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Crain AT, Nevil M, Leatham-Jensen MP, Reeves KB, Matera AG, McKay DJ, Duronio RJ. Redesigning the Drosophila histone gene cluster: An improved genetic platform for spatiotemporal manipulation of histone function. bioRxiv 2024:2024.04.25.591202. [PMID: 38712307 PMCID: PMC11071459 DOI: 10.1101/2024.04.25.591202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoan models is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such RD histone gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult. Drosophila melanogaster provides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms have been developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available to Drosophila researchers. Here we describe the development of a newly engineered platform that rectifies many of these weaknesses. We used CRISPR to precisely delete the RD histone gene array ( HisC ), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. We designed this cassette with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. We also present a method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate generation of histone mutant cells in various tissues at different stages of Drosophila development and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation.
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Zirin J, Jusiak B, Lopes R, Ewen-Campen B, Bosch JA, Risbeck A, Forman C, Villalta C, Hu Y, Perrimon N. Expanding the Drosophila toolkit for dual control of gene expression. eLife 2024; 12:RP94073. [PMID: 38569007 PMCID: PMC10990484 DOI: 10.7554/elife.94073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA system or QF system. Here, we describe a resource of reagents that facilitate combined use of the GAL4/UAS and a second binary system in various Drosophila tissues. Focusing on genes with well-characterized GAL4 expression patterns, we generated a set of more than 40 LexA-GAD and QF2 insertions by CRISPR knock-in and verified their tissue specificity in larvae. We also built constructs that encode QF2 and LexA-GAD transcription factors in a single vector. Following successful integration of this construct into the fly genome, FLP/FRT recombination is used to isolate fly lines that express only QF2 or LexA-GAD. Finally, using new compatible shRNA vectors, we evaluated both LexA and QF systems for in vivo gene knockdown and are generating a library of such RNAi fly lines as a community resource. Together, these LexA and QF system vectors and fly lines will provide a new set of tools for researchers who need to activate or repress two different genes in an orthogonal manner in the same animal.
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Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Barbara Jusiak
- Department of Physiology and Biophysics, University of California, IrvineIrvineUnited States
| | - Raphael Lopes
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Justin A Bosch
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Corey Forman
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Yanhui Hu
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
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Wuyun Q, Zhang Y, Yuan J, Zhang J, Ren C, Wang Q, Yan S, Liu W, Wang G. A classic screening marker does not affect antennal electrophysiology but strongly regulates reproductive behaviours in Bactrocera dorsalis. Insect Mol Biol 2024; 33:136-146. [PMID: 37877756 DOI: 10.1111/imb.12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
The key phenotype white eye (white) has been used for decades to selectively remove females before release in sterile insect technique programs and as an effective screening marker in genetic engineering. Bactrocera dorsalis is a representative tephritid pest causing damage to more than 150 fruit crops. Yet, the function of white in important biological processes remains unclear in B. dorsalis. In this study, the impacts of the white gene on electrophysiology and reproductive behaviour in B. dorsalis were tested. The results indicated that knocking out Bdwhite disrupted eye pigmentation in adults, consistent with previous reports. Bdwhite did not affect the antennal electrophysiology response to 63 chemical components with various structures. However, reproductive behaviours in both males and females were significantly reduced in Bdwhite-/- . Both pre-copulatory and copulation behaviours were significantly reduced in Bdwhite-/- , and the effect was male-specific. Mutant females significantly delayed their oviposition towards γ-octalactone, and the peak of oviposition behaviour towards orange juice was lost. These results show that Bdwhite might not be an ideal screening marker in functional gene research aiming to identify molecular targets for behaviour-modifying chemicals. Instead, owing to its strong effect on B. dorsalis sexual behaviours, the downstream genes regulated by Bdwhite or the genes from white-linked areas could be alternate molecular targets that promote the development of better behavioural modifying chemical-based pest management techniques.
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Affiliation(s)
- QiQige Wuyun
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Yan Zhang
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jinxi Yuan
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jie Zhang
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Cong Ren
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Qi Wang
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Shanchun Yan
- Key Laboratory of Sustainable Management of Forest Ecosystem, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Wei Liu
- Institute of Agricultural Genome, Chinese Academy of Agricultural Sciences (Shenzhen), Shenzhen Branch of Lingnan Modern Agricultural Science and Technology Laboratory, Key Laboratory of Agricultural Gene Data Analysis, Ministry of Agriculture and Rural Affairs, Shenzhen, China
| | - Guirong Wang
- Institute of Agricultural Genome, Chinese Academy of Agricultural Sciences (Shenzhen), Shenzhen Branch of Lingnan Modern Agricultural Science and Technology Laboratory, Key Laboratory of Agricultural Gene Data Analysis, Ministry of Agriculture and Rural Affairs, Shenzhen, China
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Mise K, Long J, Galvan DL, Ye Z, Fan G, Sharma R, Serysheva II, Moore TI, Jeter CR, Anna Zal M, Araki M, Wada J, Schumacker PT, Chang BH, Danesh FR. NDUFS4 regulates cristae remodeling in diabetic kidney disease. Nat Commun 2024; 15:1965. [PMID: 38438382 PMCID: PMC10912198 DOI: 10.1038/s41467-024-46366-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generate diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that conditional male mice with genetic overexpression of Ndufs4 exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping protein STOML2 in linking NDUFS4 with improved cristae morphology. Together, we provide the evidence on the central role of NDUFS4 as a regulator of cristae remodeling and mitochondrial function in kidney podocytes. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.
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Affiliation(s)
- Koki Mise
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Jianyin Long
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel L Galvan
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zengchun Ye
- Division of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rajesh Sharma
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Travis I Moore
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Collene R Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Anna Zal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Motoo Araki
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Paul T Schumacker
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Benny H Chang
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Farhad R Danesh
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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Mise K, Long J, Galvan DL, Ye Z, Fan G, Serysheva II, Moore TI, Wada J, Schumacker PT, Chang BH, Danesh FR. NDUFS4 Regulates Cristae Remodeling in Diabetic Kidney Disease. Res Sq 2023:rs.3.rs-3070079. [PMID: 37461606 PMCID: PMC10350115 DOI: 10.21203/rs.3.rs-3070079/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generated diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model to investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that these conditional mice exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping proteins in linking NDUFS4 with improved cristae morphology. Taken together, we discover the central role of NDUFS4 as a powerful regulator of cristae remodeling, respiratory supercomplexes assembly, and mitochondrial ultrastructure in vitro and in vivo. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.
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Affiliation(s)
- Koki Mise
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Jianyin Long
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel L. Galvan
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zengchun Ye
- Division of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Irina I. Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Travis I. Moore
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Paul T. Schumacker
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Benny H. Chang
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Farhad R. Danesh
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX
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Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80. Proc Natl Acad Sci U S A 2023; 120:e2304730120. [PMID: 37276389 PMCID: PMC10268248 DOI: 10.1073/pnas.2304730120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
The split-Gal4 system allows for intersectional genetic labeling of highly specific cell types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell type-specific genetic drivers based on in silico predictions generated by single-cell RNAseq (scRNAseq) datasets, and we describe an algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible.
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Affiliation(s)
- Ben Ewen-Campen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Haojiang Luan
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Rohit Singh
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Neha Joshi
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02143
| | - Benjamin H. White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- HHMI, Boston, MA02115
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7
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Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80. bioRxiv 2023:2023.03.24.534001. [PMID: 36993523 PMCID: PMC10055387 DOI: 10.1101/2023.03.24.534001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues in Drosophila . However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a new split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is fully repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell-type specific genetic drivers based on in silico predictions generated by single cell RNAseq (scRNAseq) datasets, and we describe a new algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible. Significance statement The split-Gal4 system allows Drosophila researchers to drive transgene expression with extraordinary cell type specificity. However, the existing split-Gal4 system cannot be controlled temporally, and therefore cannot be applied to many important areas of research. Here, we present a new split-Gal4 system based on a self-excising split-intein, which is fully controllable by Gal80, as well as a related drug-inducible split GeneSwitch system. This approach can both leverage and inform single-cell RNAseq datasets, and we introduce an algorithm to identify pairs of genes that precisely and narrowly mark a desired cell cluster. Our split-intein Gal4 system will be of value to the Drosophila research community, and allow for the creation of highly specific genetic drivers that are also inducible/repressible.
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Affiliation(s)
- Ben Ewen-Campen
- These authors contributed equally
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Haojiang Luan
- These authors contributed equally
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Jun Xu
- These authors contributed equally
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, China
| | - Rohit Singh
- These authors contributed equally
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Neha Joshi
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge MA 02143
| | - Benjamin H White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- HHMI, Boston, MA 02115, USA
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Venken KJ, Matinyan N, Gonzalez Y, Sarrion-Perdigones A, Dierick HA. Synthetic Assembly DNA Cloning to Build Plasmids for Multiplexed Transgenic Selection, Counterselection or Any Other Genetic Strategies Using Drosophila melanogaster. Curr Protoc 2023; 3:e653. [PMID: 36757602 PMCID: PMC10281009 DOI: 10.1002/cpz1.653] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We recently described a drug-based selectable and counterselectable genetic platform for the animal model system Drosophila melanogaster, consisting of four resistance and two sensitivity markers that allow direct selection for, or counterselection against, a desired genotype. This platform eliminates the need to identify modified progeny by traditional laborious screening using the dominant eye and body color markers, white+ and yellow+ , respectively. The four resistance markers permit selection of animals using G418 sulfate, puromycin HCl, blasticidin S, or hygromycin B, while the two sensitivity markers allow counterselection of animals against ganciclovir or acyclovir and 5-fluorocytosine. The six markers can be used alone or in combination to perform co-selection, combination selection, and counterselection, as well as co-counterselection. To make this novel selection and counterselection genetics platform easily accessible to and rapidly implementable by the scientific community, we used a synthetic assembly DNA cloning platform, GoldenBraid 2.0 (GB2.0). GB2.0 relies on two Type IIs restriction enzymes that are alternatingly used during successive cloning steps to make increasingly complex genetic constructs. Here we describe, as an example, how to perform synthetic assembly DNA cloning using GB2.0 to build such complex plasmids via the assembly of both components of the binary LexA/LexA-Op overexpression system, a G418 sulfate-selectable LexA transactivator plasmid, and a blasticidin S-selectable LexA-Op responder plasmid. We demonstrate the functionality of these plasmids by including the expression pattern obtained after co-injection, followed by co-selection using G418 sulfate and blasticidin S, resulting in co-transgenesis of both plasmids. Protocols are provided on how to obtain, adapt, and clone DNA parts for synthetic assembly cloning after de novo DNA synthesis or PCR amplification of desired DNA parts and how to assemble those DNA parts into multipartite transcription units, followed by how to further assemble multiple transcription units into genetic constructs of increasing complexity to perform multiplexed transgenic selection and counterselection, or any other genetic strategies using Drosophila melanogaster. The protocols we present can be easily adapted to incorporate any of the six selectable and counterselectable markers, or any other, markers, to generate plasmids of unmatched complexity for various genetic applications. A protocol on how to generate transgenic animals using these synthetically assembled plasmids is described in an accompanying Current Protocols article (Venken, Matinyan, Gonzalez, & Dierick, 2023). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Obtaining and cloning a de novo-synthesized DNA part for synthetic assembly DNA cloning Basic Protocol 2: Obtaining and cloning a DNA part amplified by PCR from existing DNA resources for synthetic assembly DNA cloning Alternate Protocol: Obtaining, adapting, and cloning a DNA part amplified by PCR from existing DNA resources for synthetic assembly DNA cloning Basic Protocol 3: Synthetic assembly DNA cloning of individual DNA parts into a multipartite transcription unit Basic Protocol 4: Synthetic assembly DNA cloning of multiple transcription units into genetic constructs of increasing complexity.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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Venken KJ, Matinyan N, Gonzalez Y, Dierick HA. Serial Recombineering Cloning to Build Selectable and Tagged Genomic P[acman] BAC Clones for Selection Transgenesis and Functional Gene Analysis using Drosophila melanogaster. Curr Protoc 2023; 3:e675. [PMID: 36757632 PMCID: PMC9923880 DOI: 10.1002/cpz1.675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Transgenes with genomic DNA fragments that encompass genes of interest are the gold standard for complementing null alleles in rescue experiments in the fruit fly Drosophila melanogaster. Of particular interest are genomic DNA clones available as bacterial artificial chromosomes (BACs) or fosmids from publicly available genomic DNA libraries. Genes contained within BAC and fosmid clones can be easily modified by recombineering cloning to insert peptide or protein tags to localize, visualize, or manipulate gene products, and to create point mutations or deletions for structure-function analysis of the inserted genes. However, since transgenesis efficiency is inversely correlated with transgene size, obtaining transgenic animals for increasingly larger BAC and fosmid clones requires increasingly laborious screening efforts using the transgenesis marker commonly used for these transgenes, the dominant eye color marker white+ . We recently described a drug-based selectable genetic platform for Drosophila melanogaster, which included four resistance markers that allow direct selection of transgenic animals, eliminating the need to identify transgenic progeny by laborious phenotypic screening. By integrating these resistance markers into BAC transgenes, we were able to isolate animals containing large transgenes by direct selection, avoiding laborious screening. Here we present procedures on how to upgrade BAC clones by serial recombineering cloning to build both selectable and tagged BAC transgenes, for selection transgenesis and functional gene analysis, respectively. We illustrate these procedures using a BAC clone encompassing the gene encoding the synaptic vesicle protein, cysteine string protein. We demonstrate that the modified BAC clone, serially recombineered with a selectable marker for selection transgenesis and an N-terminal green fluorescent protein tag for gene expression analysis, is functional by showing the expression pattern obtained after successful selection transgenesis. The protocols cover: (1) cloning and preparation of the recombineering templates needed for serial recombineering cloning to incorporate selectable markers and protein tags; (2) preparing electrocompetent cells needed to perform serial recombineering cloning; and (3) the serial recombineering workflow to generate both selectable and tagged genomic BAC reporter transgenes for selection transgenesis and functional gene analysis in Drosophila melanogaster. The protocols we describe can be easily adapted to incorporate any of four selectable markers, protein tags, or any other modification for structure-function analysis of the genes present within any of the BAC or fosmid clones. A protocol for generating transgenic animals using serially recombineered BAC clones is presented in an accompanying Current Protocols article (Venken, Matinyan, Gonzalez, & Dierick, 2023a). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Cloning and preparation of recombineering templates used for serial recombineering cloning. Basic Protocol 2: Making electrocompetent cells of the bacterial strains used to perform serial recombineering cloning or induction of plasmid copy number. Basic Protocol 3: Serial recombineering cloning to generate both selectable and tagged genomic P[acman] BAC reporter transgenes for selection transgenesis and gene expression analysis in Drosophila melanogaster.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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Venken KJ, Matinyan N, Gonzalez Y, Dierick HA. Multiplexed Transgenic Selection and Counterselection Strategies to Expedite Genetic Manipulation Workflows Using Drosophila melanogaster. Curr Protoc 2023; 3:e652. [PMID: 36757287 PMCID: PMC9923875 DOI: 10.1002/cpz1.652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We recently described a set of four selectable and two counterselectable markers that provide resistance and sensitivity, respectively, against their corresponding drugs using the model organism Drosophila melanogaster. The four selectable markers provide animals with resistance against G418 sulfate, puromycin HCl, blasticidin S, or hygromycin B, whereas the two counterselection markers make animals sensitive to ganciclovir/acyclovir or 5-fluorocytosine. Unlike classical phenotypic markers, whether visual or fluorescent, which require extensive screening of progeny of a genetic cross for desired genotypes, resistance and sensitivity markers eliminate this laborious procedure by directly selecting for, or counterselecting against, the desired genotypes. We demonstrated the usefulness of these markers with three applications: 1) generating dual transgenic animals for binary overexpression (e.g., GAL4/UAS) analysis in a single step through the process of co-injection, followed by co-selection resulting in co-transgenesis; 2) obtaining balancer chromosomes that are both selectable and counterselectable to manipulate crossing schemes for, or against, the presence of the modified balancer chromosome; and 3) making both selectable and fluorescently tagged P[acman] BAC transgenic animals for gene expression and proteomic analysis. Here, we describe detailed procedures for how to use these drug-based selection and counterselection markers in the fruit fly D. melanogaster when making dual transgenic animals for binary overexpression as an example. Dual transgenesis integrates site-specifically into two sites in the genome in a single step, namely both components of the binary GAL4/UAS overexpression system, via a G418 sulfate-selectable GAL4 transactivator plasmid and a blasticidin S-selectable UAS responder plasmid. The process involves co-injecting the two plasmids, followed by co-selection using G418 sulfate and blasticidin S, resulting in co-transgenesis of the two plasmids in the fly genome. We demonstrate the functionality of the procedure based on the expression pattern obtained after dual transgenesis of the two plasmids. We provide protocols on how to prepare drugged fly food vials, determine the effective drug concentration for markers used during transgenic selection and counterselection strategies, and prepare and confirm plasmid DNA for microinjection, followed by the microinjection procedure itself and setting up crossing schemes to isolate desired progeny through selection and/or counterselection. These protocols can be easily adapted to any combination of the six selectable and counterselectable markers we described or any new marker that is resistant or sensitive to a novel drug. Protocols on how to build plasmids by synthetic-assembly DNA cloning or modify plasmids by serial recombineering to perform a plethora of selection, counterselection, or any other genetic strategies are presented in two accompanying Current Protocols articles. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparing drugged fly food vials for transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 2: Determining the effective drug concentration for resistance and sensitivity markers used during transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 3: Preparing and confirming plasmid DNA for microinjection to perform transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 4: Microinjecting plasmid DNA into fly embryos to perform transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 5: Crossing schemes to isolate desired progeny through transgenic selection and counterselection strategies using D. melanogaster.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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Dierick HA, Ben-Shahar Y, Raman B, Gabbiani F. Genetic and viral approaches to record or manipulate neurons in insects. Curr Opin Insect Sci 2021; 48:79-88. [PMID: 34710643 PMCID: PMC8648980 DOI: 10.1016/j.cois.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 05/11/2023]
Abstract
The development of genetically encoded tools to record and manipulate neurons in vivo has greatly increased our understanding of how neuronal activity affects behavior. Recent advances enable the use of these tools in species not typically considered genetically tractable. This progress is revolutionizing neuroscience in general, and insect neuroethology in particular. Here we cover the latest innovations and some of their applications in phylogenetically diverse insect species. We discuss the importance and implications of these approaches for both basic and translational research. We focus on genetically encoded and virally encoded tools used for calcium imaging, optogenetics, and synaptic silencing. Finally, we discuss potential future developments of universally applicable, modular, and user-friendly genetic toolkits for neuroethological studies of insect behavior.
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Affiliation(s)
- Herman A Dierick
- Dep. of Human and Molecular Genetics, Baylor College of Medicine, United States
| | | | - Baranidharan Raman
- Dep. of Bioengineering, Washington University in St. Louis, United States
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Matinyan N, Gonzalez Y, Dierick HA, Venken KJT. Determining effective drug concentrations for selection and counterselection genetics in Drosophila melanogaster. STAR Protoc 2021; 2:100783. [PMID: 34585147 PMCID: PMC8458262 DOI: 10.1016/j.xpro.2021.100783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We recently integrated into fly genetics a set of four selection and two counterselection markers and their corresponding drugs that can be used individually or in combination. These markers eliminate the need to visually screen progeny. Before using these markers in new genetic backgrounds, effective selection/counterselection concentrations should be established for each marker/drug combination. This protocol describes how to set up, perform, and analyze a drug titration curve to determine the effective selection/counterselection drug concentrations for their corresponding markers. For complete details on the use and execution of this protocol, please refer to Matinyan et al., 2021. Selection/counterselection in Drosophila melanogaster Establish a drug titration curve for a selection/counterselection marker Identify the optimal drug concentration for a selection/counterselection marker
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Affiliation(s)
- Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Herman A Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.,McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX 77030, USA
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