1
|
Aguillon R, Rinsky M, Simon-Blecher N, Doniger T, Appelbaum L, Levy O. CLOCK evolved in cnidaria to synchronize internal rhythms with diel environmental cues. eLife 2024; 12:RP89499. [PMID: 38743049 PMCID: PMC11093582 DOI: 10.7554/elife.89499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
The circadian clock enables anticipation of the day/night cycle in animals ranging from cnidarians to mammals. Circadian rhythms are generated through a transcription-translation feedback loop (TTFL or pacemaker) with CLOCK as a conserved positive factor in animals. However, CLOCK's functional evolutionary origin and mechanism of action in basal animals are unknown. In the cnidarian Nematostella vectensis, pacemaker gene transcript levels, including NvClk (the Clock ortholog), appear arrhythmic under constant darkness, questioning the role of NvCLK. Utilizing CRISPR/Cas9, we generated a NvClk allele mutant (NvClkΔ), revealing circadian behavior loss under constant dark (DD) or light (LL), while maintaining a 24 hr rhythm under light-dark condition (LD). Transcriptomics analysis revealed distinct rhythmic genes in wild-type (WT) polypsunder LD compared to DD conditions. In LD, NvClkΔ/Δ polyps exhibited comparable numbers of rhythmic genes, but were reduced in DD. Furthermore, under LD, the NvClkΔ/Δ polyps showed alterations in temporal pacemaker gene expression, impacting their potential interactions. Additionally, differential expression of non-rhythmic genes associated with cell division and neuronal differentiation was observed. These findings revealed that a light-responsive pathway can partially compensate for circadian clock disruption, and that the Clock gene has evolved in cnidarians to synchronize rhythmic physiology and behavior with the diel rhythm of the earth's biosphere.
Collapse
Affiliation(s)
- Raphael Aguillon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat GanIsrael
- The Multidisciplinary Brain Research Center, Bar-Ilan UniversityRamat GanIsrael
| | - Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat GanIsrael
| | - Noa Simon-Blecher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat GanIsrael
| | - Tirza Doniger
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat GanIsrael
| | - Lior Appelbaum
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat GanIsrael
- The Multidisciplinary Brain Research Center, Bar-Ilan UniversityRamat GanIsrael
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat GanIsrael
| |
Collapse
|
2
|
Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, Shen Z, Rao K. Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome. Genome Biol Evol 2024; 16:evae037. [PMID: 38408866 PMCID: PMC10919887 DOI: 10.1093/gbe/evae037] [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: 07/31/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024] Open
Abstract
The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.
Collapse
Affiliation(s)
- Liang Guo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong Province 510300, China
| | - Danilo Malara
- Stazione Zoologica Anton Dohrn, Integrated Marine Ecology Department, CRIMAC, Calabria Marine Centre, Amendolara 87071, Italy
| | - Pietro Battaglia
- Integrated Marine Ecology Department, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina 98168, Italy
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21300, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden 11900, Malaysia
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - D Allen Davis
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36830, USA
| | - Yu Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| | - Zhongyuan Shen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| | - Ke Rao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| |
Collapse
|
3
|
Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024; 2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_2] [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] [Indexed: 07/17/2024]
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.
Collapse
Affiliation(s)
- Z Begum Yagci
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Gautami R Kelkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Tyler J Johnson
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Dilara Sen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
4
|
Kijima T, Kurokawa D, Sasakura Y, Ogasawara M, Aratake S, Yoshida K, Yoshida M. CatSper mediates not only chemotactic behavior but also the motility of ascidian sperm. Front Cell Dev Biol 2023; 11:1136537. [PMID: 38020915 PMCID: PMC10652287 DOI: 10.3389/fcell.2023.1136537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Sperm motility, including chemotactic behavior, is regulated by changes in the intracellular Ca2+ concentration, and the sperm-specific Ca2+ channel CatSper has been shown to play an important role in the regulation of intracellular Ca2+. In particular, in mammals, CatSper is the only functional Ca2+ channel in the sperm, and mice deficient in the genes comprising the pore region of the Ca2+ channel are infertile due to the inhibition of sperm hyperactivation. CatSper is also thought to be involved in sea urchin chemotaxis. In contrast, in ascidian Ciona intestinalis, SAAF, a sperm attractant, interacts with Ca2+/ATPase, a Ca2+ pump. Although the existence of CatSper genes has been reported, it is not clear whether CatSper is a functional Ca2+ channel in sperm. Results: We showed that CatSper is present in the sperm flagella of C. intestinalis as in mammalian species, although a small level of gene expression was found in other tissues. The spermatozoa of CatSper3 KO animals were significantly less motile, and some motile sperms did not show any chemotactic behavior. These results suggest that CatSper plays an important role in ascidians and mammals, and is involved in spermatogenesis and basic motility mechanisms.
Collapse
Affiliation(s)
- Taiga Kijima
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa, Japan
| | - Daisuke Kurokawa
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Satoe Aratake
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa, Japan
| | - Kaoru Yoshida
- Faculty of Biomedical Engineering, Toin University of Yokohama, Yokohama, Kanagawa, Japan
| | - Manabu Yoshida
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa, Japan
| |
Collapse
|
5
|
Yilmaz O, Com E, Pineau C, Bobe J. Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio). Sci Rep 2023; 13:18795. [PMID: 37914813 PMCID: PMC10620220 DOI: 10.1038/s41598-023-46148-2] [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: 08/09/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
The specific functions and essentiality of type II vitellogenin (Vtg2) in early zebrafish development were investigated in this study. A vtg2-mutant zebrafish line was produced and effects of genomic disturbance were observed in F2 females and F3 offspring. No change in vtg2 transcript has been detected, however, Vtg2 abundance in F2 female liver was 5×, and in 1 hpf F3 vtg2-mutant embryos was 3.8× less than Wt (p < 0.05). Fecundity was unaffected while fertilization rate was more than halved in F2 vtg2-mutant females (p < 0.05). Hatching rate was significantly higher in F3 vtg2-mutant embryos in comparison to Wt embryos. Survival rate declined drastically to 29% and 18% at 24 hpf and 20 dpf, respectively, in F3 vtg2-mutant embryos. The introduced mutation caused vitelline membrane deficiencies, significant mortalities at early embryonic stages, and morphological abnormalities in the surviving F3 vtg2-mutant larvae. Overrepresentation of histones, zona pellucida proteins, lectins, and protein degradation related proteins in F3 vtg2-mutant embryos provide evidence to impaired mechanisms involved in vitellin membrane formation. Overall findings imply a potential function of Vtg2 in acquisition of vitellin membrane integrity, among other reproductive functions, and therefore, its essentiality in early zebrafish embryo development.
Collapse
Affiliation(s)
- Ozlem Yilmaz
- Norwegian Institute of Marine Research, IMR, 5392, Storebø, Norway.
| | - Emmanuelle Com
- Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Univ Rennes, 35000, Rennes, France
- CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Univ Rennes, 35000, Rennes, France
| | - Charles Pineau
- Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Univ Rennes, 35000, Rennes, France
- CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Univ Rennes, 35000, Rennes, France
| | - Julien Bobe
- UR1037, Laboratory of Fish Physiology and Genomics, INRAE, Campus de Beaulieu, 35042, Rennes Cedex, France
| |
Collapse
|
6
|
Zhang X, Mei LC, Gao YY, Hao GF, Song BA. Web tools support predicting protein-nucleic acid complexes stability with affinity changes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1781. [PMID: 36693636 DOI: 10.1002/wrna.1781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 01/26/2023]
Abstract
Numerous biological processes, such as transcription, replication, and translation, rely on protein-nucleic acid interactions (PNIs). Demonstrating the binding stability of protein-nucleic acid complexes is vital to deciphering the code for PNIs. Numerous web-based tools have been developed to attach importance to protein-nucleic acid stability, facilitating the prediction of PNIs characteristics rapidly. However, the data and tools are dispersed and lack comprehensive integration to understand the stability of PNIs better. In this review, we first summarize existing databases for evaluating the stability of protein-nucleic acid binding. Then, we compare and evaluate the pros and cons of web tools for forecasting the interaction energies of protein-nucleic acid complexes. Finally, we discuss the application of combining models and capabilities of PNIs. We may hope these web-based tools will facilitate the discovery of recognition mechanisms for protein-nucleic acid binding stability. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Xiao Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Long-Can Mei
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
| | - Yang-Yang Gao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
| | - Bao-An Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| |
Collapse
|
7
|
Kiuchi T, Shoji K, Izumi N, Tomari Y, Katsuma S. Non-gonadal somatic piRNA pathways ensure sexual differentiation, larval growth, and wing development in silkworms. PLoS Genet 2023; 19:e1010912. [PMID: 37733654 PMCID: PMC10513339 DOI: 10.1371/journal.pgen.1010912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/09/2023] [Indexed: 09/23/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) guide PIWI proteins to target transposons in germline cells, thereby suppressing transposon activity to preserve genome integrity in metazoans' gonadal tissues. Piwi, one of three Drosophila PIWI proteins, is expressed in the nucleus and suppresses transposon activity by forming heterochromatin in an RNA cleavage-independent manner. Recently, Piwi was reported to control cell metabolism in Drosophila fat body, providing an example of piRNAs acting in non-gonadal somatic tissues. However, mutant flies of the other two PIWI proteins, Aubergine (Aub) and Argonaute3 (Ago3), show no apparent phenotype except for infertility, blurring the importance of the piRNA pathway in non-gonadal somatic tissues. The silkworm, Bombyx mori, possesses two PIWI proteins, Siwi (Aub homolog) and BmAgo3 (Ago3 homolog), whereas B. mori does not have a Piwi homolog. Siwi and BmAgo3 are mainly expressed in gonadal tissues and play a role in repressing transposon activity by cleaving transposon RNA in the cytoplasm. Here, we generated Siwi and BmAgo3 loss-of-function mutants of B. mori and found that they both showed delayed larval growth and failed to become adult moths. They also exhibited defects in wing development and sexual differentiation. Transcriptome analysis revealed that loss of somatic piRNA biogenesis pathways results in abnormal expression of not only transposons but also host genes, presumably causing severe growth defects. Our results highlight the roles of non-gonadal somatic piRNAs in B. mori development.
Collapse
Affiliation(s)
- Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Shoji
- Institute for Quantitative Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Natsuko Izumi
- Institute for Quantitative Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
8
|
Kumar R, Sinha NR, Mohan RR. Corneal gene therapy: Structural and mechanistic understanding. Ocul Surf 2023; 29:279-297. [PMID: 37244594 DOI: 10.1016/j.jtos.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Cornea, a dome-shaped and transparent front part of the eye, affords 2/3rd refraction and barrier functions. Globally, corneal diseases are the leading cause of vision impairment. Loss of corneal function including opacification involve the complex crosstalk and perturbation between a variety of cytokines, chemokines and growth factors generated by corneal keratocytes, epithelial cells, lacrimal tissues, nerves, and immune cells. Conventional small-molecule drugs can treat mild-to-moderate traumatic corneal pathology but requires frequent application and often fails to treat severe pathologies. The corneal transplant surgery is a standard of care to restore vision in patients. However, declining availability and rising demand of donor corneas are major concerns to maintain ophthalmic care. Thus, the development of efficient and safe nonsurgical methods to cure corneal disorders and restore vision in vivo is highly desired. Gene-based therapy has huge potential to cure corneal blindness. To achieve a nonimmunogenic, safe and sustained therapeutic response, the selection of a relevant genes, gene editing methods and suitable delivery vectors are vital. This article describes corneal structural and functional features, mechanistic understanding of gene therapy vectors, gene editing methods, gene delivery tools, and status of gene therapy for treating corneal disorders, diseases, and genetic dystrophies.
Collapse
Affiliation(s)
- Rajnish Kumar
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow campus, UP, 226028, India
| | - Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
| |
Collapse
|
9
|
Nawaly H, Tanaka A, Toyoshima Y, Tsuji Y, Matsuda Y. Localization and characterization θ carbonic anhydrases in Thalassiosira pseudonana. PHOTOSYNTHESIS RESEARCH 2023; 156:217-229. [PMID: 36862281 DOI: 10.1007/s11120-023-01007-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/12/2023] [Indexed: 05/03/2023]
Abstract
Carbonic anhydrase (CA) is a crucial component for the operation of CO2-concentrating mechanisms (CCMs) in the majority of aquatic photoautotrophs that maintain the global primary production. In the genome of the centric marine diatom, Thalassiosira pseudonana, there are four putative gene sequences that encode θ-type CA, which was a type of CA recently identified in marine diatoms and green algae. In the present study, specific subcellular locations of four θCAs, TpθCA1, TpθCA2, TpθCA3, and TpθCA4 were determined by expressing GFP-fused proteins of these TpθCAs in T. pseudonana. As a result, C-terminal GFP fusion proteins of TpθCA1, TpθCA2, and TpθCA3 were all localized in the chloroplast; TpθCA2 was at the central chloroplast area, and the other two TpθCAs were throughout the chloroplast. Immunogold-labeling transmission electron microscopy was further performed for the transformants expressing TpθCA1:GFP and TpθCA2:GFP with anti-GFP-monoclonal antibody. TpθCA1:GFP was localized in the free stroma area, including the peripheral pyrenoid area. TpθCA2:GFP was clearly located as a lined distribution at the central part of the pyrenoid structure, which was most likely the pyrenoid-penetrating thylakoid. Considering the presence of the sequence encoding the N-terminal thylakoid-targeting domain in the TpθCA2 gene, this localization was likely the lumen of the pyrenoid-penetrating thylakoid. On the other hand, TpθCA4:GFP was localized in the cytoplasm. Transcript analysis of these TpθCAs revealed that TpθCA2 and TpθCA3 were upregulated in atmospheric CO2 (0.04% CO2, LC) levels, while TpθCA1 and TpθCA4 were highly induced under 1% CO2 (HC) condition. The genome-editing knockout (KO) of TpθCA1, by CRISPR/Cas9 nickase, gave a silent phenotype in T. pseudonana under LC-HC conditions, which was in sharp agreement with the case of the previously reported TpθCA3 KO. In sharp contrast, TpθCA2 KO is so far unsuccessful, suggesting a housekeeping role of TpθCA2. The silent phenotype of KO strains of stromal CAs suggests that TpαCA1, TpθCA1, and TpθCA3 may have functional redundancy, but different transcript regulations in response to CO2 of these stromal CAs suggest in part their independent roles.
Collapse
Affiliation(s)
- Hermanus Nawaly
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Atsuko Tanaka
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, 903-0213, Japan
| | - Yui Toyoshima
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Yoshinori Tsuji
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Yusuke Matsuda
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan.
| |
Collapse
|
10
|
Yano N, Fedulov AV. Targeted DNA Demethylation: Vectors, Effectors and Perspectives. Biomedicines 2023; 11:biomedicines11051334. [PMID: 37239005 DOI: 10.3390/biomedicines11051334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.
Collapse
Affiliation(s)
- Naohiro Yano
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Alexey V Fedulov
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| |
Collapse
|
11
|
Weinschutz Mendes H, Neelakantan U, Liu Y, Fitzpatrick SE, Chen T, Wu W, Pruitt A, Jin DS, Jamadagni P, Carlson M, Lacadie CM, Enriquez KD, Li N, Zhao D, Ijaz S, Sakai C, Szi C, Rooney B, Ghosh M, Nwabudike I, Gorodezky A, Chowdhury S, Zaheer M, McLaughlin S, Fernandez JM, Wu J, Eilbott JA, Vander Wyk B, Rihel J, Papademetris X, Wang Z, Hoffman EJ. High-throughput functional analysis of autism genes in zebrafish identifies convergence in dopaminergic and neuroimmune pathways. Cell Rep 2023; 42:112243. [PMID: 36933215 PMCID: PMC10277173 DOI: 10.1016/j.celrep.2023.112243] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/15/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Advancing from gene discovery in autism spectrum disorders (ASDs) to the identification of biologically relevant mechanisms remains a central challenge. Here, we perform parallel in vivo functional analysis of 10 ASD genes at the behavioral, structural, and circuit levels in zebrafish mutants, revealing both unique and overlapping effects of gene loss of function. Whole-brain mapping identifies the forebrain and cerebellum as the most significant contributors to brain size differences, while regions involved in sensory-motor control, particularly dopaminergic regions, are associated with altered baseline brain activity. Finally, we show a global increase in microglia resulting from ASD gene loss of function in select mutants, implicating neuroimmune dysfunction as a key pathway relevant to ASD biology.
Collapse
Affiliation(s)
| | - Uma Neelakantan
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sarah E Fitzpatrick
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; MD-PhD Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tianying Chen
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Weimiao Wu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - April Pruitt
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA
| | - David S Jin
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Marina Carlson
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA
| | - Cheryl M Lacadie
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA; SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dejian Zhao
- Department of Genetics, Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sundas Ijaz
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Catalina Sakai
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Christina Szi
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Brendan Rooney
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Marcus Ghosh
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Ijeoma Nwabudike
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; MD-PhD Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA
| | - Andrea Gorodezky
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sumedha Chowdhury
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Meeraal Zaheer
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sarah McLaughlin
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Jia Wu
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jeffrey A Eilbott
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Brent Vander Wyk
- Department of Internal Medicine, Section of Geriatrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Xenophon Papademetris
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Ellen J Hoffman
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
12
|
Shirk BD, Shirk PD, Furlong RB, Scully ED, Wu K, Siegfried BD. Gene editing of the ABC Transporter/White locus using CRISPR/Cas9-mediated mutagenesis in the Indian Meal Moth. JOURNAL OF INSECT PHYSIOLOGY 2023; 145:104471. [PMID: 36539178 DOI: 10.1016/j.jinsphys.2022.104471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
ATP binding cassette (ABC) proteins are involved in transport of substrates across membranes including eye pigments. Mutations of ABC transporter white, brown and scarlet genes of Drosophila and other insects result in visible eye color phenotypes. White locus was identified in a genome assembly of Plodia interpunctella and was found to extend for 16,670 bp comprising 13 exons. We report here recovery of heritable mutants in white in the Indian meal moth, P. interpunctella, using CRISPR/Cas9-mediated mutagenesis. A white eye strain of P. interpunctella c.737delC (Piw-/-) was previously isolated in 1986. Guide RNA (sgRNA) was designed for exon 1 (sgRNA242). Microinjection of Cas9/sgRNA242 complex into Plodia wild type eggs (≤20 min post oviposition) produced 156 viable larvae of which 81 eclosed as adults. Forty-five (56 %) adults displayed wild type phenotype, while 26 females (32 %) and 10 males (12 %) showed full or partial white eye phenotype. The 26 white eye females were mated with Piw-/- males and 21 matings resulted in F1 white eye progeny. Thirteen of the Piw-242 lines were established and sequencing showed indels at the CRISPR/Cas9 242AM site. Based on RT-PCR analysis, most white mutations resulted in suppressed levels of transcript. These results demonstrate the utility of CRISPR/Cas9 gene editing in Plodia which suggests this technology can be used to characterize the role of various genetic elements including those that encode novel targets or confer insecticide resistance mechanisms.
Collapse
Affiliation(s)
- Bryce D Shirk
- Entomology & Nematology Department, PO Box 11620, University of Florida, Gainesville, FL 32611, USA
| | - Paul D Shirk
- Entomology & Nematology Department, PO Box 11620, University of Florida, Gainesville, FL 32611, USA; USDA-ARS CMAVE IBBRU, 1700 SW 23rd Drive, Gainesville, FL 32608, USA.
| | - Richard B Furlong
- USDA-ARS CMAVE IBBRU, 1700 SW 23rd Drive, Gainesville, FL 32608, USA
| | - Erin D Scully
- USDA-ARS, CGAHR-SPIERU, 1515 College Avenue, Manhattan, KS 66502, USA
| | - Ke Wu
- Entomology & Nematology Department, PO Box 11620, University of Florida, Gainesville, FL 32611, USA
| | - Blair D Siegfried
- Entomology & Nematology Department, PO Box 11620, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
13
|
Pan Q, Herpin A, Guiguen Y. Inactivation of the Anti-Müllerian Hormone Receptor Type 2 (amhrII) Gene in Northern Pike (Esox lucius) Results in Male-To-Female Sex Reversal. Sex Dev 2023; 16:289-294. [PMID: 35306491 DOI: 10.1159/000521003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The anti-müllerian hormone (Amh) pathway is crucial for sexual development in teleosts. A male-specific duplicate of anti-müllerian hormone (amhby) was previously identified as the northern pike (Esox lucius) master sex determination gene. However, the role of its putative cognate receptor, i.e., the anti-müllerian hormone receptor type 2 (amhrII) was unclear in this species. OBJECTIVE Here, we investigated the role of amhrII during sexual development of northern pike. METHOD We generated stable mutants with deletions in exon 9 of amhrII, inactivating the AmhrII protein using a CRISPR-Cas9-mediated gene knockout strategy. RESULT The inactivation of amhrII in northern pike results in a high level of male-to-female sex reversal. CONCLUSION This result demonstrates that amhrII is necessary for male sexual development in northern pike and supports the idea that AmhrII is a conserved regulator of the teleosts sex differentiation network.
Collapse
Affiliation(s)
- Qiaowei Pan
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | | |
Collapse
|
14
|
Bosada FM, van Duijvenboden K, Giovou AE, Rivaud MR, Uhm JS, Verkerk AO, Boukens BJ, Christoffels VM. An atrial fibrillation-associated regulatory region modulates cardiac Tbx5 levels and arrhythmia susceptibility. eLife 2023; 12:80317. [PMID: 36715501 PMCID: PMC9928424 DOI: 10.7554/elife.80317] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Heart development and rhythm control are highly Tbx5 dosage-sensitive. TBX5 haploinsufficiency causes congenital conduction disorders, whereas increased expression levels of TBX5 in human heart samples has been associated with atrial fibrillation (AF). We deleted the conserved mouse orthologues of two independent AF-associated genomic regions in the Tbx5 locus, one intronic (RE(int)) and one downstream (RE(down)) of Tbx5. In both lines, we observed a modest (30%) increase of Tbx5 in the postnatal atria. To gain insight into the effects of slight dosage increase in vivo, we investigated the atrial transcriptional, epigenetic and electrophysiological properties of both lines. Increased atrial Tbx5 expression was associated with induction of genes involved in development, ion transport and conduction, with increased susceptibility to atrial arrhythmias, and increased action potential duration of atrial cardiomyocytes. We identified an AF-associated variant in the human RE(int) that increases its transcriptional activity. Expression of the AF-associated transcription factor Prrx1 was induced in Tbx5RE(int)KO cardiomyocytes. We found that some of the transcriptional and functional changes in the atria caused by increased Tbx5 expression were normalized when reducing cardiac Prrx1 expression in Tbx5RE(int)KO mice, indicating an interaction between these two AF genes. We conclude that modest increases in expression of dose-dependent transcription factors, caused by common regulatory variants, significantly impact on the cardiac gene regulatory network and disease susceptibility.
Collapse
Affiliation(s)
- Fernanda M Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Alexandra E Giovou
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Mathilde R Rivaud
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Jae-Sun Uhm
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Cardiology, Severance Hospital, College of Medicine, Yonsei UniversitySeoulRepublic of Korea
| | - Arie O Verkerk
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Physiology, University of Maastricht, Cardiovascular Research Institute Maastricht, Maastricht University Medical CenterMaastrichtNetherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| |
Collapse
|
15
|
Sheikh Beig Goharrizi MA, Ghodsi S, Memarjafari MR. Implications of CRISPR-Cas9 Genome Editing Methods in Atherosclerotic Cardiovascular Diseases. Curr Probl Cardiol 2023; 48:101603. [PMID: 36682390 DOI: 10.1016/j.cpcardiol.2023.101603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Today, new methods have been developed to treat or modify the natural course of cardiovascular diseases (CVDs), including atherosclerosis, by the clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) system. Genome-editing tools are CRISPR-related palindromic short iteration systems such as CRISPR-Cas9, a valuable technology for achieving somatic and germinal genomic manipulation in model cells and organisms for various applications, including the creation of deletion alleles. Mutations in genomic deoxyribonucleic acid and new genes' placement have emerged. Based on World Health Organization fact sheets, 17.9 million people die from CVDs each year, an estimated 32% of all deaths worldwide. 85% of all CVD deaths are due to acute coronary events and strokes. This review discusses the applications of CRISPR-Cas9 technology throughout atherosclerotic disease research and the prospects for future in vivo genome editing therapies. We also describe several limitations that must be considered to achieve the full scientific and therapeutic potential of cardiovascular genome editing in the treatment of atherosclerosis.
Collapse
Affiliation(s)
| | - Saeed Ghodsi
- Department of Cardiology, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
16
|
Liang Y, Xu W, Zhou Y, Gao Y, Tian H, Wu X, Xu Y, Wang H. Midgut membrane protein BmSUH facilitates Bombyx mori nucleopolyhedrovirus oral infection. PLoS Pathog 2022; 18:e1010938. [PMID: 36383572 PMCID: PMC9668127 DOI: 10.1371/journal.ppat.1010938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Baculoviruses are virulent pathogens that infect a wide range of insects. They initiate infections via specific interactions between the structural proteins on the envelopes of occlusion-derived virions (ODVs) and the midgut cell surface receptors in hosts. However, host factors that are hijacked by baculoviruses for efficient infection remain largely unknown. In this study, we identified a membrane-associated protein sucrose hydrolase (BmSUH) as an ODV binding factor during Bombyx mori nucleopolyhedrovirus (BmNPV) primary infection. BmSUH was specifically expressed in the midgut microvilli where the ODV-midgut fusion happened. Knockout of BmSUH by CRISPR/Cas9 resulted in a significantly higher survival rate after BmNPV orally infection. Liquid chromatography-tandem mass spectrometry analysis and co-immunoprecipitation analysis demonstrated that PIF protein complex required for ODV binding could interact with BmSUH. Furthermore, fluorescence dequenching assay showed that the amount of ODV binding and fusion to the midgut decreased in BmSUH mutants compared to wild-type silkworm, suggesting the role of BmSUH as an ODV binding factor that mediates the ODV entry process. Based on a multilevel survey, the data showed that BmSUH acted as a host factor that facilitates BmNPV oral infection. More generally, this study indicated that disrupting essential protein-protein interactions required for baculovirus efficient entry may be broadly applicable to against viral infection. Baculoviridae is a large family of pathogens that infect insects and frequently cause fatal diseases. Bombyx mori nucleopolyhedrovirus (BmNPV) is a major threat to the sericulture industry. Although we have learned a lot about baculoviruses over the past several decades, the detailed interaction patterns between host proteins and viral proteins that lead to infection remain underexplored. Here, we determined that BmSUH, a midgut microvilli protein, was required for the efficient oral infection of BmNPV. Our research suggests that BmSUH mediates the entry of occlusion-derived virions into the midgut epithelia by interacting with per os infectivity factors. According to the findings, inhibition of viral binding to host cells is an attractive strategy to prevent infection. This study provides an approach for preventing BmNPV infection through developing genetic resistance to viruses by using CRISPR/Cas9 system to abolish the host factors that are essential for viral entry.
Collapse
Affiliation(s)
- Yanting Liang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Weifan Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yun Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huan Tian
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
| |
Collapse
|
17
|
Paul B, Shewade LH, Buchholz DR. cyp21a2 Knockout Tadpoles Survive Metamorphosis Despite Low Corticosterone. Endocrinology 2022; 164:6775874. [PMID: 36301177 DOI: 10.1210/endocr/bqac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 01/16/2023]
Abstract
Corticosteroids are so vital for organ maturation that reduced corticosteroid signaling during postembryonic development causes death in terrestrial vertebrates. Indeed, death occurs at metamorphosis in frogs lacking proopiomelanocortin (pomc) or the glucocorticoid receptor (GR; nr3c1). Some residual corticosteroids exist in pomc mutants to activate the wild-type (WT) GR and mineralocorticoid receptor (MR), and the elevated corticosteroids in GR mutants may activate MR. Thus, we expected a more severe developmental phenotype in tadpoles with inactivation of 21-hydroxylase, which should eliminate all interrenal corticosteroid biosynthesis. Using CRISPR/Cas9 in Xenopus tropicalis, we produced an 11-base pair deletion in cyp21a2, the gene encoding 21-hydroxylase. Growth and development were delayed in cyp21a2 mutant tadpoles, but unlike the other frog models, they survived metamorphosis. Consistent with an absence of 21-hydroxylase, mutant tadpoles had a 95% reduction of aldosterone in tail tissue, but they retained some corticosterone (∼40% of WT siblings), an amount, however, too low for survival in pomc mutants. Decreased corticosteroid signaling was evidenced by reduced expression of corticosteroid-response gene, klf9, and by impaired negative feedback in the hypothalamus-pituitary-interrenal axis with higher messenger RNA expression levels of crh, pomc, star, and cyp11b2 and an approximately 30-fold increase in tail content of progesterone. In vitro tail-tip culture showed that progesterone can transactivate the frog GR. The inadequate activation of GR by corticosterone in cyp21a2 mutants was likely compensated for by sufficient corticosteroid signaling from other GR ligands to allow survival through the developmental transition from aquatic to terrestrial life.
Collapse
Affiliation(s)
- Bidisha Paul
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Leena H Shewade
- Biotherapeutics Division, Codexis Inc., San Carlos, CA 94070, USA
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| |
Collapse
|
18
|
Keller TCS, Lechauve C, Keller AS, Broseghini-Filho GB, Butcher JT, Askew Page HR, Islam A, Tan ZY, DeLalio LJ, Brooks S, Sharma P, Hong K, Xu W, Padilha AS, Ruddiman CA, Best AK, Macal E, Kim-Shapiro DB, Christ G, Yan Z, Cortese-Krott MM, Ricart K, Patel R, Bender TP, Sonkusare SK, Weiss MJ, Ackerman H, Columbus L, Isakson BE. Endothelial alpha globin is a nitrite reductase. Nat Commun 2022; 13:6405. [PMID: 36302779 PMCID: PMC9613979 DOI: 10.1038/s41467-022-34154-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 10/04/2022] [Indexed: 01/29/2023] Open
Abstract
Resistance artery vasodilation in response to hypoxia is essential for matching tissue oxygen and demand. In hypoxia, erythrocytic hemoglobin tetramers produce nitric oxide through nitrite reduction. We hypothesized that the alpha subunit of hemoglobin expressed in endothelium also facilitates nitrite reduction proximal to smooth muscle. Here, we create two mouse strains to test this: an endothelial-specific alpha globin knockout (EC Hba1Δ/Δ) and another with an alpha globin allele mutated to prevent alpha globin's inhibitory interaction with endothelial nitric oxide synthase (Hba1WT/Δ36-39). The EC Hba1Δ/Δ mice had significantly decreased exercise capacity and intracellular nitrite consumption in hypoxic conditions, an effect absent in Hba1WT/Δ36-39 mice. Hypoxia-induced vasodilation is significantly decreased in arteries from EC Hba1Δ/Δ, but not Hba1WT/Δ36-39 mice. Hypoxia also does not lower blood pressure in EC Hba1Δ/Δ mice. We conclude the presence of alpha globin in resistance artery endothelium acts as a nitrite reductase providing local nitric oxide in response to hypoxia.
Collapse
Affiliation(s)
- T C Stevenson Keller
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Christophe Lechauve
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alexander S Keller
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Gilson Brás Broseghini-Filho
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Joshua T Butcher
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
| | - Henry R Askew Page
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Aditi Islam
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhe Yin Tan
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Leon J DeLalio
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Steven Brooks
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Poonam Sharma
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Kwangseok Hong
- Department of Physical Education, College of Education, Chung-Ang University, Seoul, South Korea
| | - Wenhao Xu
- Transgenic Mouse Facility, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | - Claire A Ruddiman
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Angela K Best
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Edgar Macal
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Daniel B Kim-Shapiro
- Department of Physics, Translational Science Center, Wake Forest University, Winston-Salem, NC, USA
| | - George Christ
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Zhen Yan
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Miriam M Cortese-Krott
- Cardiovascular Research Laboratory, Division of Cardiology, Pneumology and Angiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Karina Ricart
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rakesh Patel
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Timothy P Bender
- Department of Microbiology, Immunology and Cancer, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Swapnil K Sonkusare
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hans Ackerman
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Linda Columbus
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Brant E Isakson
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA.
| |
Collapse
|
19
|
Metabolic novelty originating from horizontal gene transfer is essential for leaf beetle survival. Proc Natl Acad Sci U S A 2022; 119:e2205857119. [PMID: 36161953 PMCID: PMC9546569 DOI: 10.1073/pnas.2205857119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) provides an evolutionary shortcut for recipient organisms to gain novel functions. Although reports of HGT in higher eukaryotes are rapidly accumulating, in most cases the evolutionary trajectory, metabolic integration, and ecological relevance of acquired genes remain unclear. Plant cell wall degradation by HGT-derived enzymes is widespread in herbivorous insect lineages. Pectin is an abundant polysaccharide in the walls of growing parts of plants. We investigated the significance of horizontally acquired pectin-digesting polygalacturonases (PGs) of the leaf beetle Phaedon cochleariae. Using a CRISPR/Cas9-guided gene knockout approach, we generated a triple knockout and a quadruple PG-null mutant in order to investigate the enzymatic, biological, and ecological effects. We found that pectin-digestion 1) is exclusively linked to the horizontally acquired PGs from fungi, 2) became fixed in the host genome by gene duplication leading to functional redundancy, 3) compensates for nutrient-poor diet by making the nutritious cell contents more accessible, and 4) facilitates the beetles development and survival. Our analysis highlights the selective advantage PGs provide to herbivorous insects and demonstrate the impact of HGT on the evolutionary success of leaf-feeding beetles, major contributors to species diversity.
Collapse
|
20
|
A genetically modified minipig model for Alzheimer’s disease with SORL1 haploinsufficiency. Cell Rep Med 2022; 3:100740. [PMID: 36099918 PMCID: PMC9512670 DOI: 10.1016/j.xcrm.2022.100740] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022]
Abstract
The established causal genes in Alzheimer’s disease (AD), APP, PSEN1, and PSEN2, are functionally characterized using biomarkers, capturing an in vivo profile reflecting the disease’s initial preclinical phase. Mutations in SORL1, encoding the endosome recycling receptor SORLA, are found in 2%–3% of individuals with early-onset AD, and SORL1 haploinsufficiency appears to be causal for AD. To test whether SORL1 can function as an AD causal gene, we use CRISPR-Cas9-based gene editing to develop a model of SORL1 haploinsufficiency in Göttingen minipigs, taking advantage of porcine models for biomarker investigations. SORL1 haploinsufficiency in young adult minipigs is found to phenocopy the preclinical in vivo profile of AD observed with APP, PSEN1, and PSEN2, resulting in elevated levels of β-amyloid (Aβ) and tau preceding amyloid plaque formation and neurodegeneration, as observed in humans. Our study provides functional support for the theory that SORL1 haploinsufficiency leads to endosome cytopathology with biofluid hallmarks of autosomal dominant AD. Minipig model of Alzheimer’s disease by CRISPR knockout of the causal gene SORL1 Young SORL1 het minipigs phenocopy a preclinical CSF biomarker profile of individuals with AD SORL1 haploinsufficiency causes enlarged endosomes similar to neuronal AD pathology A minipig model bridging the translational gap between AD mouse models and affected individuals
Collapse
|
21
|
Altered Expression of TMEM43 Causes Abnormal Cardiac Structure and Function in Zebrafish. Int J Mol Sci 2022; 23:ijms23179530. [PMID: 36076925 PMCID: PMC9455580 DOI: 10.3390/ijms23179530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022] Open
Abstract
Arrhythmogenic cardiomyopathy (ACM) is an inherited heart muscle disease caused by heterozygous missense mutations within the gene encoding for the nuclear envelope protein transmembrane protein 43 (TMEM43). The disease is characterized by myocyte loss and fibro-fatty replacement, leading to life-threatening ventricular arrhythmias and sudden cardiac death. However, the role of TMEM43 in the pathogenesis of ACM remains poorly understood. In this study, we generated cardiomyocyte-restricted transgenic zebrafish lines that overexpress eGFP-linked full-length human wild-type (WT) TMEM43 and two genetic variants (c.1073C>T, p.S358L; c.332C>T, p.P111L) using the Tol2-system. Overexpression of WT and p.P111L-mutant TMEM43 was associated with transcriptional activation of the mTOR pathway and ribosome biogenesis, and resulted in enlarged hearts with cardiomyocyte hypertrophy. Intriguingly, mutant p.S358L TMEM43 was found to be unstable and partially redistributed into the cytoplasm in embryonic and adult hearts. Moreover, both TMEM43 variants displayed cardiac morphological defects at juvenile stages and ultrastructural changes within the myocardium, accompanied by dysregulated gene expression profiles in adulthood. Finally, CRISPR/Cas9 mutants demonstrated an age-dependent cardiac phenotype characterized by heart enlargement in adulthood. In conclusion, our findings suggest ultrastructural remodeling and transcriptomic alterations underlying the development of structural and functional cardiac defects in TMEM43-associated cardiomyopathy.
Collapse
|
22
|
Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
Collapse
Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
| |
Collapse
|
23
|
Hu J, Su H, Cao H, Wei H, Fu X, Jiang X, Song Q, He X, Xu C, Luo K. AUXIN RESPONSE FACTOR7 integrates gibberellin and auxin signaling via interactions between DELLA and AUX/IAA proteins to regulate cambial activity in poplar. THE PLANT CELL 2022; 34:2688-2707. [PMID: 35435234 PMCID: PMC9252472 DOI: 10.1093/plcell/koac107] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/25/2022] [Indexed: 05/20/2023]
Abstract
Cambial development in the stems of perennial woody species is rigorously regulated by phytohormones. Auxin and gibberellin (GA) play crucial roles in stimulating cambial activity in poplar (Populus spp.). In this study, we show that the DELLA protein REPRESSOR of ga1-3 Like 1 (RGL1), AUXIN RESPONSE FACTOR 7 (ARF7), and Aux/INDOLE-3-ACETIC ACID 9 (IAA9) form a ternary complex that mediates crosstalk between the auxin and GA signaling pathways in poplar stems during cambial development. Biochemical analysis revealed that ARF7 physically interacts with RGL1 and IAA9 through distinct domains. The arf7 loss-of-function mutant showed markedly attenuated responses to auxin and GA, whereas transgenic poplar plants overexpressing ARF7 displayed strongly improved cambial activity. ARF7 directly binds to the promoter region of the cambial stem cell regulator WOX4 to modulate its expression, thus integrating auxin and GA signaling to regulate cambial activity. Furthermore, the direct activation of PIN-FORMED 1 expression by ARF7 in the RGL1-ARF7-IAA9 module increased GA-dependent cambial activity via polar auxin transport. Collectively, these findings reveal that the crosstalk between auxin and GA signaling mediated by the RGL1-ARF7-IAA9 module is crucial for the precise regulation of cambial development in poplar.
Collapse
Affiliation(s)
- Jian Hu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Huili Su
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hui Cao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongbin Wei
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuemei Jiang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Qin Song
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xinhua He
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Department of Land, Air and Water Resources, University of California at Davis, Davis, California 95616, USA
| | | | - Keming Luo
- Authors for correspondence: (K.L); (C.X.)
| |
Collapse
|
24
|
Kenny C, Dilshat R, Seberg HE, Van Otterloo E, Bonde G, Helverson A, Franke CM, Steingrímsson E, Cornell RA. TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes. PLoS Genet 2022; 18:e1010207. [PMID: 35580127 PMCID: PMC9159589 DOI: 10.1371/journal.pgen.1010207] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/01/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that TFAP2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the former necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.
Collapse
Affiliation(s)
- Colin Kenny
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hannah E. Seberg
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eric Van Otterloo
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Gregory Bonde
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Christopher M. Franke
- Department of Surgery, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Robert A. Cornell
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| |
Collapse
|
25
|
Tak YE, Boulay G, Lee L, Iyer S, Perry NT, Schultz HT, Garcia SP, Broye L, Horng JE, Rengarajan S, Naigles B, Volorio A, Sander JD, Gong J, Riggi N, Joung JK, Rivera MN. Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors. CELL GENOMICS 2022; 2. [PMID: 35967079 PMCID: PMC9374162 DOI: 10.1016/j.xgen.2022.100119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Y. Esther Tak
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Gaylor Boulay
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lukuo Lee
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nicholas T. Perry
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Hayley T. Schultz
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sara P. Garcia
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Liliane Broye
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Joy E. Horng
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Beverly Naigles
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Angela Volorio
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jeffry D. Sander
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jingyi Gong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
- Corresponding author
| | - J. Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Corresponding author
| | - Miguel N. Rivera
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Corresponding author
| |
Collapse
|
26
|
Cao HX, Vu GTH, Gailing O. From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. Int J Mol Sci 2022; 23:966. [PMID: 35055150 PMCID: PMC8780650 DOI: 10.3390/ijms23020966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.
Collapse
Affiliation(s)
- Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Giang Thi Ha Vu
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Gottingen, Germany
| |
Collapse
|
27
|
Baronio D, Chen YC, Decker AR, Enckell L, Fernández-López B, Semenova S, Puttonen HAJ, Cornell RA, Panula P. Vesicular monoamine transporter 2 (SLC18A2) regulates monoamine turnover and brain development in zebrafish. Acta Physiol (Oxf) 2022; 234:e13725. [PMID: 34403568 DOI: 10.1111/apha.13725] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/22/2023]
Abstract
AIM We aimed at identifying potential roles of vesicular monoamine transporter 2, also known as Solute Carrier protein 18 A2 (SLC18A2) (hereafter, Vmat2), in brain monoamine regulation, their turnover, behaviour and brain development using a novel zebrafish model. METHODS A zebrafish strain lacking functional Vmat2 was generated with the CRISPR/Cas9 system. Larval behaviour and heart rate were monitored. Monoamines and their metabolites were analysed with high-pressure liquid chromatography. Amine synthesising and degrading enzymes, and genes essential for brain development, were analysed with quantitative PCR, in situ hybridisation and immunocytochemistry. RESULTS The 5-bp deletion in exon 3 caused an early frameshift and was lethal within 2 weeks post-fertilisation. Homozygous mutants (hereafter, mutants) displayed normal low locomotor activity during night-time but aberrant response to illumination changes. In mutants dopamine, noradrenaline, 5-hydroxytryptamine and histamine levels were reduced, whereas levels of dopamine and 5-hydroxytryptamine metabolites were increased, implying elevated monoamine turnover. Consistently, there were fewer histamine, 5-hydroxytryptamine and dopamine immunoreactive cells. Cellular dopamine immunostaining, in wild-type larvae more prominent in tyrosine hydroxylase 1 (Th1)-expressing than in Th2-expressing neurons, was absent in mutants. Despite reduced dopamine levels, mutants presented upregulated dopamine-synthesising enzymes. Further, in mutants the number of histidine decarboxylase-expressing neurons was increased, notch1a and pax2a were downregulated in brain proliferative zones. CONCLUSION Lack of Vmat2 increases monoamine turnover and upregulates genes encoding amine-synthesising enzymes, including histidine decarboxylase. Notch1a and pax2a, genes implicated in stem cell development, are downregulated in mutants. The zebrafish vmat2 mutant strain may be a useful model to study how monoamine transport affects brain development and function, and for use in drug screening.
Collapse
Affiliation(s)
- Diego Baronio
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Yu-Chia Chen
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Amanda R Decker
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, USA
| | - Louise Enckell
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | | | | | | | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, USA
| | - Pertti Panula
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| |
Collapse
|
28
|
Choi JH, Duboue ER, Macurak M, Chanchu JM, Halpern ME. Specialized neurons in the right habenula mediate response to aversive olfactory cues. eLife 2021; 10:e72345. [PMID: 34878403 PMCID: PMC8691842 DOI: 10.7554/elife.72345] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
Hemispheric specializations are well studied at the functional level but less is known about the underlying neural mechanisms. We identified a small cluster of cholinergic neurons in the dorsal habenula (dHb) of zebrafish, defined by their expression of the lecithin retinol acyltransferase domain containing 2 a (lratd2a) gene and their efferent connections with a subregion of the ventral interpeduncular nucleus (vIPN). The lratd2a-expressing neurons in the right dHb are innervated by a subset of mitral cells from both the left and right olfactory bulb and are activated upon exposure to the odorant cadaverine that is repellent to adult zebrafish. Using an intersectional strategy to drive expression of the botulinum neurotoxin specifically in these neurons, we find that adults no longer show aversion to cadaverine. Mutants with left-isomerized dHb that lack these neurons are also less repelled by cadaverine and their behavioral response to alarm substance, a potent aversive cue, is diminished. However, mutants in which both dHb have right identity appear more reactive to alarm substance. The results implicate an asymmetric dHb-vIPN neural circuit in the processing of repulsive olfactory cues and in modulating the resultant behavioral response.
Collapse
Affiliation(s)
- Jung-Hwa Choi
- Carnegie Institution for Science, Department of EmbryologyBaltimoreUnited States
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
- Wilkes Honors College, Florida Atlantic UniversityJupiterUnited States
| | - Michelle Macurak
- Carnegie Institution for Science, Department of EmbryologyBaltimoreUnited States
| | - Jean-Michel Chanchu
- Carnegie Institution for Science, Department of EmbryologyBaltimoreUnited States
| | - Marnie E Halpern
- Carnegie Institution for Science, Department of EmbryologyBaltimoreUnited States
| |
Collapse
|
29
|
Cui Z, Liu H, Zhang H, Huang Z, Tian R, Li L, Fan W, Chen Y, Chen L, Zhang S, Das BC, Severinov K, Hitzeroth II, Debata PR, Jin Z, Liu J, Huang Z, Xie W, Xie H, Lang B, Ma J, Weng H, Tian X, Hu Z. The comparison of ZFNs, TALENs, and SpCas9 by GUIDE-seq in HPV-targeted gene therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1466-1478. [PMID: 34938601 PMCID: PMC8655392 DOI: 10.1016/j.omtn.2021.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/10/2021] [Indexed: 12/26/2022]
Abstract
Zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR-associated Cas9 endonucleases are three major generations of genome editing tools. However, no parallel comparison about the efficiencies and off-target activity of the three nucleases has been reported, which is critical for the final clinical decision. We for the first time developed the genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) method in ZFNs and TALENs with novel bioinformatics algorithms to evaluate the off-targets. By targeting human papillomavirus 16 (HPV16), we compared the performance of ZFNs, TALENs, and SpCas9 in vivo. Our data showed that ZFNs with similar targets could generate distinct massive off-targets (287–1,856), and the specificity could be reversely correlated with the counts of middle “G” in zinc finger proteins (ZFPs). We also compared the TALENs with different N-terminal domains (wild-type [WT]/αN/βN) and G recognition modules (NN/NH) and found the design (αN or NN) to improve the efficiency of TALEN inevitably increased off-targets. Finally, our results showed that SpCas9 was more efficient and specific than ZFNs and TALENs. Specifically, SpCas9 had fewer off-target counts in URR (SpCas9, n = 0; TALEN, n = 1; ZFN, n = 287), E6 (SpCas9, n = 0; TALEN, n = 7), and E7 (SpCas9, n = 4; TALEN, n = 36). Taken together, we suggest that for HPV gene therapies, SpCas9 is a more efficient and safer genome editing tool. Our off-target data could be used to improve the design of ZFNs and TALENs, and the universal in vivo off-target detection pipeline for three generations of artificial nucleases provided useful tools for genome engineering-based gene therapy.
Collapse
Affiliation(s)
- Zifeng Cui
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Hui Liu
- Department of Pathology, Xi’an People’s Hospital (Xi’an Fourth Hospital), Shaanxi, China
| | - Hongfeng Zhang
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhaoyue Huang
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Rui Tian
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Lifang Li
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Weiwen Fan
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Yili Chen
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Lijie Chen
- Graduate School, Bengbu Medical College, Bengbu, Anhui 233000, China
| | - Sen Zhang
- Graduate School, Bengbu Medical College, Bengbu, Anhui 233000, China
| | - Bhudev C. Das
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology 100 Novaya Street, Skolkovo, Moscow Region 143025, Russia
| | - Inga Isabel Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7701, South Africa
| | - Priya Ranjan Debata
- Department of Zoology, North Orissa University, Takatpur, Baripada, Odisha 757003, India
| | - Zhuang Jin
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Jiashuo Liu
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Zheying Huang
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Weiling Xie
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Hongxian Xie
- Generulor Company Bio-X Lab, Guangzhou 510006, Guangdong, China
| | - Bin Lang
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao 999078, China
| | - Ji Ma
- Department of Pathology, The Central Hospital of Sui Zhou, Hubei, China
| | - Haiyan Weng
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
- Corresponding author: Haiyan Weng, Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China.
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, Hubei, China
- Corresponding author: Xun Tian, Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, Hubei, China.
| | - Zheng Hu
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
- Corresponding author: Zheng Hu, Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China.
| |
Collapse
|
30
|
A supernumerary "B-sex" chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus. Curr Biol 2021; 31:4800-4809.e9. [PMID: 34496222 DOI: 10.1016/j.cub.2021.08.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 01/30/2023]
Abstract
Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.1,2 B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species3,4 that have often been considered as selfish genetic elements that behave as genome parasites.5,6 The observation that in some species Bs can be either restricted or predominant in one sex7-14 raised the interesting hypothesis that Bs could play a role in sex determination.15 The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a "B-sex" chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species.
Collapse
|
31
|
Ma J, Chen J, Louro B, Martins RS, Canario AV. Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
32
|
Nicolas HA, Hua K, Quigley H, Ivare J, Tesson F, Akimenko MA. A CRISPR/Cas9 zebrafish lamin A/C mutant model of muscular laminopathy. Dev Dyn 2021; 251:645-661. [PMID: 34599606 DOI: 10.1002/dvdy.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/13/2021] [Accepted: 09/16/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Lamin A/C gene (LMNA) mutations frequently cause cardiac and/or skeletal muscle diseases called striated muscle laminopathies. We created a zebrafish muscular laminopathy model using CRISPR/Cas9 technology to target the zebrafish lmna gene. RESULTS Heterozygous and homozygous lmna mutants present skeletal muscle damage at 1 day post-fertilization (dpf), and mobility impairment at 4 to 7 dpf. Cardiac structure and function analyses between 1 and 7 dpf show mild and transient defects in the lmna mutants compared to wild type (WT). Quantitative RT-PCR analysis of genes implicated in striated muscle laminopathies show a decrease in jun and nfκb2 expression in 7 dpf homozygous lmna mutants compared to WT. Homozygous lmna mutants have a 1.26-fold protein increase in activated Erk 1/2, kinases associated with striated muscle laminopathies, compared to WT at 7 dpf. Activated Protein Kinase C alpha (Pkc α), a kinase that interacts with lamin A/C and Erk 1/2, is also upregulated in 7 dpf homozygous lmna mutants compared to WT. CONCLUSIONS This study presents an animal model of skeletal muscle laminopathy where heterozygous and homozygous lmna mutants exhibit prominent skeletal muscle abnormalities during the first week of development. Furthermore, this is the first animal model that potentially implicates Pkc α in muscular laminopathies.
Collapse
Affiliation(s)
- Hannah A Nicolas
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Khang Hua
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Hailey Quigley
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Joshua Ivare
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Frédérique Tesson
- Interdisciplinary School of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Andrée Akimenko
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
33
|
Elorriaga E, Klocko AL, Ma C, du Plessis M, An X, Myburg AA, Strauss SH. Genetic containment in vegetatively propagated forest trees: CRISPR disruption of LEAFY function in Eucalyptus gives sterile indeterminate inflorescences and normal juvenile development. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1743-1755. [PMID: 33774917 PMCID: PMC8428835 DOI: 10.1111/pbi.13588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/27/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
Eucalyptus is among the most widely planted taxa of forest trees worldwide. However, its spread as an exotic or genetically engineered form can create ecological and social problems. To mitigate gene flow via pollen and seeds, we mutated the Eucalyptus orthologue of LEAFY (LFY) by transforming a Eucalyptus grandis × urophylla wild-type hybrid and two Flowering Locus T (FT) overexpressing (and flowering) lines with CRISPR Cas9 targeting its LFY orthologue, ELFY. We achieved high rates of elfy biallelic knockouts, often approaching 100% of transgene insertion events. Frameshift mutations and deletions removing conserved amino acids caused strong floral alterations, including indeterminacy in floral development and an absence of male and female gametes. These mutants were otherwise visibly normal and did not differ statistically from transgenic controls in juvenile vegetative growth rate or leaf morphology in greenhouse trials. Genes upstream or near to ELFY in the floral development pathway were overexpressed, whereas floral organ identity genes downstream of ELFY were severely depressed. We conclude that disruption of ELFY function appears to be a useful tool for sexual containment, without causing statistically significant or large adverse effects on juvenile vegetative growth or leaf morphology.
Collapse
Affiliation(s)
- Estefania Elorriaga
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
- Present address:
Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Amy L. Klocko
- Department of BiologyUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
| | - Cathleen Ma
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
| | - Marc du Plessis
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaSouth Africa
| | - Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijingChina
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
| |
Collapse
|
34
|
Ferre-Fernández JJ, Sorokina EA, Thompson S, Collery RF, Nordquist E, Lincoln J, Semina EV. Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome. Hum Mol Genet 2021; 29:2723-2735. [PMID: 32720677 DOI: 10.1093/hmg/ddaa163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022] Open
Abstract
The Forkhead Box C1 (FOXC1) gene encodes a forkhead/winged helix transcription factor involved in embryonic development. Mutations in this gene cause dysgenesis of the anterior segment of the eye, most commonly Axenfeld-Rieger syndrome (ARS), often with other systemic features. The developmental mechanisms and pathways regulated by FOXC1 remain largely unknown. There are two conserved orthologs of FOXC1 in zebrafish, foxc1a and foxc1b. To further examine the role of FOXC1 in vertebrates, we generated foxc1a and foxc1b single knockout zebrafish lines and bred them to obtain various allelic combinations. Three genotypes demonstrated visible phenotypes: foxc1a-/- single homozygous and foxc1-/- double knockout homozygous embryos presented with similar characteristics comprised of severe global vascular defects and early lethality, as well as microphthalmia, periocular edema and absence of the anterior chamber of the eye; additionally, fish with heterozygous loss of foxc1a combined with homozygosity for foxc1b (foxc1a+/-;foxc1b-/-) demonstrated craniofacial defects, heart anomalies and scoliosis. All other single and combined genotypes appeared normal. Analysis of foxc1 expression detected a significant increase in foxc1a levels in homozygous and heterozygous mutant eyes, suggesting a mechanism for foxc1a upregulation when its function is compromised; interestingly, the expression of another ARS-associated gene, pitx2, was responsive to the estimated level of wild-type Foxc1a, indicating a possible role for this protein in the regulation of pitx2 expression. Altogether, our results support a conserved role for foxc1 in the formation of many organs, consistent with the features observed in human patients, and highlight the importance of correct FOXC1/foxc1 dosage for vertebrate development.
Collapse
Affiliation(s)
- Jesús-José Ferre-Fernández
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena A Sorokina
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Samuel Thompson
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Ross F Collery
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Emily Nordquist
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Joy Lincoln
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA.,Division of Pediatric Cardiology, Herma Heart Institute, Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena V Semina
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA.,Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| |
Collapse
|
35
|
Chen Z, Zhu S, Kindig K, Wang S, Chou SW, Davis RW, Dercoli MR, Weaver H, Stepanyan R, McDermott BM. Tmc proteins are essential for zebrafish hearing where Tmc1 is not obligatory. Hum Mol Genet 2021; 29:2004-2021. [PMID: 32167554 DOI: 10.1093/hmg/ddaa045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
Perception of sound is initiated by mechanically gated ion channels at the tips of stereocilia. Mature mammalian auditory hair cells require transmembrane channel-like 1 (TMC1) for mechanotransduction, and mutations of the cognate genetic sequences result in dominant or recessive heritable deafness forms in humans and mice. In contrast, zebrafish lateral line hair cells, which detect water motion, require Tmc2a and Tmc2b. Here, we use standard and multiplex genome editing in conjunction with functional and behavioral assays to determine the reliance of zebrafish hearing and vestibular organs on Tmc proteins. Surprisingly, our approach using multiple mutant alleles demonstrates that hearing in zebrafish is not dependent on Tmc1, nor is it fully dependent on Tmc2a and Tmc2b. Hearing however is absent in triple-mutant zebrafish that lack Tmc1, Tmc2a and Tmc2b. These outcomes reveal a striking resemblance of Tmc protein reliance in the vestibular sensory epithelia of mammals to the maculae of zebrafish. Moreover, our findings disclose a logic of Tmc use where hearing depends on a complement of Tmc proteins beyond those employed to sense water motion.
Collapse
Affiliation(s)
- Zongwei Chen
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shaoyuan Zhu
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kayla Kindig
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shengxuan Wang
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shih-Wei Chou
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Robin Woods Davis
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michael R Dercoli
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hannah Weaver
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruben Stepanyan
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Brian M McDermott
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| |
Collapse
|
36
|
Ritchey B, Hai Q, Han J, Barnard J, Smith JD. Genetic variant in 3' untranslated region of the mouse pycard gene regulates inflammasome activity. eLife 2021; 10:e68203. [PMID: 34197316 PMCID: PMC8248980 DOI: 10.7554/elife.68203] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Quantitative trait locus mapping for interleukin-1β release after inflammasome priming and activation was performed on bone-marrow-derived macrophages (BMDM) from an AKRxDBA/2 mouse strain intercross. The strongest associated locus mapped very close to the Pycard gene on chromosome 7, which codes for the inflammasome adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC). The DBA/2 and AKR Pycard genes only differ at a single-nucleotide polymorphism (SNP) in their 3' untranslated region (UTR). DBA/2 vs. AKR BMDM had increased levels of Pycard mRNA expression and ASC protein, and increased inflammasome speck formation, which was associated with increased Pycard mRNA stability without an increased transcription rate. CRISPR/Cas9 gene editing was performed on DBA/2 embryonic stem cells to change the Pycard 3'UTR SNP from the DBA/2 to the AKR allele. This single base change significantly reduced Pycard expression and inflammasome activity after cells were differentiated into macrophages due to reduced Pycard mRNA stability.
Collapse
Affiliation(s)
- Brian Ritchey
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - Qimin Hai
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - Juying Han
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - Jonathan D Smith
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve UniversityClevelandUnited States
| |
Collapse
|
37
|
Bosada FM, Rivaud MR, Uhm JS, Verheule S, van Duijvenboden K, Verkerk AO, Christoffels VM, Boukens BJ. A Variant Noncoding Region Regulates Prrx1 and Predisposes to Atrial Arrhythmias. Circ Res 2021; 129:420-434. [PMID: 34092116 DOI: 10.1161/circresaha.121.319146] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Fernanda M Bosada
- Department of Medical Biology (F.M.B., J.-S.U., K.v.D., A.O.V., V.M.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Mathilde R Rivaud
- Department of Experimental Cardiology (M.R.R., A.O.V., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Jae-Sun Uhm
- Department of Medical Biology (F.M.B., J.-S.U., K.v.D., A.O.V., V.M.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands.,Department of Cardiology, Severance Hospital, College of Medicine, Yonsei University, Seoul, South Korea (J.-S.U.)
| | - Sander Verheule
- Department of Physiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, the Netherlands (S.V.)
| | - Karel van Duijvenboden
- Department of Medical Biology (F.M.B., J.-S.U., K.v.D., A.O.V., V.M.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Arie O Verkerk
- Department of Medical Biology (F.M.B., J.-S.U., K.v.D., A.O.V., V.M.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands.,Department of Experimental Cardiology (M.R.R., A.O.V., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology (F.M.B., J.-S.U., K.v.D., A.O.V., V.M.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology (F.M.B., J.-S.U., K.v.D., A.O.V., V.M.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands.,Department of Experimental Cardiology (M.R.R., A.O.V., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| |
Collapse
|
38
|
Siva N, Gupta S, Gupta A, Shukla JN, Malik B, Shukla N. Genome-editing approaches and applications: a brief review on CRISPR technology and its role in cancer. 3 Biotech 2021; 11:146. [PMID: 33732568 PMCID: PMC7910401 DOI: 10.1007/s13205-021-02680-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/05/2021] [Indexed: 02/08/2023] Open
Abstract
The development of genome-editing technologies in 1970s has discerned a new beginning in the field of science. Out of different genome-editing approaches such as Zing-finger nucleases, TALENs, and meganucleases, clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR/Cas9) is a recent and versatile technology that has the ability of making changes to the genome of different organisms with high specificity. Cancer is a complex process that is characterized by multiple genetic and epigenetic changes resulting in abnormal cell growth and proliferation. As cancer is one of the leading causes of deaths worldwide, a large number of studies are done to understand the molecular mechanisms underlying the development of cancer. Because of its high efficiency and specificity, CRISPR/Cas9 has emerged as a novel and powerful tool in the field of cancer research. CRISPR/Cas9 has the potential to accelerate cancer research by dissecting tumorigenesis process, generating animal and cellular models, and identify drug targets for chemotherapeutic approaches. However, despite having tremendous potential, there are certain challenges associated with CRISPR/Cas9 such as safe delivery to the target, potential off-target effects and its efficacy which needs to be addressed prior to its clinical application. In this review, we give a gist of different genome-editing technologies with a special focus on CRISPR/Cas9 development, its mechanism of action and its applications, especially in different type of cancers. We also highlight the importance of CRISPR/Cas9 in generating animal models of different cancers. Finally, we present an overview of the clinical trials and discuss the challenges associated with translating CRISPR/Cas9 in clinical use.
Collapse
Affiliation(s)
- Narmadhaa Siva
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
| | - Ayam Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer, India
| | - Babita Malik
- Department of Chemistry, Manipal University Jaipur, Jaipur, India
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
- Department of Chemistry, Manipal University Jaipur, Jaipur, India
| |
Collapse
|
39
|
Laverde-Paz MJ, Nuytemans K, Wang L, Vance JM, Pericak-Vance MA, Dykxhoorn DM, Cukier HN. Derivation of stem cell line UMi028-A-2 containing a CRISPR/Cas9 induced Alzheimer's disease risk variant p.S1038C in the TTC3 gene. Stem Cell Res 2021; 52:102258. [PMID: 33626494 DOI: 10.1016/j.scr.2021.102258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/28/2022] Open
Abstract
The UMi028-A-2 human induced pluripotent stem cell line carries a homozygous mutation (rs377155188, C>G, p.S1038C) in the tetratricopeptide repeat domain 3 (TTC3) gene that was introduced via CRISPR/Cas9 genome editing. The line was originally derived from a neurologically normal male and has been thoroughly characterized following editing. The p.S1038C variant has been shown to potentially contribute to the risk of late onset Alzheimer's disease and is a resource to further investigate the consequences of TTC3 and this alteration in disease pathology.
Collapse
Affiliation(s)
- Mayra Juliana Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136.
| |
Collapse
|
40
|
Ho HKY, Bigliardi PL, Stelmashenko O, Ramasamy S, Postlethwaite M, Bigliardi-Qi M. Functionally expressed bitter taste receptor TAS2R14 in human epidermal keratinocytes serves as a chemosensory receptor. Exp Dermatol 2021; 30:216-225. [PMID: 33253444 DOI: 10.1111/exd.14250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/30/2020] [Accepted: 11/23/2020] [Indexed: 01/23/2023]
Abstract
Traditionally, it is theorized that skin sensation is initiated when cutaneous sensory afferents and Merkel cells receive sensory stimuli, while epidermal keratinocytes were deemed to have no role. However, mounting evidence has shown that keratinocytes can initiate skin sensation by receiving sensory stimuli and transmitting sensory information to sensory afferents. Knowledge regarding the mechanisms by which keratinocytes receive exogenous stimuli is limited, with TRP channels and olfactory receptors having been proposed to serve as receptors for exogenous stimuli in keratinocytes. Recently, expression analyses have demonstrated the expression of multiple TAS2R genes in human skin. TAS2Rs are chemosensory GPCRs employed by taste cells to detect bitter-tasting substances. However, only subtypes TAS2R1 and TAS2R38 have been characterized in epidermal keratinocytes. We present evidence suggesting that subtype TAS2R14 is functionally expressed in epidermal keratinocytes. TAS2R14 transcripts and protein were detected in primary and N/TERT-1 keratinocytes. Additionally, keratinocytes responded to α-thujone, a TAS2R14 ligand, with an increase in intracellular free Ca2+ concentration. The tastant-evoked Ca2+ signals were found to be mediated by wild-type TAS2R14 and heterotrimeric G proteins. We conclude that TAS2R14 serves as a chemosensory receptor in epidermal keratinocytes and hypothesize that it enables the cells to recognize potentially harmful chemical substances.
Collapse
Affiliation(s)
- Hilary Kung-Yu Ho
- Agency for Science, Technology and Research, Institute of Medical Biology, Singapore, Singapore
| | - Paul Lorenz Bigliardi
- Department of Dermatology, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Olga Stelmashenko
- Agency for Science, Technology and Research, Institute of Medical Biology, Singapore, Singapore
| | - Srinivas Ramasamy
- Agency for Science, Technology and Research, Skin Research Institute Singapore, Singapore, Singapore
| | - Michael Postlethwaite
- Agency for Science, Technology and Research, Institute of Medical Biology, Singapore, Singapore
| | - Mei Bigliardi-Qi
- Department of Dermatology, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| |
Collapse
|
41
|
de Vos IJHM, Wong ASW, Taslim J, Ong SLM, Syder NC, Goggi JL, Carney TJ, van Steensel MAM. The novel zebrafish model pretzel demonstrates a central role for SH3PXD2B in defective collagen remodelling and fibrosis in Frank-Ter Haar syndrome. Biol Open 2020; 9:bio054270. [PMID: 33234702 PMCID: PMC7790187 DOI: 10.1242/bio.054270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/05/2020] [Indexed: 11/20/2022] Open
Abstract
Frank-Ter Haar syndrome (FTHS, MIM #249420) is a rare skeletal dysplasia within the defective collagen remodelling spectrum (DECORS), which is characterised by craniofacial abnormalities, skeletal malformations and fibrotic soft tissues changes including dermal fibrosis and joint contractures. FTHS is caused by homozygous or compound heterozygous loss-of-function mutation or deletion of SH3PXD2B (Src homology 3 and Phox homology domain-containing protein 2B; MIM #613293). SH3PXD2B encodes an adaptor protein with the same name, which is required for full functionality of podosomes, specialised membrane structures involved in extracellular matrix (ECM) remodelling. The pathogenesis of DECORS is still incompletely understood and, as a result, therapeutic options are limited. We previously generated an mmp14a/b knockout zebrafish and demonstrated that it primarily mimics the DECORS-related bone abnormalities. Here, we present a novel sh3pxd2b mutant zebrafish, pretzel, which primarily reflects the DECORS-related dermal fibrosis and contractures. In addition to relatively mild skeletal abnormalities, pretzel mutants develop dermal and musculoskeletal fibrosis, contraction of which seems to underlie grotesque deformations that include kyphoscoliosis, abdominal constriction and lateral folding. The discrepancy in phenotypes between mmp14a/b and sh3pxd2b mutants suggests that in fish, as opposed to humans, there are differences in spatiotemporal dependence of ECM remodelling on either sh3pxd2b or mmp14a/b The pretzel model presented here can be used to further delineate the underlying mechanism of the fibrosis observed in DECORS, as well as screening and subsequent development of novel drugs targeting DECORS-related fibrosis.This paper has an associated First Person interview with the first author of the article.
Collapse
Affiliation(s)
- Ivo J H M de Vos
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), 308232, Singapore
| | - Arnette Shi Wei Wong
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), 308232, Singapore
| | - Jason Taslim
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), 308232, Singapore
| | - Sheena Li Ming Ong
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), 138648, Singapore
| | - Nicole C Syder
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), 308232, Singapore
| | - Julian L Goggi
- Singapore Bioimaging Consortium (SBIC), Agency for Science, Technology and Research (A*STAR), 138667, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 117593, Singapore
| | - Thomas J Carney
- Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), 636921, Singapore
| | - Maurice A M van Steensel
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), 308232, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), 636921, Singapore
| |
Collapse
|
42
|
Okada K, Takada S. The second pharyngeal pouch is generated by dynamic remodeling of endodermal epithelium in zebrafish. Development 2020; 147:dev194738. [PMID: 33158927 DOI: 10.1242/dev.194738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/28/2020] [Indexed: 11/20/2022]
Abstract
Pharyngeal arches (PAs) are segmented by endodermal outpocketings called pharyngeal pouches (PPs). Anterior and posterior PAs appear to be generated by different mechanisms, but it is unclear how the anterior and posterior PAs combine. Here, we addressed this issue with precise live imaging of PP development and cell tracing of pharyngeal endoderm in zebrafish embryos. We found that two endodermal bulges are initially generated in the future second PP (PP2) region, which separates anterior and posterior PAs. Subsequently, epithelial remodeling causes contact between these two bulges, resulting in the formation of mature PP2 with a bilayered morphology. The rostral and caudal bulges develop into the operculum and gill, respectively. Development of the caudal PP2 and more posterior PPs is affected by impaired retinoic acid signaling or pax1a/b dysfunction, suggesting that the rostral front of posterior PA development corresponds to the caudal PP2. Our study clarifies an aspect of PA development that is essential for generation of a seamless array of PAs in zebrafish.
Collapse
Affiliation(s)
- Kazunori Okada
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaijicho, Okazaki 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Shinji Takada
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaijicho, Okazaki 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
- Department for Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| |
Collapse
|
43
|
Koh A, Tao S, Jing Goh Y, Chaganty V, See K, Purushothaman K, Orbán L, Mathuru AS, Wohland T, Winkler C. A Neurexin2aa deficiency results in axon pathfinding defects and increased anxiety in zebrafish. Hum Mol Genet 2020; 29:3765-3780. [PMID: 33276371 DOI: 10.1093/hmg/ddaa260] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/04/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022] Open
Abstract
Neurexins are presynaptic transmembrane proteins that control synapse activity and are risk factors for autism spectrum disorder. Zebrafish, a popular model for behavioral studies, has six neurexin genes, but their functions in embryogenesis and behavior remain largely unknown. We have previously reported that nrxn2a is aberrantly spliced and specifically dysregulated in motor neurons (MNs) in models of spinal muscular atrophy. In this study, we generated nrxn2aa-/- mutants by CRISPR/Cas9 to understand nrxn2aa function at the zebrafish neuromuscular junction (NMJ) and to determine the effects of its deficiency on adult behavior. Homozygous mutant embryos derived from heterozygous parents did not show obvious defects in axon outgrowth or synaptogenesis of MNs. In contrast, maternal-zygotic (MZ) nrxn2aa-/- mutants displayed extensively branched axons and defective MNs, suggesting a cell-autonomous role for maternally provided nrxn2aa in MN development. Analysis of the NMJs revealed enlarged choice points in MNs of mutant larvae and reduced co-localization of pre- and post-synaptic terminals, indicating impaired synapse formation. Severe early NMJ defects partially recovered in late embryos when mutant transcripts became strongly upregulated. Ultimately, however, the induced defects resulted in muscular atrophy symptoms in adult MZ mutants. Zygotic homozygous mutants developed normally but displayed increased anxiety at adult stages. Together, our data demonstrate an essential role for maternal nrxn2aa in NMJ synapse establishment, while zygotic nrxn2aa expression appears dispensable for synapse maintenance. The viable nrxn2aa-/- mutant furthermore serves as a novel model to study how an increase in anxiety-like behaviors impacts other deficits.
Collapse
Affiliation(s)
- Angela Koh
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Shijie Tao
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yun Jing Goh
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Vindhya Chaganty
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Kelvin See
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | | | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Ajay S Mathuru
- Yale-NUS College, Singapore 138527, Singapore.,Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| |
Collapse
|
44
|
Bhat MA, Bhat MA, Kumar V, Wani IA, Bashir H, Shah AA, Rahman S, Jan AT. The era of editing plant genomes using CRISPR/Cas: A critical appraisal. J Biotechnol 2020; 324:34-60. [DOI: 10.1016/j.jbiotec.2020.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
|
45
|
Shewade LH, Schoephoerster JA, Patmann MD, Kulkarni SS, Buchholz DR. Corticosterone Is Essential for Survival Through Frog Metamorphosis. Endocrinology 2020; 161:5938994. [PMID: 33099610 DOI: 10.1210/endocr/bqaa193] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Indexed: 12/12/2022]
Abstract
Thyroid hormone (TH) is required for frog metamorphosis, and corticosterone (CORT) increases TH signaling to accelerate metamorphic progression. However, a requirement for CORT in metamorphosis has been difficult to assess prior to the recent development of gene-editing technologies. We addressed this long-standing question using transcription activator-like effector nuclease (TALEN) gene disruption to knock out proopiomelanocortin (pomc) and disrupt CORT production in Xenopus tropicalis. As expected, mutant tadpoles had a reduced peak of plasma CORT at metamorphosis with correspondingly reduced expression of the CORT-response gene Usher syndrome type-1G (ush1g). Mutants had reduced rates of growth and development and exhibited lower expression levels of 2 TH response genes, Krüppel-like factor 9 (klf9) and TH receptor β (thrb). In response to exogenous TH, mutants had reduced TH response gene induction and slower morphological change. Importantly, death invariably occurred during tail resorption, unless rescued by exogenous CORT and, remarkably, by exogenous TH. The ability of exogenous TH by itself to overcome death in pomc mutants indicates that the CORT-dependent increase in TH signaling may ensure functional organ transformation required for survival through metamorphosis and/or may shorten the nonfeeding metamorphic transition to avoid lethal inanition.
Collapse
Affiliation(s)
- Leena H Shewade
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | | | - Matthew D Patmann
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Saurabh S Kulkarni
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| |
Collapse
|
46
|
Bruce HS, Patel NH. Knockout of crustacean leg patterning genes suggests that insect wings and body walls evolved from ancient leg segments. Nat Ecol Evol 2020; 4:1703-1712. [PMID: 33262517 DOI: 10.1038/s41559-020-01349-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/15/2020] [Indexed: 01/06/2023]
Abstract
The origin of insect wings has long been debated. Central to this debate is whether wings are a novel structure on the body wall resulting from gene co-option, or evolved from an exite (outgrowth; for example, a gill) on the leg of an ancestral crustacean. Here, we report the phenotypes for the knockout of five leg patterning genes in the crustacean Parhyale hawaiensis and compare these with their previously published phenotypes in Drosophila and other insects. This leads to an alignment of insect and crustacean legs that suggests that two leg segments that were present in the common ancestor of insects and crustaceans were incorporated into the insect body wall, moving the proximal exite of the leg dorsally, up onto the back, to later form insect wings. Our results suggest that insect wings are not novel structures, but instead evolved from existing, ancestral structures.
Collapse
Affiliation(s)
- Heather S Bruce
- University of California, Berkeley, Berkeley, CA, USA. .,Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| |
Collapse
|
47
|
Song P, Fogerty J, Cianciolo LT, Stupay R, Perkins BD. Cone Photoreceptor Degeneration and Neuroinflammation in the Zebrafish Bardet-Biedl Syndrome 2 ( bbs2) Mutant Does Not Lead to Retinal Regeneration. Front Cell Dev Biol 2020; 8:578528. [PMID: 33324636 PMCID: PMC7726229 DOI: 10.3389/fcell.2020.578528] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/03/2020] [Indexed: 11/17/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a heterogeneous and pleiotropic autosomal recessive disorder characterized by obesity, retinal degeneration, polydactyly, renal dysfunction, and mental retardation. BBS results from defects in primary and sensory cilia. Mutations in 21 genes have been linked to BBS and proteins encoded by 8 of these genes form a multiprotein complex termed the BBSome. Mutations in BBS2, a component of the BBSome, result in BBS as well as non-syndromic retinal degeneration in humans and rod degeneration in mice, but the role of BBS2 in cone photoreceptor survival is not clear. We used zebrafish bbs2–/– mutants to better understand how loss of bbs2 leads to photoreceptor degeneration. Zebrafish bbs2–/– mutants exhibited impaired visual function as larvae and adult zebrafish underwent progressive cone photoreceptor degeneration. Cone degeneration was accompanied by increased numbers of activated microglia, indicating an inflammatory response. Zebrafish exhibit a robust ability to regenerate lost photoreceptors following retinal damage, yet cone degeneration and inflammation was insufficient to trigger robust Müller cell proliferation. In contrast, high intensity light damage stimulated Müller cell proliferation and photoreceptor regeneration in both wild-type and bbs2–/– mutants, although the bbs2–/– mutants could only restore cones to pre-damaged densities. In summary, these findings suggest that cone degeneration leads to an inflammatory response in the retina and that BBS2 is necessary for cone survival. The zebrafish bbs2 mutant also represents an ideal model to identify mechanisms that will enhance retinal regeneration in degenerating diseases.
Collapse
Affiliation(s)
- Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Lauren T Cianciolo
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Rachel Stupay
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Brian D Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| |
Collapse
|
48
|
Klapholz B, Levy H, Kumbha R, Hosny N, D'Angelo ME, Hering BJ, Burlak C. Highly efficient multiplex genetic engineering of porcine primary fetal fibroblasts. Surg Open Sci 2020; 4:26-31. [PMID: 33937740 PMCID: PMC8074785 DOI: 10.1016/j.sopen.2020.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/30/2020] [Accepted: 11/06/2020] [Indexed: 10/30/2022] Open
Abstract
Background Genetically engineered porcine donors are a potential solution for the shortage of human organs for transplantation. Incompatibilities between humans and porcine donors are largely due to carbohydrate xenoantigens on the surface of porcine cells, provoking an immune response which leads to xenograft rejection. Materials and Methods Multiplex genetic knockout of GGTA1, β4GalNT2, and CMAH is predicted to increase the rate of xenograft survival, as described previously for GGTA1. In this study, the clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein 9 system was used to target genes relevant to xenotransplantation, and a method for highly efficient editing of multiple genes in primary porcine fibroblasts was described. Results Editing efficiencies greater than 85% were achieved for knockout of GGTA1, β4GalNT2, and CMAH. Conclusion The high-efficiency protocol presented here reduces scale and cost while accelerating the production of genetically engineered primary porcine fibroblast cells for in vitro studies and the production of animal models.
Collapse
Affiliation(s)
- Benjamin Klapholz
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, UK
| | - Heather Levy
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Ramesh Kumbha
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Nora Hosny
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Michael E D'Angelo
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, UK
| | - Bernhard J Hering
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Christopher Burlak
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota Medical School, Minneapolis, MN, USA
| |
Collapse
|
49
|
Jewett CE, Appel BH, Prekeris R. The Rab11 effectors Fip5 and Fip1 regulate zebrafish intestinal development. Biol Open 2020; 9:bio055822. [PMID: 32973079 PMCID: PMC7595698 DOI: 10.1242/bio.055822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/09/2020] [Indexed: 01/09/2023] Open
Abstract
The Rab11 apical recycling endosome pathway is a well-established regulator of polarity and lumen formation; however, Rab11-vesicular trafficking also directs a diverse array of other cellular processes, raising the question of how Rab11 vesicles achieve specificity in space, time and content of cargo delivery. In part, this specificity is achieved through effector proteins, yet the role of Rab11 effector proteins in vivo remains vague. Here, we use CRISPR/Cas9 gene editing to study the role of the Rab11 effector Fip5 during zebrafish intestinal development. Zebrafish contain two paralogous genes, fip5a and fip5b, that are orthologs of human FIP5 We find that fip5a- and fip5b-mutant fish show phenotypes characteristic of microvillus inclusion disease, including microvilli defects and lysosomal accumulation. Single and double mutant analyses suggest that fip5a and fip5b function in parallel and regulate trafficking pathways required for assembly of keratin at the terminal web. Remarkably, in some genetic backgrounds, the absence of Fip5 triggers protein upregulation of a closely related family member, Fip1. This compensation mechanism occurs both during zebrafish intestinal development and in tissue culture models of lumenogenesis. In conclusion, our data implicate the Rab11 effectors Fip5 and Fip1 in a trafficking pathway required for apical microvilli formation.
Collapse
Affiliation(s)
- Cayla E Jewett
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Bruce H Appel
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| |
Collapse
|
50
|
Identification and Characterization of a Transcribed Distal Enhancer Involved in Cardiac Kcnh2 Regulation. Cell Rep 2020; 28:2704-2714.e5. [PMID: 31484079 DOI: 10.1016/j.celrep.2019.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 06/05/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. Mutations in KCNH2 that cause a reduction of the repolarizing current can result in cardiac arrhythmias associated with long-QT syndrome. Here, we investigate the regulation of KCNH2 and identify multiple active enhancers. A transcribed enhancer ∼85 kbp downstream of Kcnh2 physically contacts the promoters of two Kcnh2 isoforms in a cardiac-specific manner in vivo. Knockdown of its ncRNA transcript results in reduced expression of Kcnh2b and two neighboring mRNAs, Nos3 and Abcb8, in vitro. Genomic deletion of the enhancer, including the ncRNA transcription start site, from the mouse genome causes a modest downregulation of both Kcnh2a and Kcnh2b in the ventricles. These findings establish that the regulation of Kcnh2a and Kcnh2b is governed by a complex regulatory landscape that involves multiple partially redundantly acting enhancers.
Collapse
|