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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...specific desiccation sensors activate transcription factors and signaling cascades, and how allelic expression bias contributes to this regulation, remains to be discovered. Although we detected allele-specific expression under stress, the random division of homologous chromosomes in our data set prevents...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...92697, USA ↵8 These authors contributed equally to this work. Corresponding authors: tanz@hs.uci.edu, kyokomor@uci.edu, xiangmix@uci.eduAbstractFacioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low...
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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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Research: 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
- Alice Cortesi,
- Matthieu Pesant,
- Shruti Sinha,
- Federica Marasca,
- Eleonora Sala,
- Francesco Gregoretti,
- Laura Antonelli,
- Gennaro Oliva,
- Chiara Chiereghin,
- Giulia Soldà,
- and Beatrice Bodega
Genome Res. June 2019 29: 883-895; Published in Advance May 16, 2019, doi:10.1101/gr.233288.117
...to this work. Corresponding author: bodega@ingm.orgAbstractDespite increasing insights in structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human , remains elusive. Facioscapulohumeral muscular dystrophy (FSHD) is associated with deletion of D4Z4 repeat...
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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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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
..., Salt Lake City, Utah 84112, USA Corresponding author: russell.butterfield@hsc.utah.eduAbstractFascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the Chromosome 4q telomere allowing...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...that balance biological relevance, sensitivity, and interpretability to ultimately answer a deceptively simple question: What TFs directly regulate the expression of my GOI?Cellular processes are regulated by transcription machinery binding the promoters and enhancers of target genes to activate gene...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
.... 2014; Veloso et al. 2014) and recent indirect estimates via TT-seq and PRO-seq signal ratios (Mimoso and Adelman 2023).We also explored the relationship between RNAPII elongation rate and transcriptional activity. A modest positive correlation with mean nascent transcript coverage was observed (Fig. 4E...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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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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