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Methods: A New Method for Rapidly Generating Gene-Targeting Vectors by Engineering BACs Through Homologous Recombination in Bacteria
- Vinícius Cotta-de-Almeida,
- Susan Schonhoff,
- Tomoyuki Shibata,
- Andrew Leiter,
- and Scott B. Snapper
Genome Res. September 2003 13: 2190-2194; Published in Advance January 1, 2003, doi:10.1101/gr.1356503
...efficient Escherichia coli -based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73 : 56 –65. ↵ Liu, P., Jenkins, N.A., and Copeland, N.G. 2003 . A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res...
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METHODS: Highly Efficient Modification of Bacterial Artificial Chromosomes (BACs) Using Novel Shuttle Vectors Containing the R6Kγ Origin of Replication
- Shiaoching Gong,
- Xiangdong William Yang,
- Chenjian Li,
- and Nathaniel Heintz
Genome Res. December 1, 2002 12: 1992-1998; doi:10.1101/gr.476202
...original BAC modification system, the temperature-sensitive pSV1.RecA shuttle vector may replicate in the BAC host cells at a low level to generate a background of false positives, which may reduce the co-integration efficiency (defined as the number of correct co-integrates among the total number...
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METHODS: An Efficient Method for High-Fidelity BAC/PAC Retrofitting with a Selectable Marker for Mammalian Cell Transfection
- Zunde Wang,
- Peter Engler,
- Angelika Longacre,
- and Ursula Storb
Genome Res. January 1, 2001 11: 137-142; doi:10.1101/gr.159001
...with large inserts. It also requires subsequent transformation of the retrofitted BAC/PAC into Escherichia coli , which is both very inefficient and deleterious to the genomic insert. Recombination-based approaches allow the direct integration of a selectable marker cassette into BAC/PAC clones without...
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Letter: ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells
- Lee H. Wong,
- James D. McGhie,
- Marcus Sim,
- Melissa A. Anderson,
- Soyeon Ahn,
- Ross D. Hannan,
- Amee J. George,
- Kylie A. Morgan,
- Jeffrey R. Mann,
- and K.H. Andy Choo
Genome Res. March 2010 20: 351-360; Published in Advance January 28, 2010, doi:10.1101/gr.101477.109
...(wild type) with ATRX in ES cells (Fig. 6A). To investigate how the loss of K4 in MYCH3.3 might affect ATRX and H3.3 interaction, we generated a MYC-H3.3 construct carrying a mutation in K4. The mutationwas introduced using PCR-based sitedirected mutagenesis, followed by transient transfection into ES...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...). These R-loops, which form within the G-rich switch regions, may contribute to recombination-based deletions and drive antibody class diversity. Similarly, R-loops play a regulatory role in gene expression in plants, in which their stabilization over the COOLAIR promoter in Arabidopsis was shown to repress...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...of haplotypes restricted to few strains, often with evidence for recombination. Based on sequence similarity, at least some of these rarer haplotypes originated by homologous recombination between Tf1 and Tf2 and remained active thereafter.We next examined whether the patterns of TE diversity in S. pombe...
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Method: 2C-Cas9: a versatile tool for clonal analysis of gene function
- Vincenzo Di Donato,
- Flavia De Santis,
- Thomas O. Auer,
- Noé Testa,
- Héctor Sánchez-Iranzo,
- Nadia Mercader,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. May 2016 26: 681-692; Published in Advance March 8, 2016, doi:10.1101/gr.196170.115
...of these animal models in genetic studies (Perrimon 1998; Wijgerde et al. 2002). In these models, the use of recombination-based approaches such as Cre/LoxP has been accepted as a gold standard technique for conditional mutagenesis. Until now, a similar approach has not been available in zebrafish. The phenotypic...
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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
...correction via recombination, base editing, or gene correction via microhomology-mediated end joining require highly precise targeting (Canver et al. 2015; Rees and Liu 2018; Gyorgy et al. 2019; Iyer et al. 2019). To achieve single-nucleotide precision in targeting, a plethora of Cas9 orthologs harboring...
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Research: Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers
- Tao Deng,
- Z. Iris Zhu,
- Shaofei Zhang,
- Yuri Postnikov,
- Di Huang,
- Marion Horsch,
- Takashi Furusawa,
- Johannes Beckers,
- Jan Rozman,
- Martin Klingenspor,
- Oana Amarie,
- Jochen Graw,
- Birgit Rathkolb,
- Eckhard Wolf,
- Thure Adler,
- Dirk H. Busch,
- Valérie Gailus-Durner,
- Helmut Fuchs,
- Martin Hrabě de Angelis,
- Arjan van der Velde,
- Lino Tessarollo,
- Ivan Ovcherenko,
- David Landsman,
- and Michael Bustin
Genome Res. September 2015 25: 1295-1308; Published in Advance July 8, 2015, doi:10.1101/gr.192229.115
...targeted to Hmgn2 were injected into C57BL/6 blastocysts and generated chimeras that transmitted the mutated allele to the progeny. The neomycin resistance (neo) and the Hmgn2 gene were removed by crossing with beta actin Cremice. The mice containing the targeted allele were backcrossed into the C57BL/6...
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Research: Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
- Ankit Malhotra,
- Michael Lindberg,
- Gregory G. Faust,
- Mitchell L. Leibowitz,
- Royden A. Clark,
- Ryan M. Layer,
- Aaron R. Quinlan,
- and Ira M. Hall
Genome Res. May 2013 23: 762-776; Published in Advance February 14, 2013, doi:10.1101/gr.143677.112
...Tumor genomes are generally thought to evolve through a gradual accumulation of mutations, but the observation that extraordinarily complex rearrangements can arise through single mutational events suggests that evolution may be accelerated by punctuated changes in genome architecture. To assess...

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