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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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Song X, Goicoechea JL, Ammiraju JSS, Luo M, He R, Lin J, Lee SJ, Sisneros N, Watts T, Kudrna DA, Golser W, Ashley E, Collura K, Braidotti M, Yu Y, Matzkin LM, McAllister BF, Markow TA, Wing RA. The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research. Genetics 2011; 187:1023-30. [PMID: 21321134 PMCID: PMC3070512 DOI: 10.1534/genetics.111.126540] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 02/05/2011] [Indexed: 11/18/2022] Open
Abstract
The genus Drosophila has been the subject of intense comparative phylogenomics characterization to provide insights into genome evolution under diverse biological and ecological contexts and to functionally annotate the Drosophila melanogaster genome, a model system for animal and insect genetics. Recent sequencing of 11 additional Drosophila species from various divergence points of the genus is a first step in this direction. However, to fully reap the benefits of this resource, the Drosophila community is faced with two critical needs: i.e., the expansion of genomic resources from a much broader range of phylogenetic diversity and the development of additional resources to aid in finishing the existing draft genomes. To address these needs, we report the first synthesis of a comprehensive set of bacterial artificial chromosome (BAC) resources for 19 Drosophila species from all three subgenera. Ten libraries were derived from the exact source used to generate 10 of the 12 draft genomes, while the rest were generated from a strategically selected set of species on the basis of salient ecological and life history features and their phylogenetic positions. The majority of the new species have at least one sequenced reference genome for immediate comparative benefit. This 19-BAC library set was rigorously characterized and shown to have large insert sizes (125-168 kb), low nonrecombinant clone content (0.3-5.3%), and deep coverage (9.1-42.9×). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny.
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Affiliation(s)
- Xiang Song
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jose Luis Goicoechea
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jetty S. S. Ammiraju
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Meizhong Luo
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Ruifeng He
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jinke Lin
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - So-Jeong Lee
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Nicholas Sisneros
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Tom Watts
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - David A. Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Wolfgang Golser
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Elizabeth Ashley
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Kristi Collura
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Michele Braidotti
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Yeisoo Yu
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Luciano M. Matzkin
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Bryant F. McAllister
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Therese Ann Markow
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Rod A. Wing
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
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