1
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Xu Q, Zhang Y, Xu W, Liu D, Jin W, Chen X, Hong N. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. Nucleic Acids Res 2024; 52:3106-3120. [PMID: 38364856 PMCID: PMC11014328 DOI: 10.1093/nar/gkae095] [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: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Chromatin accessibility plays a critical role in the regulation of cell fate decisions. Although gene expression changes have been extensively profiled at the single-cell level during early embryogenesis, the dynamics of chromatin accessibility at cis-regulatory elements remain poorly studied. Here, we used a plate-based single-cell ATAC-seq method to profile the chromatin accessibility dynamics of over 10 000 nuclei from zebrafish embryos. We investigated several important time points immediately after zygotic genome activation (ZGA), covering key developmental stages up to dome. The results revealed key chromatin signatures in the first cell fate specifications when cells start to differentiate into enveloping layer (EVL) and yolk syncytial layer (YSL) cells. Finally, we uncovered many potential cell-type specific enhancers and transcription factor motifs that are important for the cell fate specifications.
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Affiliation(s)
- Qiushi Xu
- Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Yunlong Zhang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wei Xu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangdong, China
| | - Dong Liu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
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2
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Minařík M, Modrell MS, Gillis JA, Campbell AS, Fuller I, Lyne R, Micklem G, Gela D, Pšenička M, Baker CVH. Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. Front Cell Dev Biol 2024; 12:1327924. [PMID: 38562141 PMCID: PMC10982350 DOI: 10.3389/fcell.2024.1327924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.
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Affiliation(s)
- Martin Minařík
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Melinda S. Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - J. Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Alexander S. Campbell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Isobel Fuller
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - David Gela
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Clare V. H. Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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3
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Concha ML, Reig G. Origin, form and function of extraembryonic structures in teleost fishes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210264. [PMID: 36252221 PMCID: PMC9574637 DOI: 10.1098/rstb.2021.0264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/12/2022] [Indexed: 12/18/2022] Open
Abstract
Teleost eggs have evolved a highly derived early developmental pattern within vertebrates as a result of the meroblastic cleavage pattern, giving rise to a polar stratified architecture containing a large acellular yolk and a small cellular blastoderm on top. Besides the acellular yolk, the teleost-specific yolk syncytial layer (YSL) and the superficial epithelial enveloping layer are recognized as extraembryonic structures that play critical roles throughout embryonic development. They provide enriched microenvironments in which molecular feedback loops, cellular interactions and mechanical signals emerge to sculpt, among other things, embryonic patterning along the dorsoventral and left-right axes, mesendodermal specification and the execution of morphogenetic movements in the early embryo and during organogenesis. An emerging concept points to a critical role of extraembryonic structures in reinforcing early genetic and morphogenetic programmes in reciprocal coordination with the embryonic blastoderm, providing the necessary boundary conditions for development to proceed. In addition, the role of the enveloping cell layer in providing mechanical, osmotic and immunological protection during early stages of development, and the autonomous nutritional support provided by the yolk and YSL, have probably been key aspects that have enabled the massive radiation of teleosts to colonize every ecological niche on the Earth. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
- Miguel L. Concha
- Integrative Biology Program, Institute of Biomedical Sciences (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Santiago 8380453, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago 7800003, Chile
| | - Germán Reig
- Escuela de Tecnología Médica y del Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 7800003, Chile
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4
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Abstract
POUV is a relatively newly emerged class of POU transcription factors present in jawed vertebrates (Gnathostomata). The function of POUV-class proteins is inextricably linked to zygotic genome activation (ZGA). A large body of evidence now extends the role of these proteins to subsequent developmental stages. While some functions resemble those of other POU-class proteins and are related to neuroectoderm development, others have emerged de novo. The most notable of the latter functions is pluripotency control by Oct4 in mammals. In this review, we focus on these de novo functions in the best-studied species harbouring POUV proteins-zebrafish, Xenopus (anamniotes) and mammals (amniotes). Despite the broad diversity of their biological functions in vertebrates, POUV proteins exert a common feature related to their role in safeguarding the undifferentiated state of cells. Here we summarize numerous pieces of evidence for these specific functions of the POUV-class proteins and recap available loss-of-function data.
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Affiliation(s)
- Evgeny I. Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey N. Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
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5
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Zakeri S, Aminian H, Sadeghi S, Esmaeilzadeh-Gharehdaghi E, Razmara E. Krüppel-like factors in bone biology. Cell Signal 2022; 93:110308. [PMID: 35301064 DOI: 10.1016/j.cellsig.2022.110308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 12/27/2022]
Abstract
The krüppel-like factor (KLF) family is a group of zinc finger transcription factors and contributes to different cellular processes such as differentiation, proliferation, migration, and apoptosis. While different studies show the roles of this family in skeletal development-specifically in chondrocyte and osteocyte development and bone homeostasis-there are few reviews summarizing their importance. To fill this gap, this review discusses current knowledge on different functions of the KLF family during skeletal development, including their roles in stem cell maintenance and differentiation, cell apoptosis, and cell cycle. To understand the importance of the KLF family, we also review genotype-phenotype correlations in different animal models. We also discuss how KLF proteins function through different signaling pathways and display their paramount importance in skeletal development. To highlight their roles in cartilage- or bone-related cells, we also use single-cell RNA sequencing publicly available data on mouse hindlimb. We also challenge our knowledge of how the KLF family is epigenetically regulated-e.g., using DNA methylation, histone modifications, and noncoding RNAs-during chondrocyte and osteocyte development.
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Affiliation(s)
- Sina Zakeri
- Department of Veterinary Science, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Hesam Aminian
- Department of Biology, Faculty of Sciences, Nour Danesh Institute of Higher Education, Meymeh, Isfahan, Iran
| | - Soheila Sadeghi
- Department of Biology, Faculty of Basic Sciences, Sanandaj Branch, Islamic Azad University, Kurdistan, Iran
| | | | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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6
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Leon A, Subirana L, Magre K, Cases I, Tena JJ, Irimia M, Gomez-Skarmeta JL, Escriva H, Bertrand S. Gene regulatory networks of epidermal and neural fate choice in a chordate. Mol Biol Evol 2022; 39:6547258. [PMID: 35276009 PMCID: PMC9004418 DOI: 10.1093/molbev/msac055] [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] [Indexed: 11/16/2022] Open
Abstract
Neurons are a highly specialized cell type only found in metazoans. They can be scattered throughout the body or grouped together, forming ganglia or nerve cords. During embryogenesis, centralized nervous systems develop from the ectoderm, which also forms the epidermis. How pluripotent ectodermal cells are directed toward neural or epidermal fates, and to which extent this process is shared among different animal lineages, are still open questions. Here, by using micromere explants, we were able to define in silico the putative gene regulatory networks (GRNs) underlying the first steps of the epidermis and the central nervous system formation in the cephalochordate amphioxus. We propose that although the signal triggering neural induction in amphioxus (i.e., Nodal) is different from vertebrates, the main transcription factors implicated in this process are conserved. Moreover, our data reveal that transcription factors of the neural program seem to not only activate neural genes but also to potentially have direct inputs into the epidermal GRN, suggesting that the Nodal signal might also contribute to neural fate commitment by repressing the epidermal program. Our functional data on whole embryos support this result and highlight the complex interactions among the transcription factors activated by the signaling pathways that drive ectodermal cell fate choice in chordates.
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Affiliation(s)
- Anthony Leon
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Kevin Magre
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
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7
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Li H, Xu W, Xiang S, Tao L, Fu W, Liu J, Liu W, Xiao Y, Peng L. Defining the Pluripotent Marker Genes for Identification of Teleost Fish Cell Pluripotency During Reprogramming. Front Genet 2022; 13:819682. [PMID: 35222539 PMCID: PMC8874021 DOI: 10.3389/fgene.2022.819682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pluripotency is a transient state in early embryos, which is regulated by an interconnected network of pluripotency-related genes. The pluripotent state itself seems to be highly dynamic, which leads to significant differences in the description of induced pluripotent stem cells from different species at the molecular level. With the application of cell reprogramming technology in fish, the establishment of a set of molecular standards for defining pluripotency will be important for the research and potential application of induced pluripotent stem cells in fish. In this study, by BLAST search and expression pattern analysis, we screen out four pluripotent genes (Oct4, Nanog, Tdgf1, and Gdf3) in zebrafish (Danio rerio) and crucian carp (Carassius). These genes were highly expressed in the short period of early embryonic development, but significantly down-regulated after differentiation. Moreover, three genes (Oct4, Nanog and Tdgf1) have been verified that are suitable for identifying the pluripotency of induced pluripotent stem cells in zebrafish and crucian carp. Our study expands the understanding of the pluripotent markers of induced pluripotent stem cells in fish.
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Affiliation(s)
- Huajin Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenting Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Sijia Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Leiting Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Jinhui Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenbin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Liangyue Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Liangyue Peng,
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8
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Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nat Commun 2022; 13:788. [PMID: 35145080 PMCID: PMC8831532 DOI: 10.1038/s41467-022-28434-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 01/24/2022] [Indexed: 12/28/2022] Open
Abstract
Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that two factors modify chromatin in a largely independent manner. We distinguish four types of direct enhancers by differential requirements for Pou5f3 or Sox19b. We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of Pou5f3 and Sox19b leads to premature expression of genes, involved in regulation of organogenesis and differentiation. Zygotic genome activation in zebrafish relies on pluripotency transcription factors Pou5f3 and Sox19b. Here the authors investigate how these factors interact in vivo by analyzing the changes in chromatin state and time-resolved transcription in Pou5f3 and Sox19b single and double mutant embryos.
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9
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Zhang X, Wu Z, Bu M, Hu R, Zhang X, Li W, Chen L. The CCAAT/Enhancer Binding Protein Beta (cebpb) is essential for the development of enveloping layer (EVL) in zebrafish. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Wang X, Zhao J, Zhu Z. Exogenous Expression of pou5f3 Facilitates the Development of Somatic Cell Nuclear Transfer Embryos in Zebrafish at the Early Stage. Cell Reprogram 2021; 23:191-197. [PMID: 34101505 DOI: 10.1089/cell.2021.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enucleated oocytes can reprogram differentiated nuclei to totipotency after somatic cell nuclear transfer (SCNT), which is valuable in understanding nuclear reprogramming and generating genetically modified animals. To date, reprogramming efficiency is low and the development of SCNT embryos is not going as well as anticipated. To further disclose the reprogramming mechanisms during SCNT zebrafish embryo development, we examined the expression patterns of transcription regulation factors and regulated them by mRNA and morpholino microinjection. In this study, we show that stem cell-related transcription factors are downregulated in zebrafish SCNT embryos at the blastula stage. Exogenous expression of pou5f3 at the single-cell stage improves SCNT embryo development from the blastula to the gastrula stage. We also found that exogenous expression of klf4 or sox2 decreases SCNT embryo development from the blastula to the gastrula stage, while expression of nanog is necessary for the development of SCNT embryos. Our results conclude that zebrafish pou5f3 facilitates the development of SCNT embryos from the blastula to gastrula stage.
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Affiliation(s)
- Xuegeng Wang
- College of Life Sciences, Peking University, Beijing, P.R. China.,Institute of Modern Aquaculture Science and Engineering, College of Life Sciences, South China Normal University, Guangzhou, P.R. China
| | - Jue Zhao
- College of Life Sciences, Peking University, Beijing, P.R. China
| | - Zuoyan Zhu
- College of Life Sciences, Peking University, Beijing, P.R. China
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11
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Parshina EA, Zaraisky AG, Martynova NY. The Role of Maternal pou5f3.3/oct60 Gene in the Regulation of Initial Stages of Tissue Differentiation during Xenopus laevis Embryogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020060242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Rogers KW, ElGamacy M, Jordan BM, Müller P. Optogenetic investigation of BMP target gene expression diversity. eLife 2020; 9:58641. [PMID: 33174840 PMCID: PMC7728441 DOI: 10.7554/elife.58641] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Signaling molecules activate distinct patterns of gene expression to coordinate embryogenesis, but how spatiotemporal expression diversity is generated is an open question. In zebrafish, a BMP signaling gradient patterns the dorsal-ventral axis. We systematically identified target genes responding to BMP and found that they have diverse spatiotemporal expression patterns. Transcriptional responses to optogenetically delivered high- and low-amplitude BMP signaling pulses indicate that spatiotemporal expression is not fully defined by different BMP signaling activation thresholds. Additionally, we observed negligible correlations between spatiotemporal expression and transcription kinetics for the majority of analyzed genes in response to BMP signaling pulses. In contrast, spatial differences between BMP target genes largely collapsed when FGF and Nodal signaling were inhibited. Our results suggest that, similar to other patterning systems, combinatorial signaling is likely to be a major driver of spatial diversity in BMP-dependent gene expression in zebrafish.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Mohammad ElGamacy
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.,Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.,Heliopolis Biotechnology Ltd, London, United Kingdom
| | - Benjamin M Jordan
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.,Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany
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13
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Parshina EA, Eroshkin FM, Оrlov EE, Gyoeva FK, Shokhina AG, Staroverov DB, Belousov VV, Zhigalova NA, Prokhortchouk EB, Zaraisky AG, Martynova NY. Cytoskeletal Protein Zyxin Inhibits the Activity of Genes Responsible for Embryonic Stem Cell Status. Cell Rep 2020; 33:108396. [PMID: 33207197 DOI: 10.1016/j.celrep.2020.108396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/14/2020] [Accepted: 10/26/2020] [Indexed: 10/22/2022] Open
Abstract
Zyxin is a cytoskeletal LIM-domain protein that regulates actin cytoskeleton assembly and gene expression. In the present work, we find that zyxin downregulation in Xenopus laevis embryos reduces the expression of numerous genes that regulate cell differentiation, but it enhances that of several genes responsible for embryonic stem cell status, specifically klf4, pou5f3.1, pou5f3.2, pou5f3.3, and vent2.1/2. For pou5f3 family genes (mammalian POU5F1/OCT4 homologs), we show that this effect is the result of mRNA stabilization due to complex formation with the Y-box protein Ybx1. When bound to Ybx1, zyxin interferes with the formation of these complexes, thereby stimulating pou5f3 mRNA degradation. In addition, in zebrafish embryos and human HEK293 cells, zyxin downregulation increases mRNA levels of the pluripotency genes KLF4, NANOG, and POU5F1/OCT4. Our findings indicate that zyxin may play a role as a switch among morphogenetic cell movement, differentiation, and embryonic stem cell status.
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Affiliation(s)
- Elena A Parshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Fedor M Eroshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Eugeny E Оrlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Fatima K Gyoeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Arina G Shokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda A Zhigalova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Egor B Prokhortchouk
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
| | - Natalia Y Martynova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
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14
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Krüppel-like factor 17 upregulates uterine corin expression and promotes spiral artery remodeling in pregnancy. Proc Natl Acad Sci U S A 2020; 117:19425-19434. [PMID: 32719113 DOI: 10.1073/pnas.2003913117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Spiral artery remodeling is an important physiological process in the pregnant uterus which increases blood flow to the fetus. Impaired spiral artery remodeling contributes to preeclampsia, a major disease in pregnancy. Corin, a transmembrane serine protease, is up-regulated in the pregnant uterus to promote spiral artery remodeling. To date, the mechanism underlying uterine corin up-regulation remains unknown. Here we show that Krüppel-like factor (KLF) 17 is a key transcription factor for uterine corin expression in pregnancy. In cultured human uterine endometrial cells, KLF17 binds to the CORIN promoter and enhances the promoter activity. Disruption of the KLF17 gene in the endometrial cells abolishes CORIN expression. In mice, Klf17 is up-regulated in the pregnant uterus. Klf17 deficiency prevents uterine Corin expression in pregnancy. Moreover, Klf17-deficient mice have poorly remodeled uterine spiral arteries and develop gestational hypertension and proteinuria. Together, our results reveal an important function of KLF17 in regulating Corin expression and uterine physiology in pregnancy.
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15
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Characterization of biklf/klf17-deficient zebrafish in posterior lateral line neuromast and hatching gland development. Sci Rep 2019; 9:13680. [PMID: 31558744 PMCID: PMC6763433 DOI: 10.1038/s41598-019-50149-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/29/2019] [Indexed: 11/08/2022] Open
Abstract
Krüpple-like factors (Klfs) are highly conserved zinc-finger transcription factors that regulate various developmental processes, such as haematopoiesis and cardiovascular development. In zebrafish, transient knockdown analysis of biklf/klf17 using antisense morpholino suggests the involvement of biklf/klf17 in primitive erythropoiesis and hatching gland development; however, the continuous physiological importance of klf17 remains uncharacterized under the genetic ablation of the klf17 gene among vertebrates. We established the klf17-disrupted zebrafish lines using the CRISPR/Cas9 technology and performed phenotypic analysis throughout early embryogenesis. We found that the klf17-deficient embryos exhibited abnormal lateral line neuromast deposition, whereas the production of primitive erythrocytes and haemoglobin production were observed in the klf17-deficient embryos. The expression of lateral line neuromast genes, klf17 and s100t, in the klf17-deficient embryos was detected in posterior lateral line neuromasts abnormally positioned at short intervals. Furthermore, the klf17-deficient embryos failed to hatch and died without hatching around 15 days post-fertilization (dpf), whereas the dechorionated klf17-deficient embryos and wild-type embryos were alive at 15 dpf. The klf17-deficient embryos abolished hatching gland cells and Ctsl1b protein expression, and eliminated the expression of polster and hatching gland marker genes, he1.1, ctsl1b and cd63. Thus, the klf17 gene plays important roles in posterior lateral line neuromast and hatching gland development.
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16
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Abstract
Soon after fertilization the zebrafish embryo generates the pool of cells that will give rise to the germline and the three somatic germ layers of the embryo (ectoderm, mesoderm and endoderm). As the basic body plan of the vertebrate embryo emerges, evolutionarily conserved developmental signaling pathways, including Bmp, Nodal, Wnt, and Fgf, direct the nearly totipotent cells of the early embryo to adopt gene expression profiles and patterns of cell behavior specific to their eventual fates. Several decades of molecular genetics research in zebrafish has yielded significant insight into the maternal and zygotic contributions and mechanisms that pattern this vertebrate embryo. This new understanding is the product of advances in genetic manipulations and imaging technologies that have allowed the field to probe the cellular, molecular and biophysical aspects underlying early patterning. The current state of the field indicates that patterning is governed by the integration of key signaling pathways and physical interactions between cells, rather than a patterning system in which distinct pathways are deployed to specify a particular cell fate. This chapter focuses on recent advances in our understanding of the genetic and molecular control of the events that impart cell identity and initiate the patterning of tissues that are prerequisites for or concurrent with movements of gastrulation.
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Affiliation(s)
- Florence L Marlow
- Icahn School of Medicine Mount Sinai Department of Cell, Developmental and Regenerative Biology, New York, NY, United States.
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17
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Baumgartner EA, Compton ZJ, Evans S, Topczewski J, LeClair EE. Identification of regulatory elements recapitulating early expression of L-plastin in the zebrafish enveloping layer and embryonic periderm. Gene Expr Patterns 2019; 32:53-66. [PMID: 30940554 PMCID: PMC6655599 DOI: 10.1016/j.gep.2019.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/22/2019] [Accepted: 03/24/2019] [Indexed: 12/18/2022]
Abstract
We have cloned and characterized an intronic fragment of zebrafish lymphocyte cytosolic protein 1 (lcp1, also called L-plastin) that drives expression to the zebrafish enveloping layer (EVL). L-plastin is a calcium-dependent actin-bundling protein belonging to the plastin/fimbrin family of proteins, and is necessary for the proper migration and attachment of several adult cell types, including leukocytes and osteoclasts. However, in zebrafish lcp1 is abundantly expressed much earlier, during differentiation of the EVL. The cells of this epithelial layer migrate collectively, spreading vegetally over the yolk. L-plastin expression persists into the larval periderm, a transient epithelial tissue that forms the first larval skin. This finding establishes that L-plastin is activated in two different embryonic waves, with a distinct regulatory switch between the early EVL and the later leukocyte. To better study L-plastin expressing cells we attempted CRISPR/Cas9 homology-driven recombination (HDR) to insert a self-cleaving peptide (Cre-P2A-EGFP-CAAX) downstream of the native lcp1 promoter. This produced a stable zebrafish line expressing Cre recombinase in EVL nuclei and green fluorescence in EVL cell membranes. In vivo tracking of these labeled cells provided enhanced views of EVL migration behavior, membrane extensions, and mitotic events. Finally, we experimentally dissected key elements of the targeted lcp1 locus, discovering a ∼300 bp intronic sequence sufficient to drive EVL expression. The lcp1: Cre-P2A-EGFP-CAAX zebrafish should be useful for studying enveloping layer specification, gastrulation movements and periderm development in this widely used vertebrate model. In addition, the conserved regulatory sequences we have isolated predict that L-plastin orthologs may have a similar early expression pattern in other vertebrate embryos.
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Affiliation(s)
| | | | - Spencer Evans
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, USA
| | - Jacek Topczewski
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, USA; Department of Pediatrics, Northwestern University Feinberg School of Medicine, USA; Department of Biochemistry and Molecular Biology, Medical University of Lublin, Poland
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18
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Pawlak M, Kedzierska KZ, Migdal M, Karim AN, Ramilowski JA, Bugajski L, Hashimoto K, Marconi A, Piwocka K, Carninci P, Winata CL. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Genome Res 2019; 29:506-519. [PMID: 30760547 PMCID: PMC6396412 DOI: 10.1101/gr.244491.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/09/2019] [Indexed: 12/19/2022]
Abstract
Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mechanism still exist because little is known about their downstream targets and interactive regulatory network. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption in vivo, we performed time-series analyses of the transcriptome and genome-wide chromatin accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. Loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile, indicating their role in heart development. Among regions with differential chromatin accessibility in mutants were highly conserved noncoding elements that represent putative enhancers driving heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart tube morphogenesis and looping, and were associated with metabolic shift and hematopoietic/cardiac fate switch during CM maturation. Our results revealed the dynamic regulatory landscape throughout heart development and identified interactive molecular networks driving key events of heart morphogenesis.
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Affiliation(s)
- Michal Pawlak
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Katarzyna Z Kedzierska
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Abu Nahia Karim
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | | | - Lukasz Bugajski
- Nencki Institute of Experimental Biology, Laboratory of Cytometry, 02-093 Warsaw, Poland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Aleksandra Marconi
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Katarzyna Piwocka
- Nencki Institute of Experimental Biology, Laboratory of Cytometry, 02-093 Warsaw, Poland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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19
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Park CS, Lewis A, Chen T, Lacorazza D. Concise Review: Regulation of Self-Renewal in Normal and Malignant Hematopoietic Stem Cells by Krüppel-Like Factor 4. Stem Cells Transl Med 2019; 8:568-574. [PMID: 30790473 PMCID: PMC6525558 DOI: 10.1002/sctm.18-0249] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/07/2019] [Indexed: 12/11/2022] Open
Abstract
Pluripotent and tissue‐specific stem cells, such as blood‐forming stem cells, are maintained through a balance of quiescence, self‐renewal, and differentiation. Self‐renewal is a specialized cell division that generates daughter cells with the same features as the parental stem cell. Although many factors are involved in the regulation of self‐renewal, perhaps the most well‐known factors are members of the Krüppel‐like factor (KLF) family, especially KLF4, because of the landmark discovery that this protein is required to reprogram somatic cells into induced pluripotent stem cells. Because KLF4 regulates gene expression through transcriptional activation or repression via either DNA binding or protein‐to‐protein interactions, the outcome of KLF4‐mediated regulation largely depends on the cellular context, cell cycle regulation, chromatin structure, and the presence of oncogenic drivers. This study first summarizes the current understanding of the regulation of self‐renewal by KLF proteins in embryonic stem cells through a KLF circuitry and then delves into the potential function of KLF4 in normal hematopoietic stem cells and its emerging role in leukemia‐initiating cells from pediatric patients with T‐cell acute lymphoblastic leukemia via repression of the mitogen‐activated protein kinase 7 pathway. stem cells translational medicine2019;8:568–574
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Affiliation(s)
- Chun S Park
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Andrew Lewis
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Taylor Chen
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Daniel Lacorazza
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
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20
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Nagasawa T, Kawaguchi M, Yano T, Isoyama S, Yasumasu S, Okabe M. Translocation of promoter-conserved hatching enzyme genes with intron-loss provides a new insight in the role of retrocopy during teleostean evolution. Sci Rep 2019; 9:2448. [PMID: 30792427 PMCID: PMC6385490 DOI: 10.1038/s41598-019-38693-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/17/2018] [Indexed: 11/12/2022] Open
Abstract
The hatcing enzyme gene (HE) encodes a protease that is indispensable for the hatching process and is conserved during vertebrate evolution. During teleostean evolution, it is known that HE experienced a drastic transfiguration of gene structure, namely, losing all of its introns. However, these facts are contradiction with each other, since intron-less genes typically lose their original promoter because of duplication via mature mRNA, called retrocopy. Here, using a comparative genomic assay, we showed that HEs have changed their genomic location several times, with the evolutionary timings of these translocations being identical to those of intron-loss. We further showed that HEs maintain the promoter sequence upstream of them after translocation. Therefore, teleostean HEs are unique genes which have changed intra- (exon-intron) and extra-genomic structure (genomic loci) several times, although their indispensability for the reproductive process of hatching implies that HE genes are translocated by retrocopy with their promoter sequence.
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Affiliation(s)
- Tatsuki Nagasawa
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Research Fellow of the Japan Society for the Promotion of Science (JSPS), Tokyo, 102-0083, Japan.,Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Tohru Yano
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Sho Isoyama
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
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21
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Pfeffer PL. Building Principles for Constructing a Mammalian Blastocyst Embryo. BIOLOGY 2018; 7:biology7030041. [PMID: 30041494 PMCID: PMC6164496 DOI: 10.3390/biology7030041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
The self-organisation of a fertilised egg to form a blastocyst structure, which consists of three distinct cell lineages (trophoblast, epiblast and hypoblast) arranged around an off-centre cavity, is unique to mammals. While the starting point (the zygote) and endpoint (the blastocyst) are similar in all mammals, the intervening events have diverged. This review examines and compares the descriptive and functional data surrounding embryonic gene activation, symmetry-breaking, first and second lineage establishment, and fate commitment in a wide range of mammalian orders. The exquisite detail known from mouse embryogenesis, embryonic stem cell studies and the wealth of recent single cell transcriptomic experiments are used to highlight the building principles underlying early mammalian embryonic development.
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Affiliation(s)
- Peter L Pfeffer
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
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22
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King BL, Rosenstein MC, Smith AM, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen Med 2018; 3:10. [PMID: 29872545 PMCID: PMC5973935 DOI: 10.1038/s41536-018-0049-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 12/16/2022] Open
Abstract
Regeneration is an endogenous process of tissue repair that culminates in complete restoration of tissue and organ function. While regenerative capacity in mammals is limited to select tissues, lower vertebrates like zebrafish and salamanders are endowed with the capacity to regenerate entire limbs and most adult tissues, including heart muscle. Numerous profiling studies have been conducted using these research models in an effort to identify the genetic circuits that accompany tissue regeneration. Most of these studies, however, are confined to an individual injury model and/or research organism and focused primarily on protein encoding transcripts. Here we describe RegenDbase, a new database with the functionality to compare and contrast gene regulatory pathways within and across tissues and research models. RegenDbase combines pipelines that integrate analysis of noncoding RNAs in combination with protein encoding transcripts. We created RegenDbase with a newly generated comprehensive dataset for adult zebrafish heart regeneration combined with existing microarray and RNA-sequencing studies on multiple injured tissues. In this current release, we detail microRNA-mRNA regulatory circuits and the biological processes these interactions control during the early stages of heart regeneration. Moreover, we identify known and putative novel lncRNAs and identify their potential target genes based on proximity searches. We postulate that these candidate factors underscore robust regenerative capacity in lower vertebrates. RegenDbase provides a systems-level analysis of tissue regeneration genetic circuits across injury and animal models and addresses the growing need to understand how noncoding RNAs influence these changes in gene expression.
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Affiliation(s)
- Benjamin L. King
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
| | - Michael C. Rosenstein
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Present Address: RockStep Solutions, Portland, ME 04101 USA
| | - Ashley M. Smith
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Christina A. Dykeman
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Grace A. Smith
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- University of Maine Honors College, University of Maine, Orono, ME 04469 USA
| | - Viravuth P. Yin
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
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23
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Román AC, Vicente-Page J, Pérez-Escudero A, Carvajal-González JM, Fernández-Salguero PM, de Polavieja GG. Histone H4 acetylation regulates behavioral inter-individual variability in zebrafish. Genome Biol 2018; 19:55. [PMID: 29695303 PMCID: PMC5922312 DOI: 10.1186/s13059-018-1428-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 03/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animals can show very different behaviors even in isogenic populations, but the underlying mechanisms to generate this variability remain elusive. We use the zebrafish (Danio rerio) as a model to test the influence of histone modifications on behavior. RESULTS We find that laboratory and isogenic zebrafish larvae show consistent individual behaviors when swimming freely in identical wells or in reaction to stimuli. This behavioral inter-individual variability is reduced when we impair the histone deacetylation pathway. Individuals with high levels of histone H4 acetylation, and specifically H4K12, behave similarly to the average of the population, but those with low levels deviate from it. More precisely, we find a set of genomic regions whose histone H4 acetylation is reduced with the distance between the individual and the average population behavior. We find evidence that this modulation depends on a complex of Yin-yang 1 (YY1) and histone deacetylase 1 (HDAC1) that binds to and deacetylates these regions. These changes are not only maintained at the transcriptional level but also amplified, as most target regions are located near genes encoding transcription factors. CONCLUSIONS We suggest that stochasticity in the histone deacetylation pathway participates in the generation of genetic-independent behavioral inter-individual variability.
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Affiliation(s)
- Angel-Carlos Román
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília s/n, 1400-038, Lisbon, Portugal. .,Instituto Cajal, Consejo Superior de Investigaciones Científicas, Av. Doctor Arce, 37, 28002, Madrid, Spain.
| | - Julián Vicente-Page
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília s/n, 1400-038, Lisbon, Portugal.,Instituto Cajal, Consejo Superior de Investigaciones Científicas, Av. Doctor Arce, 37, 28002, Madrid, Spain
| | - Alfonso Pérez-Escudero
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Av. Doctor Arce, 37, 28002, Madrid, Spain.,Physics Department, MIT, Cambridge, Massachusetts, USA
| | - Jose M Carvajal-González
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Gonzalo G de Polavieja
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília s/n, 1400-038, Lisbon, Portugal. .,Instituto Cajal, Consejo Superior de Investigaciones Científicas, Av. Doctor Arce, 37, 28002, Madrid, Spain.
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24
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Comprehensive analysis of target genes in zebrafish embryos reveals gbx2 involvement in neurogenesis. Dev Biol 2017; 430:237-248. [DOI: 10.1016/j.ydbio.2017.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 11/21/2022]
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25
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Jiang Y, Han K, Cai M, Wang Y, Zhang Z. Characterization and Spatiotemporal Expression of Klf4 in Large Yellow Croaker Larimichthys crocea. DNA Cell Biol 2017; 36:655-671. [DOI: 10.1089/dna.2017.3663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yonghua Jiang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
| | - Kunhuang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
| | - Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
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26
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Wu W, Jin YQ, Gao Z. Directly reprogramming fibroblasts into adipogenic, neurogenic and hepatogenic differentiation lineages by defined factors. Exp Ther Med 2017; 13:2685-2690. [PMID: 28587331 PMCID: PMC5450766 DOI: 10.3892/etm.2017.4365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/06/2017] [Indexed: 12/14/2022] Open
Abstract
The reprogramming of adult cells into pluripotent cells or directly into alternative adult cell types represents a great potential technology for regenerative medicine. In the present study, the potential of key developmental adipogenic, neurogenic and hepatogenic regulators to reprogram human fibroblasts into adipocytes, neurocytes and hepatocytes was investigated. The results demonstrated that direct reprogramming of octamer-binding transcription factor 4 (Oct4) and CCAAT-enhancer-binding protein (C/EBP)β activated C/EBPα and peroxisome proliferator-activated receptor-γ expression, inducing the conversion of fibroblasts into adipocytes. Similarly, direct reprogramming of the transcription factors sex determining region-box 2, trans-acting T-cell specific transcription factor (GATA-3) and neurogenic differentiation 1 in fibroblasts may induce neurogenic differentiation through hemagglutinating virus of Japan envelope (HVJ-E) transfection. Moreover, hepatogenic differentiation was induced by combining the direct reprogramming of Oct4, GATA-3, hepatocyte nuclear factor 1 homeobox α and forkhead box protein A2 in fibroblasts. These results demonstrate that specific transcription factors and reprogramming factors are able to directly reprogram fibroblasts into adipogenic, neurogenic and hepatogenic differentiation lineages by HVJ-E transfection.
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Affiliation(s)
- Wei Wu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
| | - Yu-Qing Jin
- Department of Plastic and Reconstructive Surgery, Shanghai General Hospital, Shanghai 200080, P.R. China
| | - Zhen Gao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
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27
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Xiaohuan H, Yang Z, Linyan L, Zhenhua F, Linyan Z, Zhijian W, Ling W, Deshou W, Jing W. Characterization of the POU5F1 Homologue in Nile Tilapia: From Expression Pattern to Biological Activity. Stem Cells Dev 2016; 25:1386-95. [PMID: 27473876 DOI: 10.1089/scd.2016.0143] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
POU5F1 (OCT4) is a crucial transcription factor for induction and maintenance of cellular pluripotency, as well as survival of germ cells in mammals. However, the homologues of POU5F1 in teleost fish, including zebrafish and medaka, now named Pou5f3, exhibit considerable differences in expression pattern and pluripotency-maintaining activity. To what extent the POU5F1 homologues are conserved in vertebrates has been unclear. In this study, we report that the POU5F1 homologue from the Nile tilapia (Oreochromis niloticus), OnPou5f3, displays an expression pattern and biological activity somewhat different from those in zebrafish or medaka. The expression of Onpou5f3 at both mRNA and protein levels was abundant in early development embryos until blastula stages, barely detectable as proceeding, and then displayed a transiently strong expression domain in the brain region during neurula stages similar to zebrafish but not medaka. Afterward, OnPou5f3 appeared as germline-restricted (including primordial germ cells and female and male gonad germ cells) expression just like medaka. Notably, OnPou5f3 depletion through morpholino oligos caused blastula blockage or lethality and failure of survival and proliferation of blastula cell-derived cells. These findings indicate that equivalent POU5F1-like expression and activity of Pou5f3 might be conserved accompanying with species-specific expression pattern during evolution. Our study provides insight into the evolutionary conservation of the POU5F1 homologues across vertebrates.
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Affiliation(s)
- Huang Xiaohuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Zhao Yang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Liu Linyan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Fan Zhenhua
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Zhou Linyan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Wang Zhijian
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Wei Ling
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Wang Deshou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
| | - Wei Jing
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University , Chongqing, China
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Evolution and functions of Oct4 homologs in non-mammalian vertebrates. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:770-9. [PMID: 27058398 DOI: 10.1016/j.bbagrm.2016.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/13/2022]
Abstract
PouV class transcription factor Oct4/Pou5f1 is a central regulator of indefinite pluripotency in mammalian embryonic stem cells (ESCs) but also participates in cell lineage specification in mouse embryos and in differentiating cell cultures. The molecular basis for this versatility, which is shared between Oct4 and its non-mammalian homologs Pou5f1 and Pou5f3, is not yet completely understood. Here, I review the current understanding of the evolution of PouV class transcription factors and discuss equivalent and diverse roles of Oct4 homologs in pluripotency, differentiation, and cell behavior in different vertebrate embryos. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
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Onichtchouk D, Driever W. Zygotic Genome Activators, Developmental Timing, and Pluripotency. Curr Top Dev Biol 2016; 116:273-97. [PMID: 26970624 DOI: 10.1016/bs.ctdb.2015.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The transcription factors Pou5f1, Sox2, and Nanog are central regulators of pluripotency in mammalian ES and iPS cells. In vertebrate embryos, Pou5f1/3, SoxB1, and Nanog control zygotic genome activation and participate in lineage decisions. We review the current knowledge of the roles of these genes in developing vertebrate embryos from fish to mammals and suggest a model for pluripotency gene regulatory network functions in early development.
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Affiliation(s)
- Daria Onichtchouk
- Developmental Biology Unit, Institute Biology I, Faculty of Biology, and Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University, Freiburg, Germany.
| | - Wolfgang Driever
- Developmental Biology Unit, Institute Biology I, Faculty of Biology, and Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University, Freiburg, Germany.
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30
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Liu H, Leslie EJ, Jia Z, Smith T, Eshete M, Butali A, Dunnwald M, Murray J, Cornell RA. Irf6 directly regulates Klf17 in zebrafish periderm and Klf4 in murine oral epithelium, and dominant-negative KLF4 variants are present in patients with cleft lip and palate. Hum Mol Genet 2015; 25:766-76. [PMID: 26692521 PMCID: PMC4743694 DOI: 10.1093/hmg/ddv614] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/14/2015] [Indexed: 02/05/2023] Open
Abstract
Non-syndromic (NS) cleft lip with or without cleft palate (CL/P) is a common disorder with a strong genetic underpinning. Genome-wide association studies have detected common variants associated with this disorder, but a large portion of the genetic risk for NSCL/P is conferred by unidentified rare sequence variants. Mutations in IRF6 (Interferon Regulatory Factor 6) and GRHL3 (Grainyhead-like 3) cause Van der Woude syndrome, which includes CL/P. Both genes encode members of a regulatory network governing periderm differentiation in model organisms. Here, we report that Krüppel-like factor 17 (Klf17), like Grhl3, acts downstream of Irf6 in this network in zebrafish periderm. Although Klf17 expression is absent from mammalian oral epithelium, a close homologue, Klf4, is expressed in this tissue and is required for the differentiation of epidermis. Chromosome configuration capture and reporter assays indicated that IRF6 directly regulates an oral-epithelium enhancer of KLF4. To test whether rare missense variants of KLF4 contribute risk for NSCL/P, we sequenced KLF4 in approximately 1000 NSCL/P cases and 300 controls. By one statistical test, missense variants of KLF4 as a group were enriched in cases versus controls. Moreover, two patient-derived KLF4 variants disrupted periderm differentiation upon forced expression in zebrafish embryos, suggesting that they have dominant-negative effect. These results indicate that rare NSCL/P risk variants can be found in members of the gene regulatory network governing periderm differentiation.
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Affiliation(s)
- Huan Liu
- Department of Anatomy and Cell Biology, College of Medicine, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhonglin Jia
- Department of Pediatrics, College of Medicine and, State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China and
| | - Tiffany Smith
- Department of Anatomy and Cell Biology, College of Medicine
| | - Mekonen Eshete
- Department of Burns and Plastic Surgery, Addis Ababa University, Addis Ababa, Ethiopia
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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31
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Gao Y, Cao Q, Lu L, Zhang X, Zhang Z, Dong X, Jia W, Cao Y. Kruppel-like factor family genes are expressed during Xenopus embryogenesis and involved in germ layer formation and body axis patterning. Dev Dyn 2015. [PMID: 26198170 DOI: 10.1002/dvdy.24310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Kruppel-like factors (Klfs) are a family of transcription factors consisting of 17 members in mammals, Klf1-Klf17, which are involved in fundamental cellular physiological procedures, such as cell proliferation, differentiation, and apoptosis. However, their functions in embryonic development have been poorly understood. Our previous study has demonstrated that the pluripotency factor Klf4 participates in germ layer formation and axis patterning of Xenopus embryos by means of the regulation of key developmental signals. In the present study, we further investigated comprehensively the expression and functions of the klf family genes, klf2, klf5, klf6, klf7, klf8, klf11, klf15, and klf17, during the embryogenesis of Xenopus laevis. RESULTS Spatio-temporal expression analyses demonstrate that these genes are transcribed both maternally and zygotically in Xenopus embryos, and during organogenesis and tissue differentiation, they are localized to a variety of placodes and tissues. Gain and loss of function studies manifest that Klf factors play different roles in germ layer formation and body axis patterning. Moreover, each Klf factor exhibits distinct regulatory effects on the expression of genes that are essential for germ layer formation and body axis patterning. CONCLUSIONS These results suggest that Klf factors are involved in the fine-tuning of these genes during early embryogenesis.
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Affiliation(s)
- Yan Gao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Qing Cao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Lei Lu
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Xuena Zhang
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Zan Zhang
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Xiaohua Dong
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Wenshuang Jia
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Ying Cao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
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Presnell JS, Schnitzler CE, Browne WE. KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. Genome Biol Evol 2015; 7:2289-309. [PMID: 26232396 PMCID: PMC4558859 DOI: 10.1093/gbe/evv141] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
The Krüppel-like factor and specificity protein (KLF/SP) genes play key roles in critical biological processes including stem cell maintenance, cell proliferation, embryonic development, tissue differentiation, and metabolism and their dysregulation has been implicated in a number of human diseases and cancers. Although many KLF/SP genes have been characterized in a handful of bilaterian lineages, little is known about the KLF/SP gene family in nonbilaterians and virtually nothing is known outside the metazoans. Here, we analyze and discuss the origins and evolutionary history of the KLF/SP transcription factor family and associated transactivation/repression domains. We have identified and characterized the complete KLF/SP gene complement from the genomes of 48 species spanning the Eukarya. We have also examined the phylogenetic distribution of transactivation/repression domains associated with this gene family. We report that the origin of the KLF/SP gene family predates the divergence of the Metazoa. Furthermore, the expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via both acquisitions of pre-existing ancient domains as well as by the appearance of novel domains exclusive to this gene family and is strongly associated with the expansion of cell type complexity.
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Affiliation(s)
| | - Christine E Schnitzler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health
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Verma A, Rajput S, De S, Kumar R, Chakravarty AK, Datta TK. Genome-wide profiling of sperm DNA methylation in relation to buffalo (Bubalus bubalis) bull fertility. Theriogenology 2014; 82:750-9.e1. [DOI: 10.1016/j.theriogenology.2014.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/31/2014] [Accepted: 06/07/2014] [Indexed: 10/25/2022]
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Graf A, Krebs S, Heininen-Brown M, Zakhartchenko V, Blum H, Wolf E. Genome activation in bovine embryos: Review of the literature and new insights from RNA sequencing experiments. Anim Reprod Sci 2014; 149:46-58. [DOI: 10.1016/j.anireprosci.2014.05.016] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/09/2014] [Accepted: 05/26/2014] [Indexed: 11/30/2022]
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35
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Frankenberg SR, Frank D, Harland R, Johnson AD, Nichols J, Niwa H, Schöler HR, Tanaka E, Wylie C, Brickman JM. The POU-er of gene nomenclature. Development 2014; 141:2921-3. [DOI: 10.1242/dev.108407] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The pluripotency factor POU5F1 (OCT4) is well known as a key regulator of stem cell fate. Homologues of POU5F1 exist throughout vertebrates, but the evolutionary and functional relationships between the various family members have been unclear. The level to which function has been conserved within this family provides insight into the evolution of early embryonic potency. Here, we seek to clarify the relationship between POU5F1 homologues in the vertebrate lineage, both phylogenetically and functionally. We resolve the confusion over the identity of the zebrafish gene, which was originally named pou2, then changed to pou5f1 and again, more recently, to pou5f3. We argue that the use of correct nomenclature is crucial when discussing the degree to which the networks regulating early embryonic differentiation are conserved.
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Affiliation(s)
| | - Dale Frank
- Department of Biochemistry, The Rappaport Family Institute for Research in the Medical Sciences, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Richard Harland
- University of California Berkeley, Department of Molecular & Cell Biology, 142 Life Sciences Addition # 3200, Berkeley, CA 94720-3200, USA
| | - Andrew D. Johnson
- School of life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Hitoshi Niwa
- Laboratory for Pluripotent Stem Cell Studies, RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 6500047, Japan
| | - Hans R. Schöler
- Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, Münster 48149, Germany
| | - Elly Tanaka
- DFG Research Center for Regenerative Therapies – CRTD, Technische Universität Dresden, Fetscherstrasse 105, Dresden 01307, Germany
| | - Chris Wylie
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH 45227, USA
| | - Joshua M. Brickman
- The Danish Stem Cell Centre (DanStem), University of Copenhagen, Blegdamsvej 3B, Copenhagen N DK-2200, Denmark
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Kotkamp K, Kur E, Wendik B, Polok BK, Ben-Dor S, Onichtchouk D, Driever W. Pou5f1/Oct4 promotes cell survival via direct activation of mych expression during zebrafish gastrulation. PLoS One 2014; 9:e92356. [PMID: 24643012 PMCID: PMC3958507 DOI: 10.1371/journal.pone.0092356] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/17/2014] [Indexed: 01/29/2023] Open
Abstract
Myc proteins control cell proliferation, cell cycle progression, and apoptosis, and play important roles in cancer as well in establishment of pluripotency. Here we investigated the control of myc gene expression by the Pou5f1/Oct4 pluripotency factor in the early zebrafish embryo. We analyzed the expression of all known zebrafish Myc family members, myca, mycb, mych, mycl1a, mycl1b, and mycn, by whole mount in situ hybridization during blastula and gastrula stages in wildtype and maternal plus zygotic pou5f1 mutant (MZspg) embryos, as well as by quantitative PCR and in time series microarray data. We found that the broad blastula and gastrula stage mych expression, as well as late gastrula stage mycl1b expression, both depend on Pou5f1 activity. We analyzed ChIP-Seq data and found that both Pou5f1 and Sox2 bind to mych and mycl1b control regions. The regulation of mych by Pou5f1 appears to be direct transcriptional activation, as overexpression of a Pou5f1 activator fusion protein in MZspg embryos induced strong mych expression even when translation of zygotically expressed mRNAs was suppressed. We further showed that MZspg embryos develop enhanced apoptosis already during early gastrula stages, when apoptosis was not be detected in wildtype embryos. However, Mych knockdown alone did not induce early apoptosis, suggesting potentially redundant action of several early expressed myc genes, or combination of several pathways affected in MZspg. Experimental mych overexpression in MZspg embryos did significantly, but not completely suppress the apoptosis phenotype. Similarly, p53 knockdown only partially suppressed apoptosis in MZspg gastrula embryos. However, combined knockdown of p53 and overexpression of Mych completely rescued the MZspg apoptosis phenotype. These results reveal that Mych has anti-apoptotic activity in the early zebrafish embryo, and that p53-dependent and Myc pathways are likely to act in parallel to control apoptosis at these stages.
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Affiliation(s)
- Kay Kotkamp
- Developmental Biology, Institute Biology I, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Esther Kur
- Developmental Biology, Institute Biology I, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Björn Wendik
- Developmental Biology, Institute Biology I, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Bożena K. Polok
- Developmental Biology, Institute Biology I, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Shifra Ben-Dor
- Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Daria Onichtchouk
- Developmental Biology, Institute Biology I, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany
| | - Wolfgang Driever
- Developmental Biology, Institute Biology I, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany
- * E-mail:
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