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Ochi H, Kato T, Zorn A, Hayashi T, Inoue T, Kondo M, Taira M, Michiue T. Versatile utilities of amphibians (part 5). Dev Growth Differ 2023; 65:459-460. [PMID: 37881023 DOI: 10.1111/dgd.12889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
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Ogino H, Kamei Y, Hayashi T, Sakamoto J, Suzuki M, Igawa T, Kondo M, Taira M. Invention sharing is the mother of developmental biology (part 4). Dev Growth Differ 2023; 65:286-287. [PMID: 37610050 DOI: 10.1111/dgd.12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2023] [Indexed: 08/24/2023]
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Takahashi-Kanemitsu A, Lu M, Knight CT, Yamamoto T, Hayashi T, Mii Y, Ooki T, Kikuchi I, Kikuchi A, Barker N, Susaki EA, Taira M, Hatakeyama M. The Helicobacter pylori CagA oncoprotein disrupts Wnt/PCP signaling and promotes hyperproliferation of pyloric gland base cells. Sci Signal 2023; 16:eabp9020. [PMID: 37463245 DOI: 10.1126/scisignal.abp9020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/24/2023] [Indexed: 07/20/2023]
Abstract
Helicobacter pylori strains that deliver the oncoprotein CagA into gastric epithelial cells are the major etiologic agents of upper gastric diseases including gastric cancer. CagA promotes gastric carcinogenesis through interactions with multiple host proteins. Here, we show that CagA also disrupts Wnt-dependent planar cell polarity (Wnt/PCP), which orients cells within the plane of an epithelium and coordinates collective cell behaviors such as convergent extension to enable epithelial elongation during development. Ectopic expression of CagA in Xenopus laevis embryos impaired gastrulation, neural tube formation, and axis elongation, processes driven by convergent extension movements that depend on the Wnt/PCP pathway. Mice specifically expressing CagA in the stomach epithelium had longer pyloric glands and mislocalization of the tetraspanin proteins VANGL1 and VANGL2 (VANGL1/2), which are critical components of Wnt/PCP signaling. The increased pyloric gland length was due to hyperproliferation of cells at the gland base, where Lgr5+ stem and progenitor cells reside, and was associated with fewer differentiated enteroendocrine cells. In cultured human gastric epithelial cells, the N terminus of CagA interacted with the C-terminal cytoplasmic tails of VANGL1/2, which impaired Wnt/PCP signaling by inducing the mislocalization of VANGL1/2 from the plasma membrane to the cytoplasm. Thus, CagA may contribute to the development of gastric cancer by subverting a Wnt/PCP-dependent mechanism that restrains pyloric gland stem cell proliferation and promotes enteroendocrine differentiation.
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Ochi H, Michiue T, Kato T, Zorn A, Hayashi T, Inoue T, Kondo M, Taira M. Versatile utilities of amphibians (part 4). Dev Growth Differ 2023; 65:4-5. [PMID: 36740732 DOI: 10.1111/dgd.12838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 02/07/2023]
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Michiue T, Kato T, Ochi H, Zorn A, Hayashi T, Inoue T, Kondo M, Taira M. Versatile utilities of amphibians (Part 3). Dev Growth Differ 2022; 64:472-473. [PMID: 36579413 DOI: 10.1111/dgd.12829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2022] [Indexed: 12/30/2022]
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Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Rep 2022; 38:110364. [PMID: 35172134 PMCID: PMC8917868 DOI: 10.1016/j.celrep.2022.110364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/30/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023] Open
Abstract
Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
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Matsuda S, Schaefer JV, Mii Y, Hori Y, Bieli D, Taira M, Plückthun A, Affolter M. Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nat Commun 2021; 12:6435. [PMID: 34750371 PMCID: PMC8576045 DOI: 10.1038/s41467-021-26726-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
How morphogen gradients control patterning and growth in developing tissues remains largely unknown due to lack of tools manipulating morphogen gradients. Here, we generate two membrane-tethered protein binders that manipulate different aspects of Decapentaplegic (Dpp), a morphogen required for overall patterning and growth of the Drosophila wing. One is "HA trap" based on a single-chain variable fragment (scFv) against the HA tag that traps HA-Dpp to mainly block its dispersal, the other is "Dpp trap" based on a Designed Ankyrin Repeat Protein (DARPin) against Dpp that traps Dpp to block both its dispersal and signaling. Using these tools, we found that, while posterior patterning and growth require Dpp dispersal, anterior patterning and growth largely proceed without Dpp dispersal. We show that dpp transcriptional refinement from an initially uniform to a localized expression and persistent signaling in transient dpp source cells render the anterior compartment robust against the absence of Dpp dispersal. Furthermore, despite a critical requirement of dpp for the overall wing growth, neither Dpp dispersal nor direct signaling is critical for lateral wing growth after wing pouch specification. These results challenge the long-standing dogma that Dpp dispersal is strictly required to control and coordinate overall wing patterning and growth.
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Kuretani A, Yamamoto T, Taira M, Michiue T. Evolution of hes gene family in vertebrates: the hes5 cluster genes have specifically increased in frogs. BMC Ecol Evol 2021; 21:147. [PMID: 34325655 PMCID: PMC8320183 DOI: 10.1186/s12862-021-01879-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Background hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes genes, including early embryogenesis and neurogenesis, have been elucidated in vertebrates. However, their orthologous relationships remain unclear partly because of less conservation of relatively short amino acid sequences, the fact that the genome was not analyzed as it is today, and species-specific genome duplication. This results in complicated gene names in vertebrates, which are not consistent in orthologs. We previously revealed that Xenopus frogs have two clusters of hes5, named “the hes5.1 cluster” and “the hes5.3 cluster”, but the origin and the conservation have not yet been revealed. Results Here, we elucidated the orthologous and paralogous relationships of all hes genes of human, mouse, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark and three species of frogs, Xenopus tropicalis (X. tropicalis), X. laevis, Nanorana parkeri, by phylogenetic and synteny analyses. Any duplicated hes5 were not found in mammals, whereas hes5 clusters in teleost were conserved although not as many genes as the three frog species. In addition, hes5 cluster-like structure was found in the elephant shark genome, but not found in cyclostomata. Conclusion These data suggest that the hes5 cluster existed in the gnathostome ancestor but became a single gene in mammals. The number of hes5 cluster genes were specifically large in frogs. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01879-6.
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Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
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Mii Y, Nakazato K, Pack CG, Ikeda T, Sako Y, Mochizuki A, Taira M, Takada S. Quantitative analyses reveal extracellular dynamics of Wnt ligands in Xenopus embryos. eLife 2021; 10:55108. [PMID: 33904408 PMCID: PMC8139832 DOI: 10.7554/elife.55108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
The mechanism of intercellular transport of Wnt ligands is still a matter of debate. To better understand this issue, we examined the distribution and dynamics of Wnt8 in Xenopus embryos. While Venus-tagged Wnt8 was found on the surfaces of cells close to Wnt-producing cells, we also detected its dispersal over distances of 15 cell diameters. A combination of fluorescence correlation spectroscopy and quantitative imaging suggested that only a small proportion of Wnt8 ligands diffuses freely, whereas most Wnt8 molecules are bound to cell surfaces. Fluorescence decay after photoconversion showed that Wnt8 ligands bound on cell surfaces decrease exponentially, suggesting a dynamic exchange of bound forms of Wnt ligands. Mathematical modeling based on this exchange recapitulates a graded distribution of bound, but not free, Wnt ligands. Based on these results, we propose that Wnt distribution in tissues is controlled by a dynamic exchange of its abundant bound and rare free populations.
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Hasegawa M, Taira M, Kanaya T, Araki K, Watanabe T, Tominaga Y, Kugo Y, Ishida H, Narita A, Ueno T, Ueno T, Sawa Y. Clinical Outcomes for Children with Left Ventricular Noncompaction and Cardiomyopathy. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Kondo M, Matsuo M, Igarashi K, Haramoto Y, Yamamoto T, Yasuoka Y, Taira M. De novo transcription of multiple Hox cluster genes takes place simultaneously in early Xenopus tropicalis embryos. Biol Open 2019; 8:bio.038422. [PMID: 30651235 PMCID: PMC6451350 DOI: 10.1242/bio.038422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
hox genes are found as clusters in the genome in most bilaterians. The order of genes in the cluster is supposed to be correlated with the site of expression along the anterior-posterior body axis and the timing of expression during development, and these correlations are called spatial and temporal collinearity, respectively. Here we studied the expression dynamics of all hox genes of the diploid species Xenopus tropicalis in four Hox clusters (A–D) by analyzing high-temporal-resolution RNA-seq databases and the results showed that temporal collinearity is not supported, which is consistent with our previous data from allotetraploid Xenopuslaevis. Because the temporal collinearity hypothesis implicitly assumes the collinear order of gene activation, not mRNA accumulation, we determined for the first time the timing of when new transcripts of hox genes are produced, by detecting pre-spliced RNA in whole embryos with reverse transcription and quantitative PCR (RT-qPCR) for all hoxa genes as well as several selected hoxb, hoxc and hoxd genes. Our analyses showed that, coinciding with the RNA-seq results, hoxa genes started to be transcribed in a non-sequential order, and found that multiple genes start expression almost simultaneously or more posterior genes could be expressed earlier than anterior ones. This tendency was also found in hoxb and hoxc genes. These results suggest that temporal collinearity of hox genes is not held during early development of Xenopus. Summary: qPCR analysis for de novo transcription of hox genes suggest that temporal collinearity is not held for all hox genes during early development of Xenopus tropicalis.
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Yasuoka Y, Taira M. Microinjection of DNA Constructs into Xenopus Embryos for Gene Misexpression and cis-Regulatory Module Analysis. Cold Spring Harb Protoc 2019; 2019:pdb.prot097279. [PMID: 30131366 DOI: 10.1101/pdb.prot097279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introducing exogenous DNA into an embryo can promote misexpression of a gene of interest via transcription regulated by an attached enhancer-promoter. This protocol describes plasmid DNA microinjection into Xenopus embryos for misexpression of genes after zygotic gene expression begins. It also describes a method for coinjecting a reporter plasmid with mRNA or antisense morpholinos to perform luciferase reporter assays, which are useful for quantitative analysis of cis-regulatory sequences responding to endogenous or exogenous stimuli in embryos.
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Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. ZOOLOGICAL LETTERS 2019; 5:27. [PMID: 31388442 PMCID: PMC6679436 DOI: 10.1186/s40851-019-0143-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated. RESULTS To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos. CONCLUSIONS On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.
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Narita J, Kogaki S, Ishigaki S, Torigoe F, Ishii R, Ishida H, Ozono K, Taira M, Ueno T, Sawa Y. Prolonged but Successful Weaning from Berlin Heart EXCOR After a Long-term Mechanical Unloading in Infantile DCM. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Taira M, Ueno T, Kido T, Kanaya T, Okuda N, Matsunaga Y, Toda K, Kuratani T, Sawa Y. Long Term Results of Mechanical Circulatory Support as Bridge to Transplant in Severe Heart Failure Pediatric Patients. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Satou Y, Minami K, Hosono E, Okada H, Yasuoka Y, Shibano T, Tanaka T, Taira M. Phosphorylation states change Otx2 activity for cell proliferation and patterning in the Xenopus embryo. Development 2018; 145:dev.159640. [PMID: 29440302 DOI: 10.1242/dev.159640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/01/2018] [Indexed: 12/19/2022]
Abstract
The homeodomain transcription factor Otx2 has essential roles in head and eye formation via the negative and positive regulation of its target genes, but it remains elusive how this dual activity of Otx2 affects cellular functions. In the current study, we first demonstrated that both exogenous and endogenous Otx2 are phosphorylated at multiple sites. Using Xenopus embryos, we identified three possible cyclin-dependent kinase (Cdk) sites and one Akt site, and analyzed the biological activities of phosphomimetic (4E) and nonphosphorylatable (4A) mutants for those sites. In the neuroectoderm, the 4E but not the 4A mutant downregulated the Cdk inhibitor gene p27xic1 (cdknx) and posterior genes, and promoted cell proliferation, possibly forming a positive-feedback loop consisting of Cdk, Otx2 and p27xic1 for cell proliferation, together with anteriorization. Conversely, the 4A mutant functioned as an activator on its own and upregulated the expression of eye marker genes, resulting in enlarged eyes. Consistent with these results, the interaction of Otx2 with the corepressor Tle1 is suggested to be phosphorylation dependent. These data suggest that Otx2 orchestrates cell proliferation, anteroposterior patterning and eye formation via its phosphorylation state.
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DeLay BD, Corkins ME, Hanania HL, Salanga M, Deng JM, Sudou N, Taira M, Horb ME, Miller RK. Tissue-Specific Gene Inactivation in Xenopus laevis: Knockout of lhx1 in the Kidney with CRISPR/Cas9. Genetics 2018; 208:673-686. [PMID: 29187504 PMCID: PMC5788530 DOI: 10.1534/genetics.117.300468] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/18/2017] [Indexed: 11/18/2022] Open
Abstract
Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. The allotetraploid frog, Xenopus laevis, is commonly used to study developmental processes, but because of the presence of two homeologs for many genes, it has been difficult to use as a genetic model. Few studies have successfully used CRISPR in amphibians, and currently there is no tissue-targeted knockout strategy described in Xenopus The goal of this study is to determine whether CRISPR/Cas9-mediated gene knockout can be targeted to the Xenopus kidney without perturbing essential early gene function. We demonstrate that targeting CRISPR gene editing to the kidney and the eye of F0 embryos is feasible. Our study shows that knockout of both homeologs of lhx1 results in the disruption of kidney development and function but does not lead to early developmental defects. Therefore, targeting of CRISPR to the kidney may not be necessary to bypass the early developmental defects reported upon disruption of Lhx1 protein expression or function by morpholinos, antisense RNA, or dominant negative constructs. We also establish a control for CRISPR in Xenopus by editing a gene (slc45a2) that when knocked out results in albinism without altering kidney development. This study establishes the feasibility of tissue-specific gene knockout in Xenopus, providing a cost-effective and efficient method for assessing the roles of genes implicated in developmental abnormalities that is amenable to high-throughput gene or drug screening techniques.
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Mii Y, Yamamoto T, Takada R, Mizumoto S, Matsuyama M, Yamada S, Takada S, Taira M. Roles of two types of heparan sulfate clusters in Wnt distribution and signaling in Xenopus. Nat Commun 2017; 8:1973. [PMID: 29215008 PMCID: PMC5719454 DOI: 10.1038/s41467-017-02076-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
Wnt proteins direct embryonic patterning, but the regulatory basis of their distribution and signal reception remain unclear. Here, we show that endogenous Wnt8 protein is distributed in a graded manner in Xenopus embryo and accumulated on the cell surface in a punctate manner in association with “N-sulfo-rich heparan sulfate (HS),” not with “N-acetyl-rich HS”. These two types of HS are differentially clustered by attaching to different glypicans as core proteins. N-sulfo-rich HS is frequently internalized and associated with the signaling vesicle, known as the Frizzled/Wnt/LRP6 signalosome, in the presence of Wnt8. Conversely, N-acetyl-rich HS is rarely internalized and accumulates Frzb, a secreted Wnt antagonist. Upon interaction with Frzb, Wnt8 associates with N-acetyl-rich HS, suggesting that N-acetyl-rich HS supports Frzb-mediated antagonism by sequestering Wnt8 from N-sulfo-rich HS. Thus, these two types of HS clusters may constitute a cellular platform for the distribution and signaling of Wnt8. Wnt proteins mediate embryonic development but how protein localization and patterning is regulated is unclear. Here, the authors show that distinct structures with different heparan sulfate modifications (‘N-sulfo-rich’ and ‘N-acetyl-rich’) regulate cellular localization and signal transduction of Wnt8 in Xenopus.
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Kondo M, Yamamoto T, Takahashi S, Taira M. Comprehensive analyses ofhoxgene expression inXenopus laevisembryos and adult tissues. Dev Growth Differ 2017; 59:526-539. [DOI: 10.1111/dgd.12382] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/29/2017] [Indexed: 01/04/2023]
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Inamochi Y, Fueki K, Usui N, Taira M, Wakabayashi N. Adaptive change in chewing-related brain activity while wearing a palatal plate: an functional magnetic resonance imaging study. J Oral Rehabil 2017. [DOI: 10.1111/joor.12541] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Suzuki A, Uno Y, Takahashi S, Grimwood J, Schmutz J, Mawaribuchi S, Yoshida H, Takebayashi-Suzuki K, Ito M, Matsuda Y, Rokhsar D, Taira M. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:236-244. [PMID: 27720224 DOI: 10.1016/j.ydbio.2016.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 01/21/2023]
Abstract
Extracellular factors belonging to the TGF-β family play pivotal roles in the formation and patterning of germ layers during early Xenopus embryogenesis. Here, we show that the vg1 and nodal3 genes of Xenopus laevis are present in gene clusters on chromosomes XLA1L and XLA3L, respectively, and that both gene clusters have been completely lost from the syntenic S chromosome regions. The presence of gene clusters and chromosome-specific gene loss were confirmed by cDNA FISH analyses. Sequence and expression analyses revealed that paralogous genes in the vg1 and nodal3 clusters on the L chromosomes were also altered compared to their Xenopus tropicalis orthologs. X. laevis vg1 and nodal3 paralogs have potentially become pseudogenes or sub-functionalized genes and are expressed at different levels. As X. tropicalis has a single vg1 gene on chromosome XTR1, the ancestral vg1 gene in X. laevis appears to have been expanded on XLA1L. Of note, two reported vg1 genes, vg1(S20) and vg1(P20), reside in the cluster on XLA1L. The nodal3 gene cluster is also present on X. tropicalis chromosome XTR3, but phylogenetic analysis indicates that nodal3 genes in X. laevis and X. tropicalis were independently expanded and/or evolved in concert within each cluster by gene conversion. These findings provide insights into the function and molecular evolution of TGF-β family genes in response to allotetraploidization.
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Tanaka T, Ochi H, Takahashi S, Ueno N, Taira M. Genes coding for cyclin-dependent kinase inhibitors are fragile in Xenopus. Dev Biol 2017; 426:291-300. [PMID: 27393661 DOI: 10.1016/j.ydbio.2016.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/16/2016] [Accepted: 06/16/2016] [Indexed: 11/27/2022]
Abstract
Cell proliferation is strictly regulated by the dosage balance among cell-cycle regulators such as CDK/cyclin complexes and CDK-Inhibitors. Even in the allotetraploid genome of Xenopus laevis, the dosage balance must be maintained for animals to stay alive, and the duplicated homeologous genes seem to have gradually changed, through evolution, resulting in the best genes for them to thrive. In the Xenopus laevis genome, while homeologous gene pairs of CDKs are fundamentally maintained and a few cyclin genes are amplified, homeologous gene pairs of the important CDK-Inhibitors, CDKn1c and CDKn2a, are deleted from chromosomes L and S. Although losses of CDKn1c and CDKn2a can lead to diseases in humans, their loss in X. laevis does not affect the animals' health. Also, another gene coding CDKn1b is lost besides CDKn1c and CDKn2a in the genome of Xenopus tropicalis. These findings suggest a high resistance of Xenopus to diseases. We also found that CDKn2c.S expression is higher than that of CDKn2c.L, and a conserved noncoding sequence (CNS) of CDKn2c genomic loci on X. laevis chromosome S and X. tropicalis has an enhancement activity in regulating the different expression. These findings together indicate a surprising fragility of CDK inhibitor gene loci in the Xenopus genome in spite of their importance, and may suggest that factors other than CDK-inhibitors decelerate cell-cycling in Xenopus.
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Michiue T, Yamamoto T, Yasuoka Y, Goto T, Ikeda T, Nagura K, Nakayama T, Taira M, Kinoshita T. High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis. Dev Biol 2017; 426:270-290. [DOI: 10.1016/j.ydbio.2016.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
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