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Heim F, Scharff C, Fisher SE, Riebel K, Ten Cate C. Auditory discrimination learning and acoustic cue weighing in female zebra finches with localized FoxP1 knockdowns. J Neurophysiol 2024; 131:950-963. [PMID: 38629163 DOI: 10.1152/jn.00228.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 05/21/2024] Open
Abstract
Rare disruptions of the transcription factor FOXP1 are implicated in a human neurodevelopmental disorder characterized by autism and/or intellectual disability with prominent problems in speech and language abilities. Avian orthologues of this transcription factor are evolutionarily conserved and highly expressed in specific regions of songbird brains, including areas associated with vocal production learning and auditory perception. Here, we investigated possible contributions of FoxP1 to song discrimination and auditory perception in juvenile and adult female zebra finches. They received lentiviral knockdowns of FoxP1 in one of two brain areas involved in auditory stimulus processing, HVC (proper name) or CMM (caudomedial mesopallium). Ninety-six females, distributed over different experimental and control groups were trained to discriminate between two stimulus songs in an operant Go/Nogo paradigm and subsequently tested with an array of stimuli. This made it possible to assess how well they recognized and categorized altered versions of training stimuli and whether localized FoxP1 knockdowns affected the role of different features during discrimination and categorization of song. Although FoxP1 expression was significantly reduced by the knockdowns, neither discrimination of the stimulus songs nor categorization of songs modified in pitch, sequential order of syllables or by reversed playback were affected. Subsequently, we analyzed the full dataset to assess the impact of the different stimulus manipulations for cue weighing in song discrimination. Our findings show that zebra finches rely on multiple parameters for song discrimination, but with relatively more prominent roles for spectral parameters and syllable sequencing as cues for song discrimination.NEW & NOTEWORTHY In humans, mutations of the transcription factor FoxP1 are implicated in speech and language problems. In songbirds, FoxP1 has been linked to male song learning and female preference strength. We found that FoxP1 knockdowns in female HVC and caudomedial mesopallium (CMM) did not alter song discrimination or categorization based on spectral and temporal information. However, this large dataset allowed to validate different cue weights for spectral over temporal information for song recognition.
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Affiliation(s)
- Fabian Heim
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | | | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Katharina Riebel
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Carel Ten Cate
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Leiden Institute for Brain and Cognition, Leiden, The Netherlands
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Le Beulze M, Daubech C, Balde-Camara A, Ghieh F, Vialard F. Mammal Reproductive Homeobox (Rhox) Genes: An Update of Their Involvement in Reproduction and Development. Genes (Basel) 2023; 14:1685. [PMID: 37761825 PMCID: PMC10531175 DOI: 10.3390/genes14091685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The reproductive homeobox on the X chromosome (RHOX) genes were first identified in the mouse during the 1990s and have a crucial role in reproduction. In various transcription factors with a key regulatory role, the homeobox sequence encodes a "homeodomain" DNA-binding motif. In the mouse, there are three clusters of Rhox genes (α, β, and γ) on the X chromosome. Each cluster shows temporal and/or quantitative collinearity, which regulates the progression of the embryonic development process. Although the RHOX family is conserved in mammals, the interspecies differences in the number of RHOX genes and pseudogenes testifies to a rich evolutionary history with several relatively recent events. In the mouse, Rhox genes are mainly expressed in reproductive tissues, and several have a role in the differentiation of primordial germ cells (Rhox1, Rhox6, and Rhox10) and in spermatogenesis (Rhox1, Rhox8, and Rhox13). Despite the lack of detailed data on human RHOX, these genes appear to be involved in the formation of germ cells because they are predominantly expressed during the early (RHOXF1) and late (RHOXF2/F2B) stages of germ cell development. Furthermore, the few variants identified to date are thought to induce or predispose to impaired spermatogenesis and severe oligozoospermia or azoospermia. In the future, research on the pathophysiology of the human RHOX genes is likely to confirm the essential role of this family in the reproductive process and might help us to better understand the various causes of infertility and characterize the associated human phenotypes.
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Affiliation(s)
- Morgane Le Beulze
- Equipe RHuMA, UMR-BREED, UFR Simone Veil Santé, F-78180 Montigny-le-Bretonneux, France; (M.L.B.); (C.D.); (A.B.-C.); (F.G.)
- UFR des Sciences de la Santé Simone Veil, Université de Versailles-Saint Quentin en Yvelines—Université Paris Saclay (UVSQ), INRAE, BREED, F-78350 Jouy-en-Josas, France
| | - Cécile Daubech
- Equipe RHuMA, UMR-BREED, UFR Simone Veil Santé, F-78180 Montigny-le-Bretonneux, France; (M.L.B.); (C.D.); (A.B.-C.); (F.G.)
- UFR des Sciences de la Santé Simone Veil, Université de Versailles-Saint Quentin en Yvelines—Université Paris Saclay (UVSQ), INRAE, BREED, F-78350 Jouy-en-Josas, France
| | - Aissatu Balde-Camara
- Equipe RHuMA, UMR-BREED, UFR Simone Veil Santé, F-78180 Montigny-le-Bretonneux, France; (M.L.B.); (C.D.); (A.B.-C.); (F.G.)
- UFR des Sciences de la Santé Simone Veil, Université de Versailles-Saint Quentin en Yvelines—Université Paris Saclay (UVSQ), INRAE, BREED, F-78350 Jouy-en-Josas, France
| | - Farah Ghieh
- Equipe RHuMA, UMR-BREED, UFR Simone Veil Santé, F-78180 Montigny-le-Bretonneux, France; (M.L.B.); (C.D.); (A.B.-C.); (F.G.)
- UFR des Sciences de la Santé Simone Veil, Université de Versailles-Saint Quentin en Yvelines—Université Paris Saclay (UVSQ), INRAE, BREED, F-78350 Jouy-en-Josas, France
| | - François Vialard
- Equipe RHuMA, UMR-BREED, UFR Simone Veil Santé, F-78180 Montigny-le-Bretonneux, France; (M.L.B.); (C.D.); (A.B.-C.); (F.G.)
- UFR des Sciences de la Santé Simone Veil, Université de Versailles-Saint Quentin en Yvelines—Université Paris Saclay (UVSQ), INRAE, BREED, F-78350 Jouy-en-Josas, France
- Département de Génétique, CHI de Poissy St. Germain en Laye, F-78300 Poissy, France
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Tan K, Wilkinson MF. Developmental regulators moonlighting as transposons defense factors. Andrology 2023; 11:891-903. [PMID: 36895139 PMCID: PMC11162177 DOI: 10.1111/andr.13427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/17/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND The germline perpetuates genetic information across generations. To maintain the integrity of the germline, transposable elements in the genome must be silenced, as these mobile elements would otherwise engender widespread mutations passed on to subsequent generations. There are several well-established mechanisms that are dedicated to providing defense against transposable elements, including DNA methylation, RNA interference, and the PIWI-interacting RNA pathway. OBJECTIVES Recently, several studies have provided evidence that transposon defense is not only provided by factors dedicated to this purpose but also factors with other roles, including in germline development. Many of these are transcription factors. Our objective is to summarize what is known about these "bi-functional" transcriptional regulators. MATERIALS AND METHODS Literature search. RESULTS AND CONCLUSION We summarize the evidence that six transcriptional regulators-GLIS3, MYBL1, RB1, RHOX10, SETDB1, and ZBTB16-are both developmental regulators and transposable element-defense factors. These factors act at different stages of germ cell development, including in pro-spermatogonia, spermatogonial stem cells, and spermatocytes. Collectively, the data suggest a model in which specific key transcriptional regulators have acquired multiple functions over evolutionary time to influence developmental decisions and safeguard transgenerational genetic information. It remains to be determined whether their developmental roles were primordial and their transposon defense roles were co-opted, or vice versa.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
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Mei-Lin Zhou, Ma JN, Xue L. Effect of Protein Arginine Methyltransferase 1 Gene Knockout on the Proliferation of Human Embryonic Kidney 293T Cells. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022140163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
Transposable elements (TEs) are mobile sequences that engender widespread mutations and thus are a major hazard that must be silenced. The most abundant active class of TEs in mammalian genomes is long interspersed element class 1 (LINE1). Here, we report that LINE1 transposition is suppressed in the male germline by transcription factors encoded by a rapidly evolving X-linked homeobox gene cluster. LINE1 transposition is repressed by many members of this RHOX transcription factor family, including those with different patterns of expression during spermatogenesis. One family member-RHOX10-suppresses LINE1 transposition during fetal development in vivo when the germline would otherwise be susceptible to LINE1 activation because of epigenetic reprogramming. We provide evidence that RHOX10 suppresses LINE transposition by inducing Piwil2, which encodes a key component in the Piwi-interacting RNA pathway that protects against TEs. The ability of RHOX transcription factors to suppress LINE1 is conserved in humans but is lost in RHOXF2 mutants from several infertile human patients, raising the possibility that loss of RHOXF2 causes human infertility by allowing uncontrolled LINE1 expression in the germline. Together, our results support a model in which the Rhox gene cluster is in an evolutionary arms race with TEs, resulting in expansion of the Rhox gene cluster to suppress TEs in different biological contexts.
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Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019; 222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).
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Affiliation(s)
- Alex M Zimmer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yihang K Pan
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | | | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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Li Y, Zhang X, Zhang J, Mu X, Duan Q, Wang T, Tian H. Synthesis and characterization of a hyperbranched grafting copolymer PEI-g-PLeu for gene and drug co-delivery. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2018; 29:47. [PMID: 29687339 DOI: 10.1007/s10856-018-6057-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
L-Leucine (Leu) is a hydrophobic natural amino acid and can polymerize into poly-L-Leucine (PLeu) to be an excellent biocompatible material. In this paper, a hyperbranched copolymer polyethyleneimine-g-poly-L-leucine (PEI-g-PLeu) was synthesized by ring-opening polymerization with leucine NCA as monomer and PEI as initiator, which will be used as drug and gene co-delivery system for cancer therapy. To characterize the transfection efficiency in vitro, pGL3 as the reporter gene was loaded in PEI-g-PLeu to form complexes. Doxorubicin (DOX) with cis-aconitic anhydride linker (CAD) and calf thymus DNA (as model DNA) were co-loaded in PEI-g-PLeu to obtain PEI-g-PLeu/DNA/CAD nanoparticles to measure Zeta potentials and particle sizes. Lastly, CAD and modified Bc12-shRNA(as therapeutic gene) were co-loaded in PEI-g-PLeu to get PEI-g-PLeu/CAD/DNA complexes. Our finding revealed when PEI and PLeu with the molar ratio of 1:240, and PEI-g-PLeu and DNA with the mass ratio of 1:5, PEI-g-PLeu/CAD/DNA had negligible cytotoxicity with equivalent gene transfaction efficiency compared with PEI25k. As a result, PEI-g-PLeu/CAD/DNA was a promising drug and gene co-delivery system.
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Affiliation(s)
- Yanhui Li
- School of Materials Science and Engineering, Changchun University of Science and Technology, Changchun, 130022, China.
| | - Xue Zhang
- School of Materials Science and Engineering, Changchun University of Science and Technology, Changchun, 130022, China
- Key Laboratory of Polymer Ecomaterials,Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Jingpeng Zhang
- School of Materials Science and Engineering, Changchun University of Science and Technology, Changchun, 130022, China
- Key Laboratory of Polymer Ecomaterials,Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Xin Mu
- School of Materials Science and Engineering, Changchun University of Science and Technology, Changchun, 130022, China
- Key Laboratory of Polymer Ecomaterials,Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Qian Duan
- School of Materials Science and Engineering, Changchun University of Science and Technology, Changchun, 130022, China
| | - Tinghong Wang
- Changchun Chaoyang People's Hospital, Changchun, 130022, China
| | - Huayu Tian
- Key Laboratory of Polymer Ecomaterials,Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
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Song HW, Bettegowda A, Lake BB, Zhao AH, Skarbrevik D, Babajanian E, Sukhwani M, Shum EY, Phan MH, Plank TDM, Richardson ME, Ramaiah M, Sridhar V, de Rooij DG, Orwig KE, Zhang K, Wilkinson MF. The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment. Cell Rep 2017; 17:149-164. [PMID: 27681428 DOI: 10.1016/j.celrep.2016.08.090] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 07/19/2016] [Accepted: 08/27/2016] [Indexed: 12/31/2022] Open
Abstract
The developmental origins of most adult stem cells are poorly understood. Here, we report the identification of a transcription factor-RHOX10-critical for the initial establishment of spermatogonial stem cells (SSCs). Conditional loss of the entire 33-gene X-linked homeobox gene cluster that includes Rhox10 causes progressive spermatogenic decline, a phenotype indistinguishable from that caused by loss of only Rhox10. We demonstrate that this phenotype results from dramatically reduced SSC generation. By using a battery of approaches, including single-cell-RNA sequencing (scRNA-seq) analysis, we show that Rhox10 drives SSC generation by promoting pro-spermatogonia differentiation. Rhox10 also regulates batteries of migration genes and promotes the migration of pro-spermatogonia into the SSC niche. The identification of an X-linked homeobox gene that drives the initial generation of SSCs has implications for the evolution of X-linked gene clusters and sheds light on regulatory mechanisms influencing adult stem cell generation in general.
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Affiliation(s)
- Hye-Won Song
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Anilkumar Bettegowda
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Blue B Lake
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Adrienne H Zhao
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - David Skarbrevik
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eric Babajanian
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Meena Sukhwani
- Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Eleen Y Shum
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mimi H Phan
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Terra-Dawn M Plank
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Marcy E Richardson
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Vaishnavi Sridhar
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Faculty of Science, Department of Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Kyle E Orwig
- Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Kun Zhang
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Masuda T, Wan J, Yerrabelli A, Berlinicke C, Kallman A, Qian J, Zack DJ. Off Target, but Sequence-Specific, shRNA-Associated Trans-Activation of Promoter Reporters in Transient Transfection Assays. PLoS One 2016; 11:e0167867. [PMID: 27977714 PMCID: PMC5158200 DOI: 10.1371/journal.pone.0167867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/21/2016] [Indexed: 11/23/2022] Open
Abstract
Transient transfection promoter reporter assays are commonly used in the study of transcriptional regulation, and can be used to define and characterize both cis-acting regulatory sequences and trans-acting factors. In the process of using a variety of reporter assays designed to study regulation of the rhodopsin (rho) promoter, we discovered that rhodopsin promoter-driven reporter expression could be activated by certain species of shRNA in a gene-target-independent but shRNA sequence-specific manner, suggesting involvement of a specific shRNA associated pathway. Interestingly, the shRNA-mediated increase of rhodopsin promoter activity was synergistically enhanced by the rhodopsin transcriptional regulators CRX and NRL. Additionally, the effect was cell line-dependent, suggesting that this pathway requires the expression of cell-type specific factors. Since microRNA (miRNA) and interferon response-mediated processes have been implicated in RNAi off-target phenomena, we performed miRNA and gene expression profiling on cells transfected with shRNAs that do target a specific gene but have varied effects on rho reporter expression in order to identify transcripts whose expression levels are associated with shRNA induced rhodopsin promoter reporter activity. We identified a total of 50 miRNA species, and by microarray analysis, 320 protein-coding genes, some of which were predicted targets of the identified differentially expressed miRNAs, whose expression was altered in the presence of shRNAs that stimulated rhodopsin-promoter activity in a non-gene-targeting manner. Consistent with earlier studies on shRNA off-target effects, a number of interferon response genes were among those identified to be upregulated. Taken together, our results confirm the importance of considering off-target effects when interpreting data from RNAi experiments and extend prior results by focusing on the importance of including multiple and carefully designed controls in the design and analysis of the effects of shRNA on transient transfection-based transcriptional assays.
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Affiliation(s)
- Tomohiro Masuda
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jun Wan
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anitha Yerrabelli
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cindy Berlinicke
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alyssa Kallman
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Donald J. Zack
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institut de la Vision, University Pierre and Marie Curie, Paris, France
- * E-mail:
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Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins. Biotechniques 2016; 60:69-74. [PMID: 26842351 DOI: 10.2144/000114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/11/2015] [Indexed: 01/13/2023] Open
Abstract
Manipulation of protein stability with ligand-regulated degron fusions is a powerful method for investigating gene function. We developed a selectable cassette for easy C-terminal tagging of endogenous human proteins with the E. coli dihydrofolate reductase (eDHFR) degron using CRISPR/Cas9 genome editing. This cassette permits high-efficiency recovery of correct integration events using an in-frame self-cleaving 2A peptide and the puromycin resistance gene. PCR amplified donor eDHFR cassette fragments with 100 bases of homology on each end are integrated by homology-directed repair (HDR) of guide RNA (gRNA)-targeted double-stranded DNA breaks at the 3' ends of open reading frames (ORFs). As proof of principle, we generated cell lines in which three endogenous proteins were tagged with the eDHFR degron. When the antibiotic trimethoprim is removed from the media, each of the eDHFR-tagged proteins was depleted by >90% within 2-4 h, and this depletion was reversed by re-addition of trimethoprim. Since puromycin selection permits recovery of in-frame degron fusions with high efficiency using only 100-bp long regions of homology, this method should be applicable on a genome-wide scale for generating libraries of conditional mutant cell lines.
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