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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...(Ma and Nt, 506 and 347 complete phenotypes, respectively) showed highly significant differences for all traits studied. In six of the eight bulls studied, we found that balanced daughters had significantly delayed first inseminations compared with their wild-type sisters, thus supporting growth...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...requires the presence of a homologous sequence of DNA (most commonly a sister chromatid) to serve as a template that can be used to resynthesize DNA sequences. However, except in special circumstances such as MAT switching, where the donor is heterochromatic with highly positioned nucleosomes...
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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
...and Cooper 2010; Wellinger and Zakian 2012; de Lange 2018). These functions are tightly associated with the regulation of telomere length (TL). Indeed, telomeres are protected by proteins that prevent natural chromosome ends from being recognized as double-strand breaks, which would elicit a DNA damage...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
..., respectively; the rDNA repeats, in light green; the distal satellite regions, in orange; and the telomeres, in dark green. Each distal satellite is labeled according to the HG002 v1.0.1 reference assembly, with the exception of Chromosome 13 and Chromosome 22 paternal, which are too similar to be separated...
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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
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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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: 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
...different sequencing depths. Here, we used equal sequencing depths on both haplotypes. (C,D) Fraction of sequencing outputs containing an assembly gap when the sequencing depths across the two haplotypes are uneven. This scenario models somatic mutation in DNA with variant allele frequency below 0.5. In (C...
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Research: Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
- Samantha L. Sholes,
- Kayarash Karimian,
- Ariel Gershman,
- Thomas J. Kelly,
- Winston Timp,
- and Carol W. Greider
Genome Res. April 2022 32: 616-628; Published in Advance October 26, 2021, doi:10.1101/gr.275868.121
...polymerase IV, which lacks strand displacement and exonuclease activity, was used to generate a double-stranded blunt end, as well as T4 DNA ligase to seal the nicks. Nanopore library adaptors were added to allow sequencing (Fig. 1A).View larger version: In this window In a new window Figure 1. Telomere...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...for feature encoding schemes was further analyzed across 11 species. We encoded all the 11 data sets from EpiTEAmDNA by 14 feature encoding schemes and evaluated ACC via three DL base models on independent test sets, thus quantifying feature selectivity across species and models to uncover encoding...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...of peaks. (B) The density of ChIP-seq peak positions along the Arabidopsis chromosomes, relative to their distance from the centromere (C, on the left) to the telomere of the chromosome arm they are on (T, on the right). (C) Average DNA methylation levels in WT Arabidopsis seedlings under protein...

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