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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...Francisco, San Francisco, California 94158, USA; 3Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: kpollard@gladstone.ucsf.eduAbstractChromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
....The findings described so far indicate that, of the seven defense systems considered in this study, CRISPR-Cas is the one that most often induces a net reduction in HGT rates. According to the linkage hypothesis, this could be owing to a comparatively weaker physical association between CRISPR-Cas and MGEs...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...–gene and corresponding protein–protein physical interactions, as well as transcription correlation, is revealed. We also find that gene fusion events are significantly enriched between genes of short CTG distances and are thus close in 3D space. These findings indicate that 3D chromatin structure is at least partially...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...A novel quantitative trait locus implicates Msh3 in the propensity for -wide short tandem repeat expansions in mice Mikhail O. Maksimov1,2,12, Cynthia Wu3,12, David G. Ashbrook4, Flavia Villani4, Vincenza Colonna4,5, Nima Mousavi6, Nichole Ma1, Lu Lu4, Jonathan K. Pritchard7,8, Alon Goren1...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...transfer) affects stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole--sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome Jessica Stapley 1 , Tim R. Birkhead , Terry Burke and Jon Slate Department of Animal and Plant Sciences, University of Sheffield...
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Methods: Genome-wide comparisons of variation in linkage disequilibrium
- Yik Y. Teo,
- Andrew E. Fry,
- Kanishka Bhattacharya,
- Kerrin S. Small,
- Dominic P. Kwiatkowski,
- and Taane G. Clark
Genome Res. October 2009 19: 1849-1860; Published in Advance June 18, 2009, doi:10.1101/gr.092189.109
...Genome-wide comparisons of variation in linkage disequilibrium Yik Y. Teo 1 , 3 , Andrew E. Fry 1 , Kanishka Bhattacharya 1 , Kerrin S. Small 1 , Dominic P. Kwiatkowski 1 , 2 and Taane G. Clark 1 , 2 1 Wellcome...
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Methods: Recent human effective population size estimated from linkage disequilibrium
- Albert Tenesa,
- Pau Navarro,
- Ben J. Hayes,
- David L. Duffy,
- Geraldine M. Clarke,
- Mike E. Goddard,
- and Peter M. Visscher
Genome Res. April 2007 17: 520-526; Published in Advance March 9, 2007, doi:10.1101/gr.6023607
...Recent human effective population size estimated from linkage disequilibrium Albert Tenesa 1 , 2 , 3 , Pau Navarro 3 , Ben J. Hayes 4 , David L. Duffy 5 , Geraldine M. Clarke 6 , Mike E. Goddard 4 , 7 , and Peter M...
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Resource: A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
- Kaitlin U. Laverty,
- Jake M. Stout,
- Mitchell J. Sullivan,
- Hardik Shah,
- Navdeep Gill,
- Larry Holbrook,
- Gintaras Deikus,
- Robert Sebra,
- Timothy R. Hughes,
- Jonathan E. Page,
- and Harm van Bakel
Genome Res. January 2019 29: 146-156; Published in Advance November 8, 2018, doi:10.1101/gr.242594.118
...roles in the perception of pain-inducing signals and by inhibiting the reuptake of endocannabinoids such as anandamide (Maione et al. 2011). Furthermore, CBC operates as a gastrointestinal anti-inflammatory agent in mice and protects adult neuronal stem progenitor cells in vitro (Izzo et al. 2012...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...and Keightley 2009; Bergeron et al. 2022). This has enabled mutation rates to be estimated in a wide range of taxa (Lynch et al. 2023; Wang and Obbard 2023), including humans and mice (Ohno 2019). However, the most widely available short-read sequencing technologies only allow inference of the rate and spectrum...
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