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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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Method: Direct chromosome-length haplotyping by single-cell sequencing
- David Porubský,
- Ashley D. Sanders,
- Niek van Wietmarschen,
- Ester Falconer,
- Mark Hills,
- Diana C.J. Spierings,
- Marianna R. Bevova,
- Victor Guryev,
- and Peter M. Lansdorp
Genome Res. November 2016 26: 1565-1574; Published in Advance September 19, 2016, doi:10.1101/gr.209841.116
...Direct chromosome-length haplotyping by single-cell sequencing David Porubský 1 , Ashley D. Sanders 2 , Niek van Wietmarschen 1 , Ester Falconer 2 , Mark Hills 2 , Diana C.J. Spierings 1 , Marianna R. Bevova 1...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.Structural variants (SVs) are genomic alterations that involve segments of DNA that are >50 bp (Iafrate et al. 2004; Sebat et al...
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Method: Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
- Dongqing Shi,
- Jun Wu,
- Haibao Tang,
- Hao Yin,
- Hongtao Wang,
- Ran Wang,
- Runze Wang,
- Ming Qian,
- Juyou Wu,
- Kaijie Qi,
- Zhihua Xie,
- Zhiwen Wang,
- Xiang Zhao,
- and Shaoling Zhang
Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
...for linking s to life and the environment. Nucleic Acids Res 36: D480–D484. doi:10.1093/nar/gkm882 ↵Kirkness EF, Grindberg RV, Yee-Greenbaum J, Marshall CR, Scherer SW, Lasken RS, Venter JC. 2013. Sequencing of isolated sperm cells for direct haplotyping of a human . Genome Res 23: 826–832. doi:10.1101/gr...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA; 5Centre de Recherche en Biologie cellulaire...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...; males: 24% blood, 76% sperm DNA). The average sequence depth was 26× for sire–dam–offspring trios, 17× for sibs, 10× for grand-offspring, and 27.3× for grandparents. This pedigree is well suited for the detection of germline DNM and their reliable assignment to sire, dam, or offspring.The first type...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
..., providing remarkable new information about the evolution and variation of primate s. Strand-seq generates directional libraries that, once sequenced and aligned against a reference , allow investigators to distinguish different orientation variants and to locate them at a single-cell level (Sanders et al...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...and Drosophila melanogaster s (Britten and Kohne 1968; International Human Genome Sequencing Consortium 2001; Treangen and Salzberg 2012; Hoskins et al. 2015). These sequences include repeated tandem arrays of noncoding sequences like satellite DNAs, self-replicating selfish elements like transposable elements...
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Resource: Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation
- Kang Du,
- Martin Pippel,
- Susanne Kneitz,
- Romain Feron,
- Irene da Cruz,
- Sylke Winkler,
- Brigitta Wilde,
- Edgar G. Avila Luna,
- Gene Myers,
- Yann Guiguen,
- Constantino Macias Garcia,
- and Manfred Schartl
Genome Res. March 2022 32: 583-594; Published in Advance January 26, 2022, doi:10.1101/gr.275826.121
.... For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the of the darkedged splitfin, Girardinichthys multiradiatus. The assembly is chromosome level and includes the X and Y Chromosomes. A large male-specific region...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...measured by ChIP-seq (Baker et al. 2015), DSB activity based on DMC1 single-stranded DNA sequencing ChIP-seq (DMC1-SSDS) (Smagulova et al. 2016), and crossover likelihood quantified in single-sperm sequencing data sets (Yin et al. 2019). These three data sets all derive from a B6xCAST hybrid mouse genotype...
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