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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
...speech development remains incomplete. Vocal learning evolved independently in humans and at least four nonhuman mammalian lineages (cetaceans, bats, elephants, and pinnipeds) and three avian lineages (oscine songbirds, parrots, and hummingbirds) (Petkov and Jarvis 2012). Vocal learning species share...
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Method: Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq
- Pete H. Taylor,
- Amanda Cinquin,
- and Olivier Cinquin
Genome Res. November 2016 26: 1600-1611; Published in Advance October 19, 2016, doi:10.1101/gr.200501.115
...Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq Pete H. Taylor 1 , 2 , Amanda Cinquin 1 , 2 and Olivier Cinquin 1 , 2 1Department of Developmental and Cell Biology...
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LETTER: Isolation of the repertoire of VSG expression site containing telomeres of Trypanosoma brucei 427 using transformation-associated recombination in yeast
- Marion Becker,
- Niall Aitcheson,
- Elaine Byles,
- Bill Wickstead,
- Edward Louis,
- and Gloria Rudenko
Genome Res. November 2004 14: 2319-2329; doi:10.1101/gr.2955304
...set of telomeric T. brucei 427 BESs, we have devised a modified transformation-associated recombination (TAR) procedure to construct a telomere specific library in S. cerevisiae . TAR cloning in yeast relies on recombination between a target fragment present in a TAR cloning vector and the same...
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Method: Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme
- Jianbin Wang,
- Geoffrey Friedman,
- Yannick Doyon,
- Nathaniel S. Wang,
- Carrie Jiaxin Li,
- Jeffrey C. Miller,
- Kevin L. Hua,
- Jenny Jiacheng Yan,
- Joshua E. Babiarz,
- Philip D. Gregory,
- and Michael C. Holmes
Genome Res. July 2012 22: 1316-1326; Published in Advance March 20, 2012, doi:10.1101/gr.122879.111
...ligases (for review, see Caldecott 2008). However, firm evidence for a different role for SSB/nicks has also emerged over the years. In yeast, SSBs induced by the gene II protein (gIIp) can stimulate HDR (Galli and Schiestl 1998). In mammalian cells, the ‘‘nick-only’’ mutants of the RAG proteins for V...
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METHODS: Linker-Mediated Recombinational Subcloning of Large DNA Fragments Using Yeast
- Christopher K. Raymond,
- Elizabeth H. Sims,
- and Maynard V. Olson
Genome Res. January 1, 2002 12: 190-197; doi:10.1101/gr.205201
...in vivo in yeast. Nucleic Acids Res. 25 : 451 – 452 . ↵ Orr-Weaver T. , Szostak R. ( 1985 ) Fungal recombination. Microbiol. Rev. 49 : 33 – 58 . ↵ Osoegawa K. , Mammoser A. , Wu C. , Frengen E. , Zeng C. , Catanese J. , de Jong P. ( 2001 ) A bacterial artificial chromosome library for sequencing...
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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
.... It is well suited for efficient production of modified BACs for use in a variety of in vivo studies. Bacterial artificial chromosomes (BACs) and P-1 derived artificial chromosomes (PACs) have several advantages over the traditional large DNA cloning system, the yeast artificial chromosomes (YACs...
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Methods: Identification of Novel ErbB3-Interacting Factors Using the Split-Ubiquitin Membrane Yeast Two-Hybrid System
- Safia Thaminy,
- Daniel Auerbach,
- Anthony Arnoldo,
- and Igor Stagljar
Genome Res. July 2003 13: 1744-1753; doi:10.1101/gr.1276503
...-Ubiquitin Membrane Yeast Two-Hybrid System Our central goal was to use the split-ubiquitin membrane YTH technology to identify proteins that interact with a given mammalian membrane target protein. To this end, we have constructed a new set of bait and prey vectors that allow the constitutive expression...
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METHODS: A Streamlined Process to Phenotypically Profile Heterologous cDNAs in Parallel Using Yeast Cell-Based Assays
- Stuart Tugendreich,
- Ed Perkins,
- Joe Couto,
- Peter Barthmaier,
- Dongxu Sun,
- Shawn Tang,
- Suzana Tulac,
- Allen Nguyen,
- Elaine Yeh,
- Amy Mays,
- Ellen Wallace,
- Tom Lila,
- Dave Shivak,
- Mark Prichard,
- Laura Andrejka,
- Raymond Kim,
- and Teri Melese
Genome Res. November 1, 2001 11: 1899-1912; doi:10.1101/gr.191601
...DNAs to obtain HTS compatible yeast cell-based assays. Our ability to use the in vivo biochemical activity of mammalian or viral proteins to generate a generic growth interference assay in yeast whose reversal allows the identification of small molecule inhibitors is highlighted in this paper. Although the use...
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REVIEW: Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences.
- E D Green and
- P Green
Genome Res. November 1991 1: 77-90; doi:10.1101/gr.1.2.77
....S. , Patterson, D. , Schild, D. , Featherstone, T. , Olson. M.V. Gnirke, A., Barnes, T.S. Patterson, D. Schild, D. Featherstone, T. and Olson. M.V. 1991 . Cloning and in vivo expression of the human GART gene using yeast artificial chromosomes. EMBO J. 10 : 1629 – 1634 . 38. Ochman, H., M.M. Medhora, D. Garza...
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Methods: Recombinatorial Cloning Using Heterologous Lox Sites
- Robert W. Siegel,
- Nileena Velappan,
- Peter Pavlik,
- Leslie Chasteen,
- and Andrew Bradbury
Genome Res. June 2004 14: 1119-1129; doi:10.1101/gr.1821804
...), and this has proved to be an important tool for the in vivo manipulation of eukaryotic s, including gene activation and deactivation studies in both mammalian cells and transgenic mice. Recent reports, however, have suggested recombination can occur between wild-type and 511 loxP sequences ( Lee and Saito 1998...

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