan et al. 2017) followed by motif discovery (Methods). This analysis revealed that the ConvNeXt-based models consistently learned sequence motifs corresponding to transcription factors with known roles in regulating chromatin...
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Method: Telomere-to-telomere assembly by preserving contained reads
- Sudhanva Shyam Kamath,
- Mehak Bindra,
- Debnath Pal,
- and Chirag Jain
Genome Res. November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124
...Sudhanva Shyam Kamath, Mehak Bindra, Debnath Pal and Chirag Jain Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India Corresponding author: chirag@iisc.ac.inAbstractAutomated telomere-to-telomere (T2T) de novo assembly of diploid and polyploid s...
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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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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...controlling CTCF binding remain unclear. Here, we investigate the role of repressive chromatin modifications in CTCF binding using H3K9 methyltransferase-deficient immortalized mouse embryonic fibroblasts (iMEFs) and H3K27 methyltransferase EZH1/2 inhibitor. We find that H3K9 and H3K27 methylation regulate...
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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
...epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations produced by segmentation and annotation (SAGA) methods have emerged as the predominant way to summarize these epigenomic data sets in order to annotate the . These chromatin state annotations are essential for many genomic...
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