@article {125, title = {Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.}, journal = {Nat Genet}, volume = {54}, year = {2022}, month = {2022 Jul}, pages = {1037-1050}, abstract = {

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

}, keywords = {Animals, Chromatin, Databases, Genetic, Gene Expression Regulation, Developmental, Genome, Genomics, Humans, Mice, Molecular Sequence Annotation, Organogenesis, Regulatory Sequences, Nucleic Acid, Zebrafish, Zebrafish Proteins}, issn = {1546-1718}, doi = {10.1038/s41588-022-01089-w}, author = {Baranasic, Damir and H{\"o}rtenhuber, Matthias and Balwierz, Piotr J and Zehnder, Tobias and Mukarram, Abdul Kadir and Nepal, Chirag and V{\'a}rnai, Csilla and Hadzhiev, Yavor and Jimenez-Gonzalez, Ada and Li, Nan and Wragg, Joseph and D{\textquoteright}Orazio, Fabio M and Relic, Dorde and Pachkov, Mikhail and D{\'\i}az, Noelia and Hern{\'a}ndez-Rodr{\'\i}guez, Benjam{\'\i}n and Chen, Zelin and Stoiber, Marcus and Dong, Micha{\"e}l and Stevens, Irene and Ross, Samuel E and Eagle, Anne and Martin, Ryan and Obasaju, Oluwapelumi and Rastegar, Sepand and McGarvey, Alison C and Kopp, Wolfgang and Chambers, Emily and Wang, Dennis and Kim, Hyejeong R and Acemel, Rafael D and Naranjo, Silvia and {\L}api{\'n}ski, Maciej and Chong, Vanessa and Mathavan, Sinnakaruppan and Peers, Bernard and Sauka-Spengler, Tatjana and Vingron, Martin and Carninci, Piero and Ohler, Uwe and Lacadie, Scott Allen and Burgess, Shawn M and Winata, Cecilia and van Eeden, Freek and Vaquerizas, Juan M and G{\'o}mez-Skarmeta, Jos{\'e} Luis and Onichtchouk, Daria and Brown, Ben James and Bogdanovic, Ozren and van Nimwegen, Erik and Westerfield, Monte and Wardle, Fiona C and Daub, Carsten O and Lenhard, Boris and M{\"u}ller, Ferenc} } @article {118, title = {Fish-Ing for Enhancers in the Heart.}, journal = {Int J Mol Sci}, volume = {22}, year = {2021}, month = {2021 Apr 10}, abstract = {

Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.

}, keywords = {Animals, Binding Sites, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Heart, Humans, Mutation, Transcription Factors, Zebrafish}, issn = {1422-0067}, doi = {10.3390/ijms22083914}, author = {Parisi, Costantino and Vashisht, Shikha and Winata, Cecilia Lanny} } @article {120, title = {Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region.}, journal = {Cell Mol Life Sci}, volume = {78}, year = {2021}, month = {2021 Oct}, pages = {6669-6687}, abstract = {

The atrioventricular canal (AVC) is the site where key structures responsible for functional division between heart regions are established, most importantly, the atrioventricular (AV) conduction system and cardiac valves. To elucidate the mechanism underlying AVC development and function, we utilized transgenic zebrafish line sqet31Et expressing EGFP in the AVC to isolate this cell population and profile its transcriptome at 48 and 72 hpf. The zebrafish AVC transcriptome exhibits hallmarks of mammalian AV node, including the expression of genes implicated in its development and those encoding connexins forming low conductance gap junctions. Transcriptome analysis uncovered protein-coding and noncoding transcripts enriched in AVC, which have not been previously associated with this structure, as well as dynamic expression of epithelial-to-mesenchymal transition markers and components of TGF-β, Notch, and Wnt signaling pathways likely reflecting ongoing AVC and valve development. Using transgenic line Tg(myl7:mermaid) encoding voltage-sensitive fluorescent protein, we show that abolishing the pacemaker-containing sinoatrial ring (SAR) through Isl1 loss of function resulted in spontaneous activation in the AVC region, suggesting that it possesses inherent automaticity although insufficient to replace the SAR. The SAR and AVC transcriptomes express partially overlapping species of ion channels and gap junction proteins, reflecting their distinct roles. Besides identifying conserved aspects between zebrafish and mammalian conduction systems, our results established molecular hallmarks of the developing AVC which underlies its role in structural and electrophysiological separation between heart chambers. This data constitutes a valuable resource for studying AVC development and function, and identification of novel candidate genes implicated in these processes.

}, keywords = {Animals, Animals, Genetically Modified, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Genome, Genomics, Heart Septal Defects, Heart Valves, Myocardium, Organogenesis, Pacemaker, Artificial, Wnt Signaling Pathway, Zebrafish, Zebrafish Proteins}, issn = {1420-9071}, doi = {10.1007/s00018-021-03939-y}, author = {Abu Nahia, Karim and Migda{\l}, Maciej and Quinn, T Alexander and Poon, Kar-Lai and {\L}api{\'n}ski, Maciej and Sulej, Agata and Liu, Jiandong and Mondal, Shamba S and Pawlak, Micha{\l} and Bugajski, {\L}ukasz and Piwocka, Katarzyna and Brand, Thomas and Kohl, Peter and Korzh, Vladimir and Winata, Cecilia} } @article {112, title = {Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.}, journal = {Genome Res}, volume = {29}, year = {2019}, month = {2019 03}, pages = {506-519}, 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.

}, keywords = {Animals, Cells, Cultured, Chromatin, Chromatin Assembly and Disassembly, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Heart, Myocytes, Cardiac, Transcription Factors, Transcriptome, Zebrafish, Zebrafish Proteins}, issn = {1549-5469}, doi = {10.1101/gr.244491.118}, author = {Pawlak, Michal and Kedzierska, Katarzyna Z and Migdal, Maciej and Nahia, Karim Abu and Ramilowski, Jordan A and Bugajski, Lukasz and Hashimoto, Kosuke and Marconi, Aleksandra and Piwocka, Katarzyna and Carninci, Piero and Winata, Cecilia L} } @article {113, title = {A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.}, journal = {Dev Dyn}, volume = {248}, year = {2019}, month = {2019 09}, pages = {837-849}, abstract = {

BACKGROUND: Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis.

RESULTS: We identified two novel tetrapod-teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue-specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression.

CONCLUSION: This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression.

}, keywords = {Animals, Animals, Genetically Modified, Conserved Sequence, Embryonic Development, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Green Fluorescent Proteins, Habenula, Homeodomain Proteins, Humans, Nervous System, Repressor Proteins, Transcription Factors, Zebrafish, Zebrafish Proteins}, issn = {1097-0177}, doi = {10.1002/dvdy.69}, author = {Minhas, Rashid and Paterek, Aleksandra and {\L}api{\'n}ski, Maciej and Baza{\l}a, Micha{\l} and Korzh, Vladimir and Winata, Cecilia L} } @article {74, title = {Impaired development of neural-crest cell-derived organs and intellectual disability caused by MED13L haploinsufficiency.}, journal = {Hum Mutat}, volume = {35}, year = {2014}, month = {2014 Nov}, pages = {1311-20}, abstract = {

MED13L is a component subunit of the Mediator complex, an important regulator of transcription that is highly conserved across eukaryotes. Here, we report MED13L disruption in a translocation t(12;19) breakpoint of a patient with Pierre-Robin syndrome, moderate intellectual disability, craniofacial anomalies, and muscular defects. The phenotype is similar to previously described patients with MED13L haploinsufficiency. Knockdown of MED13L orthologue in zebrafish, med13b, showed early defective migration of cranial neural crest cells (NCCs) that contributed to cartilage structure deformities in the later stage, recapitulating craniofacial anomalies seen in human patients. Notably, we observed abnormal distribution of developing neurons in different brain regions of med13b morphant embryos, which could be rescued upon introduction of full-length human MED13L mRNA. To compare with mammalian system, we suppressed MED13L expression by short-hairpin RNA in ES-derived human neural progenitors, and differentiated them into neurons. Transcriptome analysis revealed differential expression of components of Wnt and FGF signaling pathways in MED13L-deficient neurons. Our finding provides a novel insight into the mechanism of overlapping phenotypic outcome targeting NCCs derivatives organs in patients with MED13L haploinsufficiency, and emphasizes a clinically recognizable syndromic phenotype in these patients.

}, keywords = {Animals, Cell Differentiation, Cell Movement, Child, Preschool, Chromosome Breakpoints, Disease Models, Animal, Embryonic Stem Cells, Female, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Genetic Association Studies, Haploinsufficiency, Humans, Intellectual Disability, Mediator Complex, Neural Crest, Neurons, Phenotype, RNA, Messenger, Sequence Analysis, DNA, Transcriptome, Translocation, Genetic, Zebrafish}, issn = {1098-1004}, doi = {10.1002/humu.22636}, author = {Utami, Kagistia Hana and Winata, Cecilia L and Hillmer, Axel M and Aksoy, Irene and Long, Hoang Truong and Liany, Herty and Chew, Elaine G Y and Mathavan, Sinnakaruppan and Tay, Stacey K H and Korzh, Vladimir and Sarda, Pierre and Davila, Sonia and Cacheux, Valere} } @article {34, title = {Prepatterning of developmental gene expression by modified histones before zygotic genome activation.}, journal = {Dev Cell}, volume = {21}, year = {2011}, month = {2011 Dec 13}, pages = {993-1004}, abstract = {

A hallmark of anamniote vertebrate development is a window of embryonic transcription-independent cell divisions before onset of zygotic genome activation (ZGA). Chromatin determinants of ZGA are unexplored; however, marking of developmental genes by modified histones in sperm suggests a predictive role of histone marks for ZGA. In zebrafish, pre-ZGA development for ten cell cycles provides an opportunity to examine whether genomic enrichment in modified histones is present before initiation of transcription. By profiling histone H3 trimethylation on all zebrafish promoters before and after ZGA, we demonstrate here an epigenetic prepatterning of developmental gene expression. This involves pre-ZGA marking of transcriptionally inactive genes involved in homeostatic and developmental regulation by permissive H3K4me3 with or without repressive H3K9me3 or H3K27me3. Our data suggest that histone modifications are instructive for the developmental gene expression program.

}, keywords = {Animals, Body Patterning, Chromatin, Epigenesis, Genetic, Female, Gene Expression Regulation, Developmental, Histones, Male, Methylation, Multigene Family, Promoter Regions, Genetic, Spermatozoa, Zebrafish, Zebrafish Proteins}, issn = {1878-1551}, doi = {10.1016/j.devcel.2011.10.008}, author = {Lindeman, Leif C and Andersen, Ingrid S and Reiner, Andrew H and Li, Nan and Aanes, H{\r a}vard and {\O}strup, Olga and Winata, Cecilia L and Mathavan, Sinnakaruppan and M{\"u}ller, Ferenc and Alestr{\"o}m, Peter and Collas, Philippe} } @article {72, title = {Wnt signaling is required for early development of zebrafish swimbladder.}, journal = {PLoS One}, volume = {6}, year = {2011}, month = {2011}, pages = {e18431}, abstract = {

BACKGROUND: Wnt signaling plays critical roles in mammalian lung development. However, Wnt signaling in the development of the zebrafish swimbladder, which is considered as a counterpart of mammalian lungs, have not been explored. To investigate the potential conservation of signaling events in early development of the lung and swimbladder, we wish to address the question whether Wnt signaling plays a role in swimbladder development.

METHODOLOGY/PRINCIPAL FINDINGS: For analysis of zebrafish swimbladder development, we first identified, by whole-mount in situ hybridization (WISH), has2 as a mesenchymal marker, sox2 as the earliest epithelial marker, as well as hprt1l and elovl1a as the earliest mesothelial markers. We also demonstrated that genes encoding Wnt signaling members Wnt5b, Fz2, Fz7b, Lef1, Tcf3 were expressed in different layers of swimbladder. Then we utilized the heat-shock inducible transgenic lines hs:Dkk1-GFP and hs:ΔTcf-GFP to temporarily block canonical Wnt signaling. Inhibition of canonical Wnt signaling at various time points disturbed precursor cells specification, organization, anterioposterior patterning, and smooth muscle differentiation in all three tissue layers of swimbladder. These observations were also confirmed by using a chemical inhibitor (IWR-1) of Wnt signaling. In addition, we found that Hedgehog (Hh) signaling was activated by canonical Wnt signaling and imposed a negative feedback on the latter.

SIGNIFICANCE/CONCLUSION: We first provided a new set of gene markers for the three tissue layers of swimbladder in zebrafish and demonstrated the expression of several key genes of Wnt signaling pathway in developing swimbladder. Our functional analysis data indicated that Wnt/β-catenin signaling is required for swimbladder early development and we also provided evidence for the crosstalk between Wnt and Hh signaling in early swimbladder development.

}, keywords = {Air Sacs, Animals, Animals, Genetically Modified, Apoptosis, Cell Differentiation, Cell Proliferation, Embryo, Nonmammalian, Epithelium, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Genetic Markers, Green Fluorescent Proteins, Heat-Shock Response, Hedgehog Proteins, Mesoderm, Models, Biological, Morphogenesis, Myocytes, Smooth Muscle, Recombinant Fusion Proteins, Reproducibility of Results, Signal Transduction, Wnt Proteins, Zebrafish, Zebrafish Proteins}, issn = {1932-6203}, doi = {10.1371/journal.pone.0018431}, author = {Yin, Ao and Korzh, Svitlana and Winata, Cecilia L and Korzh, Vladimir and Gong, Zhiyuan} } @article {73, title = {The interaction of epithelial Ihha and mesenchymal Fgf10 in zebrafish esophageal and swimbladder development.}, journal = {Dev Biol}, volume = {359}, year = {2011}, month = {2011 Nov 15}, pages = {262-76}, abstract = {

Developmental patterning and growth of the vertebrate digestive and respiratory tracts requires interactions between the epithelial endoderm and adjacent mesoderm. The esophagus is a specialized structure that connects the digestive and respiratory systems and its normal development is critical for both. Shh signaling from the epithelium regulates related aspects of mammalian and zebrafish digestive organ development and has a prominent effect on esophageal morphogenesis. The mechanisms underlying esophageal malformations, however, are poorly understood. Here, we show that zebrafish Ihha signaling from the epithelium acting in parallel, but independently of Shh, controls epithelial and mesenchymal cell proliferation and differentiation of smooth muscles and neurons in the gut and swimbladder. In zebrafish ihha mutants, the esophageal and swimbladder epithelium is dysmorphic, and expression of fgf10 in adjacent mesenchymal cells is affected. Analysis of the development of the esophagus and swimbladder in fgf10 mutant daedalus (dae) and compound dae/ihha mutants shows that the Ihha-Fgf10 regulatory interaction is realized through a signaling feedback loop between the Ihha-expressing epithelium and Fgf10-expressing mesenchyme. Disruption of this loop further affects the esophageal and swimbladder epithelium in ihha mutants, and Ihha acts in parallel to but independently of Shha in this process. These findings contribute to the understanding of epithelial-mesenchymal interactions and highlight an interaction between Hh and Fgf signaling pathways during esophagus and swimbladder development.

}, keywords = {Air Sacs, Animals, Animals, Genetically Modified, Cell Proliferation, Embryo, Nonmammalian, Epithelium, Esophagus, Female, Fibroblast Growth Factor 10, Gastrointestinal Tract, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Green Fluorescent Proteins, Hedgehog Proteins, In Situ Hybridization, Male, Membrane Proteins, Mesoderm, Microscopy, Confocal, Mutation, Protein Binding, Receptors, Cell Surface, Signal Transduction, Zebrafish, Zebrafish Proteins}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2011.08.024}, author = {Korzh, Svitlana and Winata, Cecilia Lanni and Zheng, Weiling and Yang, Shulan and Yin, Ao and Ingham, Phillip and Korzh, Vladimir and Gong, Zhiyuan} } @article {69, title = {Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos.}, journal = {Int J Dev Biol}, volume = {54}, year = {2010}, month = {2010}, pages = {803-13}, abstract = {

Embryo development proceeds from a cascade of gene activation and repression events controlled by epigenetic modifications of DNA and histones. Little is known about epigenetic states in the developing zebrafish, despite its importance as a model organism. We report here DNA methylation and histone modification profiles of promoters of developmentally-regulated genes (pou5f1, sox2, sox3, klf4, nnr, otx1b, nes, vasa), as well as tert and bactin2, in zebrafish embryos at the mid-late blastula transition, shortly after embryonic genome activation. We identify four classes of promoters based on the following profiles: (i) those enriched in marks of active genes (H3K9ac, H4ac, H3K4me3) without transcriptionally repressing H3K9me3 or H3K27me3; (ii) those enriched in H3K9ac, H4ac and H3K27me3, without H3K9me3; one such gene was klf4, shown by in situ hybridization to be mosaically expressed, likely accounting for the detection of both activating and repressive marks on its promoter; (iii) those enriched in H3K4me3 and H3K27me3 without acetylation; and (iv) those enriched in all histone modifications examined. Culture of embryo-derived cells under differentiation conditions leads to H3K9 and H4 deacetylation and H3K9 and H3K27 trimethylation on genes that are inactivated, yielding an epigenetic profile similar to those of fibroblasts or muscle. All promoters however retain H3K4me3, indicating an uncoupling of H3K4me3 occupancy and gene expression. All non-CpG island developmentally-regulated promoters are DNA unmethylated in embryos, but hypermethylated in fibroblasts. Our results suggest that differentially expressed embryonic genes are regulated by various patterns of histone modifications on unmethylated DNA, which create a developmentally permissive chromatin state.

}, keywords = {Animals, Blastula, Cell Line, Chromatin, Chromatin Immunoprecipitation, CpG Islands, DNA Methylation, Embryo, Nonmammalian, Fibroblasts, Gene Expression Profiling, Gene Expression Regulation, Developmental, Histones, In Situ Hybridization, Lysine, Methylation, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Reverse Transcriptase Polymerase Chain Reaction, Zebrafish, Zebrafish Proteins}, issn = {1696-3547}, doi = {10.1387/ijdb.103081ll}, author = {Lindeman, Leif C and Winata, Cecilia L and Aanes, Hvard and Mathavan, Sinnakaruppan and Alestrom, Peter and Collas, Philippe} } @article {71, title = {Expression of components of Wnt and Hedgehog pathways in different tissue layers during lung development in Xenopus laevis.}, journal = {Gene Expr Patterns}, volume = {10}, year = {2010}, month = {2010 Oct-Dec}, pages = {338-44}, abstract = {

Although Wnt and Hedgehog (Hh) signaling pathways play important roles in mouse lung development, these have not been explored in the development of Xenopus lung. This may be due to the lack of specific molecular markers for different layers of tissue in Xenopus lung and/or insufficient knowledge on expression patterns of Wnt and Hh signaling components in Xenopus lung. In this study, we first described the early morphogenesis of Xenopus laevis lung by using surfactant protein C (sftpc) as a marker of lung epithelium and compared it with the expression patterns of several genes of Wnt and Hh pathways in Xenopus lungs. Our data showed that wnt7b was expressed in the entire lung epithelium from stage 37 to stage 45, while two other Wnt signaling components, wnt5a and wif1 (wnt inhibitory factor 1), were expressed in the mesenchyme layer of the entire lungs through stages 39-41. We also found that sonic hedgehog (shh) was expressed at stage 41 only in the anterior, but not in the posterior part of the lungs. These results show the expression of wnt5a, wnt7b, wif1 and shh in different layers of tissue of Xenopus lungs at early developmental stages, which implies different roles of these genes in the early development of Xenopus lungs. Our study for the first time defined specific molecular markers for description of early lung development in Xenopus, as well as provided information about expression of components of Wnt and Hh pathways in early Xenopus lungs, which should be useful for future functional studies.

}, keywords = {Animals, Epithelium, Gene Expression Regulation, Developmental, Genetic Markers, Hedgehog Proteins, In Situ Hybridization, Lung, Mesoderm, Morphogenesis, Polymerase Chain Reaction, Pulmonary Surfactants, Signal Transduction, Wnt Proteins, Xenopus Proteins, Xenopus laevis}, issn = {1872-7298}, doi = {10.1016/j.gep.2010.07.005}, author = {Yin, Ao and Winata, Cecilia L and Korzh, Svitlana and Korzh, Vladimir and Gong, Zhiyuan} }