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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...for Cas9-based editing (Kim et al. 2011; Ramakrishna et al. 2014), “TREE” reporters for base editors (Standage-Beier et al. 2019), “fluoPEER” reporters for prime editors (Schene et al. 2022), and CRISPRa selection for gain of function (Heidersbach et al. 2023). For these methods, the gene of interest...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...structure and reconstruct phylogenetic relationships of Δblock within Iberian wolves and dogs, we used the 78 SNPs spanning this genomic region to construct both a neighbor-joining (NJ) tree and a median-joining network. The NJ tree revealed that all Iberian wolves with the Δblock (N = 21) were more closely...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...of pseudouridine within in vivo systems have drawn mixed conclusions, including increasing (Schwartz et al. 2014; Dai et al. 2023), decreasing (Nakamoto et al. 2017), and having no effect on mRNA stability (Zhang et al. 2023).Genome-wide identification of RNA modificationsA-to-I and C-to-U RNA editing events can...
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In memoriam: Deborah A. Nickerson (1954 –2021)
- Aravinda Chakravarti,
- Evan E. Eichler,
- Richard A. Gibbs,
- Eric D. Green,
- Richard M. Myers,
- and Hillary E. Sussman
Genome Res. February 2022 32: v-vi; Published in Advance January 24, 2022, doi:10.1101/gr.276582.122
...Aravinda Chakravarti1,2, Evan E. Eichler3,4, Richard A. Gibbs5,6, Eric D. Green7, Richard M. Myers8 and Hillary E. Sussman9 1Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY; 2Department of Neuroscience and Physiology, New York University...
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Method: A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor
- Hengxing Lu,
- Jun Liu,
- Tao Feng,
- Zihang Guo,
- Yunjun Yin,
- Fei Gao,
- Gengsheng Cao,
- Xuguang Du,
- and Sen Wu
Genome Res. May 2021 31: 900-909; Published in Advance April 1, 2021, doi:10.1101/gr.271312.120
.... Nat Commun 6: 10237. doi:10.1038/ncomms10237 ↵Maresca M, Lin VG, Guo N, Yang Y. 2013. Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res 23: 539–546. doi:10.1101/gr.145441.112 ↵Mehravar M, Shirazi A...
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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...; Gaudelli et al. 2017; Satomura et al. 2017; Anzalone et al. 2019).For example, two guide RNAs can be designed to flank a target site and generate nicks on opposite DNA strands that together comprise an on-target DSB with reduced off-target DSBs (Ran et al. 2013). CRISPR base editors are composed of Cas9...
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Method: Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9
- Daniel Agudelo,
- Sophie Carter,
- Minja Velimirovic,
- Alexis Duringer,
- Jean-François Rivest,
- Sébastien Levesque,
- Jeremy Loehr,
- Mathilde Mouchiroud,
- Denis Cyr,
- Paula J. Waters,
- Mathieu Laplante,
- Sylvain Moineau,
- Adeline Goulet,
- and Yannick Doyon
Genome Res. January 2020 30: 107-117; Published in Advance January 3, 2020, doi:10.1101/gr.255414.119
..., and NNGAAA PAMs, respectively (Fig. 3B–D). St1BE4max variants were inactive at noncognate PAMs, indicating that they function in an orthogonal manner (Supplemental Fig. S5). We also generated an adenine base editor (St1ABEmax LMD9) to mediate the conversion of A•T to G•C in genomic DNA. We observed moderate...
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Method: Modeling Niemann–Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation
- Steven Erwood,
- Reid A. Brewer,
- Teija M.I. Bily,
- Eleonora Maino,
- Liangchi Zhou,
- Ronald D. Cohn,
- and Evgueni A. Ivakine
Genome Res. December 2019 29: 2010-2019; Published in Advance November 21, 2019, doi:10.1101/gr.250720.119
...Steven Erwood1,2, Reid A. Brewer1, Teija M.I. Bily1, Eleonora Maino1,2, Liangchi Zhou1, Ronald D. Cohn1,2,3 and Evgueni A. Ivakine1 1Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, M5G 0A4, Canada; 2Department of Molecular Genetics...
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Method: Accurate analysis of genuine CRISPR editing events with ampliCan
- Kornel Labun,
- Xiaoge Guo,
- Alejandro Chavez,
- George Church,
- James A. Gagnon,
- and Eivind Valen
Genome Res. May 2019 29: 843-847; Published in Advance March 8, 2019, doi:10.1101/gr.244293.118
...to confidently identify induced mutations after repair through nonhomologous end-joining (NHEJ) or homology directed repair (HDR). Insertions or deletions (indels) are often identified by sequencing the targeted loci and comparing the sequenced reads to a reference sequence. Deep sequencing has the advantage...
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Method: GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Martin J. Sergeant,
- Nina Luhmann,
- Cátia Vaz,
- Alexandre P. Francisco,
- João André Carriço,
- and Mark Achtman
Genome Res. September 2018 28: 1395-1404; Published in Advance July 26, 2018, doi:10.1101/gr.232397.117
...Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-004 Lisboa, Portugal Corresponding authors: zhemin.zhou@warwick.ac.uk, m.achtman@warwick.ac.ukAbstractCurrent methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial s. Grape...
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