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Fu J, Zhu W, Wang L, Luo M, Jiang B, Dong Z. Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Hypophthalmichthys nobilis) Early Development. Front Genet 2022; 12:821403. [PMID: 35126475 PMCID: PMC8809360 DOI: 10.3389/fgene.2021.821403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
The early development of fish is regulated through dynamic and complex mechanisms involving the regulation of various genes. Many genes are subjected to post-transcriptional regulation by microRNAs (miRNAs). In the Chinese aquaculture industry, the native species bighead carp (Hypophthalmichthys nobilis) is important. However, the genetic regulation related to the early development of bighead carp is unknown. Here, we generated developmental profiles by miRNA sequencing to study the dynamic regulation of miRNAs during bighead carp early development. This study identified 1 046 miRNAs, comprising 312 known miRNAs and 734 uncharacterized miRNAs. Changes in miRNA expression were identified in the six early development stages. An obviously increased expression trend was detected during the development process, with the main burst of activity occurring after the earliest stage (early blastula, DS1). Investigations revealed that several miRNAs were dominantly expressed during the development process, especially in the later stages (e.g., miR-10b-5p, miR-21, miR-92a-3p, miR-206-3p, and miR-430a-3p), suggesting that these miRNAs exerted important functions during embryonic development. The differentially expressed miRNAs (DEMs) and time-serial analysis (profiles) of DEMs were analyzed. A total of 372 miRNAs were identified as DEMs (fold-change >2, and false discovery rate <0.05), and three expression profiles of the DEMs were detected to have co-expression patterns (r > 0.7, and p < 0.05). The broad negative regulation of target genes by miRNAs was speculated, and many development-related biological processes and pathways were enriched for the targets of the DEMs, which might be associated with maternal genome degradation and embryogenesis processes. In conclusion, we revealed the repertoire of miRNAs that are active during early development of bighead carp. These findings will increase our understanding of the regulatory mechanisms of early development of fish.
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Affiliation(s)
- Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Bingjie Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- *Correspondence: Zaijie Dong, ,
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Chen L, Xu W, Liu K, Jiang Z, Han Y, Jin H, Zhang L, Shen W, Jia S, Sun Q, Meng A. 5' Half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos. SCIENCE ADVANCES 2021; 7:eabh0494. [PMID: 34797706 PMCID: PMC8604414 DOI: 10.1126/sciadv.abh0494] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
5′tRFls are small transfer RNA (tRNA) fragments derived from 5′ half of mature tRNAs. However, it is unknown whether 5′tRFls could feed back to regulate tRNA biogenesis. Here, we show that 5′tRFlGly/GCC and 5′tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5′tRFlGly/GCC and 5′tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5′tRFlGly/GCC or 5′tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels, respectively, and causes embryonic lethality that is efficiently rescued by coinjection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5′tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5′tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA gene transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.
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Affiliation(s)
- Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kunpeng Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Jiang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Han
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongbin Jin
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Guangzhou Laboratory, Guangzhou 510320, Guangdong Province, China
- Corresponding author.
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3
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Yang L, Zhu X, Ni Y, Wu D, Tian Y, Chen Z, Li M, Zhang H, Liang D. MicroRNA-34c Inhibits Osteogenic Differentiation and Valvular Interstitial Cell Calcification via STC1-Mediated JNK Pathway in Calcific Aortic Valve Disease. Front Physiol 2020; 11:829. [PMID: 32982764 PMCID: PMC7489094 DOI: 10.3389/fphys.2020.00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 06/22/2020] [Indexed: 12/20/2022] Open
Abstract
Calcific aortic valve disease (CAVD), a common heart valve disease, is increasingly prevalent worldwide and causes high morbidity and mortality. Here, we aimed to investigate a possible role for miR-34c in the development of osteogenic differentiation during CAVD and to find out the underlying mechanisms. Valvular interstitial cells (VICs) were isolated from the clinical aortic valve tissue samples of CAVD patients and patients with acute aortic dissection and collected. Then, RT-qPCR was performed to determine miR-34c expression and western blot analysis was applied to confirm the relevant protein expression in these VICs. Dual luciferase reporter gene assay was applied to confirm the relation between miR-34c and STC1. Alkaline phosphatase (ALP) staining and alizarin red staining was performed to further confirm the degree of calcification in these samples. MiR-34c was lowly expressed and STC1 was highly expressed in the CAVD tissues. Furthermore, STC1 was the target of miR-34c and was negatively regulated by miR-34c. Overexpression of miR-34c in VICs was concomitant with suppression of both STC1 expression and phosphorylation level of c-Jun N-terminal kinase (JNK). In addition, significant decrease of bone morphogenetic protein-2 (BMP2) and osteocalcin, as well as the decrease of calcification degree were also observed in VICs with miR-34c overexpressed. Taken together, miR-34c could inhibit osteogenic differentiation and calcification of VICs by suppressing the STC1/JNK signaling pathway in CAVD, making miR-34c a novel therapeutic target for the treatment of CAVD.
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Affiliation(s)
- Lieming Yang
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xinyuan Zhu
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yingying Ni
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Dawei Wu
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yikui Tian
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhi Chen
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingbiao Li
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hao Zhang
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Degang Liang
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
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4
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Neupane S, Aryal YP, Kim TY, Yeon CY, An CH, Kim JY, Yamamoto H, Lee Y, Sohn WJ, Kim JY. Signaling Modulations of miR-206-3p in Tooth Morphogenesis. Int J Mol Sci 2020; 21:E5251. [PMID: 32722078 PMCID: PMC7432545 DOI: 10.3390/ijms21155251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of naturally occurring small non-coding RNAs that post-transcriptionally regulate gene expression in organisms. Most mammalian miRNAs influence biological processes, including developmental changes, tissue morphogenesis and the maintenance of tissue identity, cell growth, differentiation, apoptosis, and metabolism. The miR-206-3p has been correlated with cancer; however, developmental roles of this miRNA are unclear. In this study, we examined the expression pattern and evaluated the developmental regulation of miR-206-3p during tooth morphogenesis using ex-vivo culture method. The expression pattern of miR-206-3p was examined in the epithelium and mesenchyme of developing tooth germ with stage-specific manners. Perturbation of the expression of miR-206-3p clearly altered expression patterns of dental-development-related signaling molecules, including Axin2, Bmp2, Fgf4, Lef1 and Shh. The gene expression complemented with change in cellular events including, apoptosis and proliferation which caused altered crown and pulp morphogenesis in renal-capsule-calcified teeth. Especially, mislocalization of β-Catenin and SMAD1/5/8 were observed alongside dramatic alterations in the expression patterns of Fgf4 and Shh. Overall, our data suggest that the miR-206-3p regulate the cellular physiology during tooth morphogenesis through modulation of the Wnt, Bmp, Fgf, and Shh signaling pathways to form proper tooth pulp and crown.
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Affiliation(s)
- Sanjiv Neupane
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu 41940, Korea; (Y.P.A.); (T.-Y.K.); (C.-Y.Y.); (Y.L.)
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Yam Prasad Aryal
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu 41940, Korea; (Y.P.A.); (T.-Y.K.); (C.-Y.Y.); (Y.L.)
| | - Tae-Young Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu 41940, Korea; (Y.P.A.); (T.-Y.K.); (C.-Y.Y.); (Y.L.)
| | - Chang-Yeol Yeon
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu 41940, Korea; (Y.P.A.); (T.-Y.K.); (C.-Y.Y.); (Y.L.)
| | - Chang-Hyeon An
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea;
| | - Ji-Youn Kim
- Department of Dental Hygiene, College of Health Science, Gachon University, Incheon 21936, Korea;
| | - Hitoshi Yamamoto
- Department of Histology and Developmental Biology, Tokyo Dental College, Tokyo 101-0061, Japan;
| | - Youngkyun Lee
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu 41940, Korea; (Y.P.A.); (T.-Y.K.); (C.-Y.Y.); (Y.L.)
| | - Wern-Joo Sohn
- Pre-Major of Cosmetics and Pharmaceutics, Daegu Haany University, Gyeongsan 38610, Korea;
| | - Jae-Young Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu 41940, Korea; (Y.P.A.); (T.-Y.K.); (C.-Y.Y.); (Y.L.)
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5
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Abstract
Pyruvate kinase (PK), as one of the key enzymes for glycolysis, can encode four different subtypes from two groups of genes, although the M2 subtype PKM2 is expressed mainly during embryonic development in normal humans, and is closely related to tissue repair and regeneration, with the deepening of research, the role of PKM2 in tumor tissue has received increasing attention. PKM2 can be aggregated into tetrameric and dimeric forms, PKM2 in the dimer state can enter the nuclear to regulate gene expression, the transformation between them can play an important role in tumor cell energy supply, epithelial-mesenchymal transition (EMT), invasion and metastasis and cell proliferation. We will use the switching effect of PKM2 in glucose metabolism as the entry point to expand and enrich the Warburg effect. In addition, PKM2 can also regulate each other with various proteins by phosphorylation, acetylation and other modifications, mediate the different intracellular localization of PKM2 and then exert specific biological functions. In this paper, we will illustrate each of these points.
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6
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MicroRNA-125b-5p improves pancreatic β-cell function through inhibiting JNK signaling pathway by targeting DACT1 in mice with type 2 diabetes mellitus. Life Sci 2019; 224:67-75. [PMID: 30684546 DOI: 10.1016/j.lfs.2019.01.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a progressive disease, accompanied by increased insulin resistance and deteriorating β-cell function. Previous studies have revealed that microRNA (miRNA) plays a crucial role in the treatment of T2DM. Hence, we aim to investigate the role of microRNA-125b-5p (miR-125b-5p) in pancreatic β-cell function and insulin sensitivity of mice with T2DM with the involvement of Dishevelled antagonist Dapper1 (DACT1) and the c-Jun NH2-terminal kinases (JNK) signaling pathway. Firstly, a mouse model of T2DM was established by administering a high-fat diet plus low dosage of streptozotocin, and function of pancreatic β-cell and insulin sensitivity in the normal and T2DM mice were detected. Then, the pancreatic β-cells were collected from pancreatic islet tissues and treated with different mimics, inhibitors and siRNAs. After that, the relationship among miR-125b-5p, DACT1, and the JNK signaling-related factors in T2DM mice was determined. Finally, cell proliferation and apoptosis were determined. Mice with T2DM had lower pancreatic β-cell function and insulin sensitivity, as well as diminished expression of miR-125b-5p but enhanced expressions of DACT1, JNK and c-Jun. miR-125b-5p inhibited DACT1 expression and the activation of the JNK signaling pathway, as well as restrained cell proliferation and promoted cell apoptosis. The current results suggest that up-regulated miR-125b-5p promotes insulin sensitivity and enhances pancreatic β-cell function through inhibiting the JNK signaling pathway by negatively mediating DACT1.
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7
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Vergara HM, Ramirez J, Rosing T, Nave C, Blandino R, Saw D, Saraf P, Piexoto G, Coombes C, Adams M, Domingo CR. miR-206 is required for changes in cell adhesion that drive muscle cell morphogenesis in Xenopus laevis. Dev Biol 2018; 438:94-110. [PMID: 29596841 DOI: 10.1016/j.ydbio.2018.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are highly conserved small non-coding RNA molecules that post-transcriptionally regulate gene expression in multicellular organisms. Within the set of muscle-specific miRNAs, miR-206 expression is largely restricted to skeletal muscle and is found exclusively within the bony fish lineage. Although many studies have implicated miR-206 in muscle maintenance and disease, its role in skeletal muscle development remains largely unknown. Here, we examine the role of miR-206 during Xenopus laevis somitogenesis. In Xenopus laevis, miR-206 expression coincides with the onset of somitogenesis. We show that both knockdown and over-expression of miR-206 result in abnormal somite formation affecting muscle cell rotation, attachment, and elongation. In particular, our data suggests that miR-206 regulates changes in cell adhesion that affect the ability of newly formed somites to adhere to the notochord as well as to the intersomitic boundaries. Additionally, we show that β-dystroglycan and F-actin expression levels are significantly reduced, suggesting that knockdown of miR-206 levels affects cellular mechanics necessary for cell shape changes and attachments that are required for proper muscle formation.
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Affiliation(s)
- Hernando Martínez Vergara
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Julio Ramirez
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Trista Rosing
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Ceazar Nave
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Rebecca Blandino
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Daniel Saw
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Parag Saraf
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Gabriel Piexoto
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Coohleen Coombes
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Melissa Adams
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Carmen R Domingo
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA.
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8
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Abstract
TGF-β family ligands function in inducing and patterning many tissues of the early vertebrate embryonic body plan. Nodal signaling is essential for the specification of mesendodermal tissues and the concurrent cellular movements of gastrulation. Bone morphogenetic protein (BMP) signaling patterns tissues along the dorsal-ventral axis and simultaneously directs the cell movements of convergence and extension. After gastrulation, a second wave of Nodal signaling breaks the symmetry between the left and right sides of the embryo. During these processes, elaborate regulatory feedback between TGF-β ligands and their antagonists direct the proper specification and patterning of embryonic tissues. In this review, we summarize the current knowledge of the function and regulation of TGF-β family signaling in these processes. Although we cover principles that are involved in the development of all vertebrate embryos, we focus specifically on three popular model organisms: the mouse Mus musculus, the African clawed frog of the genus Xenopus, and the zebrafish Danio rerio, highlighting the similarities and differences between these species.
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Affiliation(s)
- Joseph Zinski
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Benjamin Tajer
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Mary C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
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9
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Lin CY, He JY, Zeng CW, Loo MR, Chang WY, Zhang PH, Tsai HJ. microRNA-206 modulates an Rtn4a/Cxcr4a/Thbs3a axis in newly forming somites to maintain and stabilize the somite boundary formation of zebrafish embryos. Open Biol 2018; 7:rsob.170009. [PMID: 28701377 PMCID: PMC5541343 DOI: 10.1098/rsob.170009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/12/2017] [Indexed: 12/22/2022] Open
Abstract
Although microRNA-206 (miR-206) is known to regulate proliferation and differentiation of muscle fibroblasts, the role of miR-206 in early-stage somite development is still unknown. During somitogenesis of zebrafish embryos, reticulon4a (rtn4a) is specifically repressed by miR-206. The somite boundary was defective, and actin filaments were crossing over the boundary in either miR-206-knockdown or rtn4a-overexpressed embryos. In these treated embryos, C-X-C motif chemokine receptor 4a (cxcr4a) was reduced, while thrombospondin 3a (thbs3a) was increased. The defective boundary was phenocopied in either cxcr4a-knockdown or thbs3a-overexpressed embryos. Repression of thbs3a expression by cxcr4a reduced the occurrence of the boundary defect. We demonstrated that cxcr4a is an upstream regulator of thbs3a and that defective boundary cells could not process epithelialization in the absence of intracellular accumulation of the phosphorylated focal adhesion kinase (p-FAK) in boundary cells. Therefore, in the newly forming somites, miR-206-mediated downregulation of rtn4a increases cxcr4a. This activity largely decreases thbs3a expression in the epithelial cells of the somite boundary, which causes epithelialization of boundary cells through mesenchymal-epithelial transition (MET) and eventually leads to somite boundary formation. Collectively, we suggest that miR-206 mediates a novel pathway, the Rtn4a/Cxcr4a/Thbs3a axis, that allows boundary cells to undergo MET and form somite boundaries in the newly forming somites of zebrafish embryos.
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Affiliation(s)
- Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, No. 46, Section 3 Zhongzhen Road, Sanzhi Dist., New Taipei City 252, Taiwan, Republic of China
| | - Jun-Yu He
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Chih-Wei Zeng
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Moo-Rumg Loo
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Wen-Yen Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Po-Hsiang Zhang
- Institute of Biomedical Sciences, Mackay Medical College, No. 46, Section 3 Zhongzhen Road, Sanzhi Dist., New Taipei City 252, Taiwan, Republic of China
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, No. 46, Section 3 Zhongzhen Road, Sanzhi Dist., New Taipei City 252, Taiwan, Republic of China
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Burgos-Aceves MA, Cohen A, Smith Y, Faggio C. Estrogen regulation of gene expression in the teleost fish immune system. FISH & SHELLFISH IMMUNOLOGY 2016; 58:42-49. [PMID: 27633675 DOI: 10.1016/j.fsi.2016.09.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/01/2016] [Accepted: 09/10/2016] [Indexed: 05/02/2023]
Abstract
Elucidating the mechanisms of estrogens-induced immunomodulation in teleost fish is of great importance due to the observed worldwide continuing decrease in pristine environments. However, little is know about the immunotoxicological consequences of exposure to these chemicals in fish, or of the mechanisms through which these effects are mediated. In this review, we summarize the results showing estrogens (natural or synthetic) acting through estrogen receptors and regulating specific target genes, also through microRNAs (miRNAs), leading to modulation of the immune functioning. The identification and characterization of miRNAs will provide new opportunities for functional genome research on teleost immune system and can also be useful when screening for novel molecule biomarkers for environmental pollution.
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Affiliation(s)
- Mario Alberto Burgos-Aceves
- Centro de Investigaciones Biológicas de Noroeste, S.C., Mar Bermejo 195, Col. Playa Palo de Sta. Rita, La Paz BCS, 23090, México
| | - Amit Cohen
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy.
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11
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Bunkar N, Pathak N, Lohiya NK, Mishra PK. Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med 2016; 43:59-81. [PMID: 27358824 PMCID: PMC4925870 DOI: 10.5653/cerm.2016.43.2.59] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/06/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
It is well established that there is a heritable element of susceptibility to chronic human ailments, yet there is compelling evidence that some components of such heritability are transmitted through non-genetic factors. Due to the complexity of reproductive processes, identifying the inheritance patterns of these factors is not easy. But little doubt exists that besides the genomic backbone, a range of epigenetic cues affect our genetic programme. The inter-generational transmission of epigenetic marks is believed to operate via four principal means that dramatically differ in their information content: DNA methylation, histone modifications, microRNAs and nucleosome positioning. These epigenetic signatures influence the cellular machinery through positive and negative feedback mechanisms either alone or interactively. Understanding how these mechanisms work to activate or deactivate parts of our genetic programme not only on a day-to-day basis but also over generations is an important area of reproductive health research.
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Affiliation(s)
- Neha Bunkar
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India
| | - Neelam Pathak
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Nirmal Kumar Lohiya
- Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Pradyumna Kumar Mishra
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Department of Molecular Biology, National Institute for Research in Environmental Health (ICMR), Bhopal, India
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Bizuayehu TT, Johansen SD, Puvanendran V, Toften H, Babiak I. Temperature during early development has long-term effects on microRNA expression in Atlantic cod. BMC Genomics 2015; 16:305. [PMID: 25881242 PMCID: PMC4403832 DOI: 10.1186/s12864-015-1503-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background Environmental temperature has serious implications in life cycle of aquatic ectotherms. Understanding the molecular mechanisms of temperature acclimation and adaptation of marine organisms is of the uttermost importance for ecology, fisheries, and aquaculture, as it allows modeling the effects of global warming on population dynamics. Regulatory molecules are major modulators of acclimation and adaptation; among them, microRNAs (miRNAs) are versatile and substantial contributors to regulatory networks of development and adaptive plasticity. However, their role in thermal plasticity is poorly known. We have asked whether the temperature and its shift during the early ontogeny (embryonic and larval development) affect the miRNA repertoire of Atlantic cod (Gadus morhua), and if thermal experience has long-term consequences in the miRNA profile. Results We characterized miRNA during different developmental stages and in juvenile tissues using next generation sequencing. We identified 389 putative miRNA precursor loci, 120 novel precursor miRNAs, and 281 mature miRNAs. Some miRNAs showed stage- or tissue-enriched expression and miRNAs, such as the miR-17 ~ 92 cluster, myomiRs (miR-206), neuromiRs (miR-9, miR-124), miR-130b, and miR-430 showed differential expression in different temperature regimes. Long-term effect of embryonic incubation temperature was revealed on expression of some miRNAs in juvenile pituitary (miR-449), gonad (miR-27c, miR-30c, and miR-200a), and liver (let-7 h, miR-7a, miR-22, miR-34c, miR-132a, miR-192, miR-221, miR-451, miR-2188, and miR-7550), but not in brain. Some of differentially expressed miRNAs in the liver were confirmed using LNA-based rt-qPCR. The effect of temperature on methylation status of selected miRNA promoter regions was mostly inconclusive. Conclusions Temperature elevation by several degrees during embryonic and larval developmental stages significantly alters the miRNA profile, both short-term and long-term. Our results suggest that a further rise in seas temperature might affect life history of Atlantic cod. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1503-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Steinar D Johansen
- University of Nordland, Faculty of Biosciences and Aquaculture, Post Box 1490, 8049, Bodø, Norway. .,Arctic University of Norway, FHS, RNA Lab, Dept Med Biol, N-9037, Tromsø, Norway.
| | | | - Hilde Toften
- Nofima AS, Muninbakken 9-13, P.O. box 6122, NO, 9291, Tromsø, Norway.
| | - Igor Babiak
- University of Nordland, Faculty of Biosciences and Aquaculture, Post Box 1490, 8049, Bodø, Norway.
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Down-regulation of miR-206 is associated with Hirschsprung disease and suppresses cell migration and proliferation in cell models. Sci Rep 2015; 5:9302. [PMID: 25792468 PMCID: PMC4366810 DOI: 10.1038/srep09302] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/25/2015] [Indexed: 01/07/2023] Open
Abstract
Hirschsprung disease (HSCR) is a well-known congenital digestive disease that originates due to the developmental disorder of neural crest cells. MiR-206 is kown to have a relationship with digestive malfunctions. Therefore, we investigated whether or not miR-206 was involved in the pathogenesis of HSCR. qRT-PCR and Western blot assays were used to detect the expression levels of miRNA and mRNAs, and proteins in case and control tissue samples and two cell lines (293T and SH-SY5Y). The functions of miR-206 in vitro were measured by transwell assay, CCK8 assay and flow cytometry. Finally, we conducted dual-luciferase reporter assay to verify the connections between miR-206 and the target mRNA SDPR. Down-regulation of miR-206 was found in HSCR case tissue samples compared with controls, which was validated to be connected with the increased level of mRNA and protein of SDPR by qRT-PCR and dual-luciferase reporter assay. Moreover, miR-206 suppressed the cell migration and proliferation and silencing of SDPR could rescue the extent of the suppressing effects by miR-206 inhibitor. The findings suggest that miR-206 may play a significant role in the pathogenesis of HSCR, as well as inhibiting the cell migration and proliferation by targeting SDPR in disease models.
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Abstract
MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique features across Metazoa. Here, we present the current status of the knowledge about the role of miRNA in development, growth, and physiology of teleost fishes, in comparison to other vertebrates. Infraclass Teleostei is the most abundant group among vertebrate lineage. Fish are an important component of aquatic ecosystems and human life, being the prolific source of animal proteins worldwide and a vertebrate model for biomedical research. We review miRNA biogenesis, regulation, modifications, and mechanisms of action. Specific sections are devoted to the role of miRNA in teleost development, organogenesis, tissue differentiation, growth, regeneration, reproduction, endocrine system, and responses to environmental stimuli. Each section discusses gaps in the current knowledge and pinpoints the future directions of research on miRNA in teleosts.
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Affiliation(s)
| | - Igor Babiak
- Faculty of Aquaculture and Biosciences, University of Nordland, Bodø, Norway
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15
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Toivonen JM, Manzano R, Oliván S, Zaragoza P, García-Redondo A, Osta R. MicroRNA-206: a potential circulating biomarker candidate for amyotrophic lateral sclerosis. PLoS One 2014; 9:e89065. [PMID: 24586506 PMCID: PMC3930686 DOI: 10.1371/journal.pone.0089065] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/13/2014] [Indexed: 12/28/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a lethal motor neuron disease that progressively debilitates neuronal cells that control voluntary muscle activity. Biomarkers are urgently needed to facilitate ALS diagnosis and prognosis, and as indicators of therapeutic response in clinical trials. microRNAs (miRNAs), small posttranscriptional modifiers of gene expression, are frequently altered in disease conditions. Besides their important regulatory role in variety of biological processes, miRNAs can also be released into the circulation by pathologically affected tissues and display remarkable stability in body fluids. In a mouse model of ALS that expresses mutated human superoxide dismutase 1 (SOD1-G93A) skeletal muscle is one of the tissues affected early by mutant SOD1 toxicity. To find biomarkers for ALS, we studied miRNA alterations from skeletal muscle and plasma of SOD1-G93A mice, and subsequently tested the levels of the affected miRNAs in the serum from human ALS patients. Fast-twitch and slow-twitch muscles from symptomatic SOD1-G93A mice (age 90 days) and their control littermates were first studied using miRNA microarrays and then evaluated with quantitative PCR from five age groups from neonatal to the terminal disease stage (10–120 days). Among those miRNA changed in various age/gender/muscle groups (miR-206, -1, -133a, -133b, -145, -21, -24), miR-206 was the only one consistently altered during the course of the disease pathology. In both sexes, mature miR-206 was increased in fast-twitch muscles preferably affected in the SOD1-G93A model, with highest expression towards the most severely affected animals. Importantly, miR-206 was also increased in the circulation of symptomatic animals and in a group of 12 definite ALS patients tested. We conclude that miR-206 is elevated in the circulation of symptomatic SOD1-G93A mice and possibly in human ALS patients. Although larger scale studies on ALS patients are warranted, miR-206 is a promising candidate biomarker for this motor neuron disease.
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Affiliation(s)
- Janne M Toivonen
- Laboratorio de Genética Bioquímica (LAGENBIO-I3A), Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Raquel Manzano
- Laboratorio de Genética Bioquímica (LAGENBIO-I3A), Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Sara Oliván
- Laboratorio de Genética Bioquímica (LAGENBIO-I3A), Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica (LAGENBIO-I3A), Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Madrid, Spain
| | - Rosario Osta
- Laboratorio de Genética Bioquímica (LAGENBIO-I3A), Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
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Liu X, Ma Y, Zhang C, Wei S, Cao Y, Wang Q. Nodal promotes mir206 expression to control convergence and extension movements during zebrafish gastrulation. J Genet Genomics 2013; 40:515-21. [PMID: 24156917 DOI: 10.1016/j.jgg.2013.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 07/15/2013] [Accepted: 07/22/2013] [Indexed: 11/25/2022]
Abstract
Nodal, a member of the transforming growth factor β (TGF-β) superfamily, has been shown to play a role in mesendoderm induction and gastrulation movements. The activity of Nodal signaling can be modulated by microRNAs (miRNAs) as previously reported, but little is known about which miRNAs are regulated by Nodal during gastrulation. In the present study, we found that the expression of mir206, one of the most abundant miRNAs during zebrafish early embryo development, is regulated by Nodal signaling. Abrogation of Nodal signal activity results in defective convergence and extension (CE) movements, and these cell migration defects can be rescued by supplying an excess of mir206, suggesting that mir206 acts downstream of Nodal signaling to regulate CE movements. Furthermore, in mir206 morphants, the expression of cell adhesion molecule E-cadherin is significantly increased, while the key transcriptional repressor of E-cadherin, snail1a, is depressed. Our study uncovers a novel mechanism by which Nodal-regulated mir206 modulates gastrulation movements in connection with the Snail/E-cadherin pathway.
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Affiliation(s)
- Xiuli Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Liu Y, Liu Q, Jia W, Chen J, Wang J, Ye D, Guo X, Chen W, Li G, Wang G, Deng A, Kang J. MicroRNA-200a regulates Grb2 and suppresses differentiation of mouse embryonic stem cells into endoderm and mesoderm. PLoS One 2013; 8:e68990. [PMID: 23874841 PMCID: PMC3715486 DOI: 10.1371/journal.pone.0068990] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 06/03/2013] [Indexed: 12/20/2022] Open
Abstract
The mechanisms by which microRNAs (miRNAs) affect cell fate decisions remain poorly understood. Herein, we report that miR-200a can suppress the differentiation of mouse embryonic stem (ES) cells into endoderm and mesoderm. Interestingly, miR-200a directly targets growth factor receptor-bound protein 2 (Grb2), which is a key adaptor in the Erk signaling pathway. Furthermore, high levels of miR-200a dramatically decrease Grb2 levels and suppress the appearance of mesoderm and endoderm lineages in embryoid body formation, as well as suppressing the activation of Erk. Finally, Grb2 supplementation significantly rescues the miR-200a-induced layer-formation bias and the Erk suppression. Collectively, our results demonstrate that miR-200a plays critical roles in ES cell lineage commitment by directly regulating Grb2 expression and Erk signaling.
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Affiliation(s)
- Yang Liu
- Department of Laboratory Medicine and Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, People’s Republic of China
| | - Qidong Liu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Wenwen Jia
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Jie Chen
- Department of Laboratory Medicine and Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, People’s Republic of China
| | - Jianmin Wang
- Department of Laboratory Medicine and Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, People’s Republic of China
| | - Dan Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Wen Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Guoping Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Guiying Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Anmei Deng
- Department of Laboratory Medicine and Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, People’s Republic of China
- * E-mail: (JK); (AD)
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
- * E-mail: (JK); (AD)
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Ning G, Liu X, Dai M, Meng A, Wang Q. MicroRNA-92a Upholds Bmp Signaling by Targeting noggin3 during Pharyngeal Cartilage Formation. Dev Cell 2013; 24:283-95. [DOI: 10.1016/j.devcel.2012.12.016] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 09/27/2012] [Accepted: 12/24/2012] [Indexed: 12/21/2022]
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