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Wang K, Hua G, Li J, Yang Y, Zhang C, Yang L, Hu X, Scheben A, Wu Y, Gong P, Zhang S, Fan Y, Zeng T, Lu L, Gong Y, Jiang R, Sun G, Tian Y, Kang X, Hu H, Li W. Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. IMETA 2024; 3:e154. [PMID: 38868520 PMCID: PMC10989122 DOI: 10.1002/imt2.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/07/2023] [Indexed: 06/14/2024]
Abstract
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
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Affiliation(s)
- Kejun Wang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu Yang
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Chenxi Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Lan Yang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiaoyu Hu
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Armin Scheben
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Yanan Wu
- Department of preventive veterinary medicine, College of Veterinary MedicineHenan Agricultural UniversityZhengzhouChina
- International Joint Research Center for National Animal ImmunologyZhengzhouHenanChina
| | - Ping Gong
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Shuangjie Zhang
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Yanfeng Fan
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ruirui Jiang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guirong Sun
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Yadong Tian
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiangtao Kang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding and Guangdong Rice Engineering LaboratoryGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Wenting Li
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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3
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. RESEARCH SQUARE 2023:rs.3.rs-2652395. [PMID: 36993571 PMCID: PMC10055508 DOI: 10.21203/rs.3.rs-2652395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Hongzhan Huang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry L. David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
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Núñez L, Buxbaum AR, Katz ZB, Lopez-Jones M, Nwokafor C, Czaplinski K, Pan F, Rosenberg J, Monday HR, Singer RH. Tagged actin mRNA dysregulation in IGF2BP1[Formula: see text] mice. Proc Natl Acad Sci U S A 2022; 119:e2208465119. [PMID: 36067310 PMCID: PMC9477413 DOI: 10.1073/pnas.2208465119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Gene expression is tightly regulated by RNA-binding proteins (RBPs) to facilitate cell survival, differentiation, and migration. Previous reports have shown the importance of the Insulin-like Growth Factor II mRNA-Binding Protein (IGF2BP1/IMP1/ZBP1) in regulating RNA fate, including localization, transport, and translation. Here, we generated and characterized a knockout mouse to study RBP regulation. We report that IGF2BP1 is essential for proper brain development and neonatal survival. Specifically, these mice display disorganization in the developing neocortex, and further investigation revealed a loss of cortical marginal cell density at E17.5. We also investigated migratory cell populations in the IGF2BP1[Formula: see text] mice, using BrdU labeling, and detected fewer mitotically active cells in the cortical plate. Since RNA localization is important for cellular migration and directionality, we investigated the regulation of β-actin messenger RNA (mRNA), a well-characterized target with established roles in cell motility and development. To aid in our understanding of RBP and target mRNA regulation, we generated mice with endogenously labeled β-actin mRNA (IGF2BP1[Formula: see text]; β-actin-MS2[Formula: see text]). Using endogenously labeled β-actin transcripts, we report IGF2BP1[Formula: see text] neurons have increased transcription rates and total β-actin protein content. In addition, we found decreased transport and anchoring in knockout neurons. Overall, we present an important model for understanding RBP regulation of target mRNA.
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Affiliation(s)
- Leti Núñez
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | | | | | - Melissa Lopez-Jones
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | - Chiso Nwokafor
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | | | - Feng Pan
- Eli Lilly and Company, Indianapolis, IN 46285
| | | | | | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY 10461
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5
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Chitramuthu BP, Campos-García VR, Bateman A. Multiple Molecular Pathways Are Influenced by Progranulin in a Neuronal Cell Model-A Parallel Omics Approach. Front Neurosci 2022; 15:775391. [PMID: 35095393 PMCID: PMC8791029 DOI: 10.3389/fnins.2021.775391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Progranulin (PGRN) is critical in supporting a healthy CNS. Its haploinsufficiency results in frontotemporal dementia, while in experimental models of age-related neurodegenerative diseases, the targeted expression of PGRN greatly slows the onset of disease phenotypes. Nevertheless, much remains unclear about how PGRN affects its target cells. In previous studies we found that PGRN showed a remarkable ability to support the survival of NSC-34 motor neuron cells under conditions that would otherwise lead to their apoptosis. Here we used the same model to investigate other phenotypes of PGRN expression in NSC-34 cells. PGRN significantly influenced morphological differentiation, resulting in cells with enlarged cell bodies and extended projections. At a molecular level this correlated with pathways associated with the cytoskeleton and synaptic differentiation. Depletion of PGRN led to increased expression of several neurotrophic receptors, which may represent a homeostatic mechanism to compensate for loss of neurotrophic support from PGRN. The exception was RET, a neurotrophic tyrosine receptor kinase, which, when PGRN levels are high, shows increased expression and enhanced tyrosine phosphorylation. Other receptor tyrosine kinases also showed higher tyrosine phosphorylation when PGRN was elevated, suggesting a generalized enhancement of receptor activity. PGRN was found to bind to multiple plasma membrane proteins, including RET, as well as proteins in the ER/Golgi apparatus/lysosome pathway. Understanding how these various pathways contribute to PGRN action may provide routes toward improving neuroprotective therapies.
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Affiliation(s)
- Babykumari P Chitramuthu
- Division of Experimental Medicine, Faculty of Medicine and Health Sciences, McGill University, and Centre for Translational Biology, Metabolic Disorders and Complications, McGill University Health Centre Research Institute, Montréal, QC, Canada
| | - Víctor R Campos-García
- Division of Experimental Medicine, Faculty of Medicine and Health Sciences, McGill University, and Centre for Translational Biology, Metabolic Disorders and Complications, McGill University Health Centre Research Institute, Montréal, QC, Canada
| | - Andrew Bateman
- Division of Experimental Medicine, Faculty of Medicine and Health Sciences, McGill University, and Centre for Translational Biology, Metabolic Disorders and Complications, McGill University Health Centre Research Institute, Montréal, QC, Canada
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Liu H, Xu H, Lan X, Cao X, Pan C. The InDel variants of sheep IGF2BP1 gene are associated with growth traits. Anim Biotechnol 2021; 34:134-142. [PMID: 34255980 DOI: 10.1080/10495398.2021.1942029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) plays positive roles in the growth, proliferation of cells and early embryos development by binding mRNA targets. Recently, it had been shown that some polymorphic loci within IGF2BP1 gene were associated with growth traits in animals, especially in goats. Therefore, it has been hypothesized that some variants within IGF2BP1 gene may be also involved in growth traits of sheep. Nine insertion/deletion (InDel) mutations within IGF2BP1 were identified and three loci were polymorphic. Meanwhile, the association analyses between three InDels and growth traits were carried out in 745 sheep. The results showed that all InDels included 5 bp InDel in downstream region, 9 bp InDel in intron 4 and 15 bp InDel in intron 2 within IGF2BP1 were significantly associated with growth traits (p<.05). Furthermore, at 5 and 9 bp InDel loci, the individuals of heterozygous genotype (ID) had superior growing performance especially at body weight (BW). In all, three InDels were crucial variants correlated with growth traits and could be applied in marker-assisted selection (MAS) in sheep.
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Affiliation(s)
- Hongfei Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, P. R. China.,College of Animal Science and Technology, Northwest A&F University, Yangling, P. R. China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, P. R. China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, P. R. China
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Xing L, Cai Y, Yang T, Yu W, Gao M, Chai R, Ding S, Wei J, Pan J, Chen G. Epitranscriptomic m6A regulation following spinal cord injury. J Neurosci Res 2020; 99:843-857. [PMID: 33271625 DOI: 10.1002/jnr.24763] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022]
Abstract
RNA methylation is involved in multiple physiological and pathological processes. However, the role of RNA methylation in spinal cord regeneration has not been reported. In this study, we find an altered m6A (N6-methyladenosine) RNA methylation profiling following zebrafish spinal cord injury (SCI), in line with an altered transcription level of the m6A methylase Mettl3. Interestingly, many of the differential m6A-tagged genes associated with neural regeneration are hypomethylated, but their transcription levels are upregulated in SCI. Moreover, we find that METTL3 may be important for spinal cord regeneration. We also show a conserved feature of METTL3 changes in mouse SCI model, in which the expression of METTL3 is increased in both astrocytes and neural stem cells. Together, our results indicate that m6A RNA methylation is dynamic and conserved following SCI and may contribute to spinal cord regeneration.
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Affiliation(s)
- Lingyan Xing
- Key Laboratory of Neuroregeneration of Jiangsu and the Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yunyun Cai
- Department of Physiology, School of medicine, Nantong University, Nantong, China
| | - Tuo Yang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Weiwei Yu
- Key Laboratory of Neuroregeneration of Jiangsu and the Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Mengdie Gao
- Key Laboratory of Neuroregeneration of Jiangsu and the Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Rui Chai
- Key Laboratory of Neuroregeneration of Jiangsu and the Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Sujun Ding
- Department of Medical Ultrasound, Affiliated Hospital of Nantong University, Nantong, China
| | - Jinhuan Wei
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China
| | - Jingying Pan
- Department of Tissue and Embryology, Medical School of Nantong University, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Gang Chen
- Department of Tissue and Embryology, Medical School of Nantong University, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Department of Anesthesiology, Affiliated Hospital of Nantong University, Nantong, China
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Wu J, Lu C, Ge S, Mei J, Li X, Guo W. Igf2bp1 is required for hepatic outgrowth during early liver development in zebrafish. Gene 2020; 744:144632. [PMID: 32240777 DOI: 10.1016/j.gene.2020.144632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 02/09/2023]
Abstract
IGF2BPs, a subclass of RNA-binding proteins, regulate cellular differentiation, proliferation and migration during multiple organs development, but their functions in liver development still remain unclear. Here, in this study, whole-mount in situ hybridization showed that igf2bp1 was constantly and stably expressed at early stages of embryo development in zebrafish. Both the morpholino-induced knockdown and CRISPR/Cas9-mediated knockout of igf2bp1 led to a reduced-size liver phenotype. Further analysis revealed that igf2bp1 is required for hepatic outgrowth, but not for hepatoblast specification and budding. Deficiency of igf2bp1 resulted in reduced cell proliferation, but had no effect on apoptosis. Therefore, we concluded that igf2bp1 is a critical factor to regulate hepatic outgrowth via cell proliferation during early liver development in zebrafish.
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Affiliation(s)
- Junjie Wu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Yunnan Institute of Fisheries Sciences, Kunming 650111, China
| | - Chang Lu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Si Ge
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohui Li
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wenjie Guo
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Syntaphilin-Mediated Docking of Mitochondria at the Growth Cone Is Dispensable for Axon Elongation In Vivo. eNeuro 2019; 6:ENEURO.0026-19.2019. [PMID: 31481398 PMCID: PMC6751374 DOI: 10.1523/eneuro.0026-19.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 08/15/2019] [Accepted: 08/22/2019] [Indexed: 11/25/2022] Open
Abstract
Mitochondria are abundantly detected at the growth cone, the dynamic distal tip of developing axons that directs growth and guidance. It is, however, poorly understood how mitochondrial dynamics relate to growth cone behavior in vivo, and which mechanisms are responsible for anchoring mitochondria at the growth cone during axon pathfinding. Here, we show that in retinal axons elongating along the optic tract in zebrafish, mitochondria accumulate in the central area of the growth cone and are occasionally observed in filopodia extending from the growth cone periphery. Mitochondrial behavior at the growth cone in vivo is dynamic, with mitochondrial positioning and anterograde transport strongly correlating with growth cone behavior and axon outgrowth. Using novel zebrafish mutant lines that lack the mitochondrial anchoring proteins Syntaphilin a and b, we further show that Syntaphilins contribute to mitochondrial immobilization at the growth cone. Syntaphilins are, however, not required for proper growth cone morphology and axon growth in vivo, indicating that Syntaphilin-mediated anchoring of mitochondria at the growth cone plays only a minor role in elongating axons.
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Abstract
In this issue of Neuron, Cagnetta et al. (2018) describe a novel method to identify, in an unbiased manner, newly synthesized axonal proteins in response to axon guidance cues. They find that axons stimulated by different guidance cues (Netrin-1, BDNF, and Sema3A) show distinct and common signatures.
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Ning X, Feng L, Li X, Wang S, Zhang M, Wang S, Zhang L, Hu X, Bao Z. The scallop IGF2 mRNA-binding protein gene PyIMP and association of a synonymous mutation with growth traits. Genes Genet Syst 2018; 93:91-100. [PMID: 29998907 DOI: 10.1266/ggs.17-00028] [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] [Indexed: 11/23/2022] Open
Abstract
Insulin-like growth factor 2 mRNA-binding proteins (IMPs) function in localization, stability and translational control of their target RNAs. In this study, we identified an IMP gene (PyIMP) from Yesso scallop, Patinopecten yessoensis. The complete DNA sequence of PyIMP was 22,875 bp, consisting of seventeen exons and sixteen introns. The full-length cDNA sequence was 3,293 bp, with an open reading frame of 1,776 bp, encoding 592 amino acids. PyIMP exhibited characters typical of IMPs, namely two RNA recognition motifs and four hnRNP K homology domains. Real-time quantitative reverse transcription PCR analysis indicated that PyIMP was universally expressed, with higher expression levels in the gonad of adult scallops, and in gastrulae and trochophore larvae at developmental stages. A synonymous mutation SNP, c.852A>G, which showed significant associations with growth traits of Yesso scallop, was identified in this gene. Scallops with the AA genotype at this locus had significantly higher trait values than those with the GG genotype for shell length, shell height, body weight, soft tissue weight and striated muscle weight (P < 0.05). Meanwhile, the expression of PyIMP in AA type scallops was significantly higher than that in the GG type, implying a positive effect of PyIMP on scallop growth. PyIMP represents the first mRNA-binding protein gene characterized in mollusks, and SNP c.852A>G will be useful for a better understanding of the role of mRNA-binding proteins in bivalves and for scallop breeding.
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Affiliation(s)
- Xianhui Ning
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Liying Feng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Xue Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Shuyue Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Mengran Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology
| | - Lingling Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology
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12
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The Roles of Insulin-Like Growth Factor 2 mRNA-Binding Protein 2 in Cancer and Cancer Stem Cells. Stem Cells Int 2018; 2018:4217259. [PMID: 29736175 PMCID: PMC5874980 DOI: 10.1155/2018/4217259] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/12/2017] [Accepted: 01/04/2018] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins (RBPs) mediate the localization, stability, and translation of the target transcripts and fine-tune the physiological functions of the proteins encoded. The insulin-like growth factor (IGF) 2 mRNA-binding protein (IGF2BP, IMP) family comprises three RBPs, IGF2BP1, IGF2BP2, and IGF2BP3, capable of associating with IGF2 and other transcripts and mediating their processing. IGF2BP2 represents the least understood member of this family of RBPs; however, it has been reported to participate in a wide range of physiological processes, such as embryonic development, neuronal differentiation, and metabolism. Its dysregulation is associated with insulin resistance, diabetes, and carcinogenesis and may potentially be a powerful biomarker and candidate target for relevant diseases. This review summarizes the structural features, regulation, and functions of IGF2BP2 and their association with cancer and cancer stem cells.
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13
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Dong X, Xu H, Wu X, Yang L. Multiple bioanalytical method to reveal developmental biological responses in zebrafish embryos exposed to triclocarban. CHEMOSPHERE 2018; 193:251-258. [PMID: 29136572 DOI: 10.1016/j.chemosphere.2017.11.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/05/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Triclocarban (TCC) is a well-known antibacterial agent that is frequently detected in environmental, wildlife and human samples. The potential toxicological effects and action mechanism of TCC on vertebrate development has remained unclear. In the present study, we analyzed phenotypic alterations, thyroid hormone levels, thyroid hormone responsive genes, and proteomic profiles of zebrafish embryos after exposure to a series of concentrations of TCC from 6 h post-fertilization (hpf) to 120 hpf. The most nonlethal concentration (MNLC), lethal concentration 10% (LC10) and lethal concentration 50% (LC50) of TCC for exposures of 96 h were 133.3 μg/L, 147.5 μg/L and 215.8 μg/L, respectively. Our results showed that exposure to TCC decreased heart rate, delayed yolk absorption and swim bladder development at MNLC and LC10. Exposure to MNLC of TCC inhibited thyroid hormone and altered expression of thyroid hormone responsive genes. Furthermore, exposure to 1/20 MNLC of TCC altered expression of proteins related to binding and metabolism, skeletal muscle development and function, as well as proteins involved in nervous system development and immune response, indicating TCC has potential health risks in wildlife and humans at low concentration level.
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Affiliation(s)
- Xing Dong
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Hai Xu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China.
| | - Xiangyang Wu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Liuqing Yang
- School of Chemistry & Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
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14
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Expression and characterization of insulin-like growth factor II mRNA binding protein in the razor clam Sinonovacula constricta. AQUACULTURE AND FISHERIES 2017. [DOI: 10.1016/j.aaf.2017.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Donlin-Asp PG, Rossoll W, Bassell GJ. Spatially and temporally regulating translation via mRNA-binding proteins in cellular and neuronal function. FEBS Lett 2017; 591:1508-1525. [PMID: 28295262 DOI: 10.1002/1873-3468.12621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/20/2022]
Abstract
Coordinated regulation of mRNA localization and local translation are essential steps in cellular asymmetry and function. It is increasingly evident that mRNA-binding proteins play critical functions in controlling the fate of mRNA, including when and where translation occurs. In this review, we discuss the robust and complex roles that mRNA-binding proteins play in the regulation of local translation that impact cellular function in vertebrates. First, we discuss the role of local translation in cellular polarity and possible links to vertebrate development and patterning. Next, we discuss the expanding role for local protein synthesis in neuronal development and function, with special focus on how a number of neurological diseases have given us insight into the importance of translational regulation. Finally, we discuss the ever-increasing set of tools to study regulated translation and how these tools will be vital in pushing forward and addressing the outstanding questions in the field.
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Affiliation(s)
- Paul G Donlin-Asp
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Wilfried Rossoll
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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16
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Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. RNA-binding proteins in eye development and disease: implication of conserved RNA granule components. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:527-57. [PMID: 27133484 DOI: 10.1002/wrna.1355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
Abstract
The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, the orthologs or family members of several conserved transcription and signaling regulators such as Pax6, Six3, Prox1, and Bmp4 are commonly required for their development. In contrast, our understanding of posttranscriptional regulation in eye development and disease, particularly regarding the function of RNA-binding proteins (RBPs), is limited. We examine the present knowledge of RBPs in eye development in the insect model Drosophila as well as several vertebrate models such as fish, frog, chicken, and mouse. Interestingly, of the 42 RBPs that have been investigated for their expression or function in vertebrate eye development, 24 (~60%) are recognized in eukaryotic cells as components of RNA granules such as processing bodies, stress granules, or other specialized ribonucleoprotein (RNP) complexes. We discuss the distinct developmental and cellular events that may necessitate potential RBP/RNA granule-associated RNA regulon models to facilitate posttranscriptional control of gene expression in eye morphogenesis. In support of these hypotheses, three RBPs and RNP/RNA granule components Tdrd7, Caprin2, and Stau2 are linked to ocular developmental defects such as congenital cataract, Peters anomaly, and microphthalmia in human patients or animal models. We conclude by discussing the utility of interdisciplinary approaches such as the bioinformatics tool iSyTE (integrated Systems Tool for Eye gene discovery) to prioritize RBPs for deriving posttranscriptional regulatory networks in eye development and disease. WIREs RNA 2016, 7:527-557. doi: 10.1002/wrna.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University & Purdue University Indianapolis, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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