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Wu C, Liu H, Zhan Z, Zhang X, Zhang M, You J, Ma J. Unveiling dysregulated lncRNAs and networks in non-syndromic cleft lip with or without cleft palate pathogenesis. Sci Rep 2024; 14:1047. [PMID: 38200098 PMCID: PMC10781966 DOI: 10.1038/s41598-024-51747-8] [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: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital facial malformation with a complex, incompletely understood origin. Long noncoding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression, potentially shedding light on NSCL/P's etiology. This study aimed to identify critical lncRNAs and construct regulatory networks to unveil NSCL/P's underlying molecular mechanisms. Integrating gene expression profiles from the Gene Expression Omnibus (GEO) database, we pinpointed 30 dysregulated NSCL/P-associated lncRNAs. Subsequent analyses enabled the creation of competing endogenous RNA (ceRNA) networks, lncRNA-RNA binding protein (RBP) interaction networks, and lncRNA cis and trans regulation networks. RT-qPCR was used to examine the regulatory networks of lncRNA in vivo and in vitro. Furthermore, protein levels of lncRNA target genes were validated in human NSCL/P tissue samples and murine palatal shelves. Consequently, two lncRNAs and three mRNAs: FENDRR (log2FC = - 0.671, P = 0.040), TPT1-AS1 (log2FC = 0.854, P = 0.003), EIF3H (log2FC = - 1.081, P = 0.041), RBBP6 (log2FC = 0.914, P = 0.037), and SRSF1 (log2FC = 0.763, P = 0.026) emerged as potential contributors to NSCL/P pathogenesis. Functional enrichment analyses illuminated the biological functions and pathways associated with these lncRNA-related networks in NSCL/P. In summary, this study comprehensively delineates the dysregulated transcriptional landscape, identifies associated lncRNAs, and reveals pivotal sub-networks relevant to NSCL/P development, aiding our understanding of its molecular progression and setting the stage for further exploration of lncRNA and mRNA regulation in NSCL/P.
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Affiliation(s)
- Caihong Wu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Stomatological Hospital affiliated Suzhou Vocational Health College, Suzhou, China
| | - Haojie Liu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Zhuorong Zhan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Xinyu Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Mengnan Zhang
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jiawen You
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Junqing Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
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2
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Binelli A, Nigro L, Sbarberi R, Della Torre C, Magni S. To be or not to be plastics? Protein modulation and biochemical effects in zebrafish embryos exposed to three water-soluble polymers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167699. [PMID: 37832656 DOI: 10.1016/j.scitotenv.2023.167699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Water-soluble polymers (WSPs) are a particular category of polymers that, due to their capability to be soluble in water, come out of the classic definition of plastic and therefore also from its regulation and control, representing a possible new environmental problem considering the number of consumer products in which they are contained. For this reason, the aim of this study was to evaluate the possible adverse effects of three of the most used WSPs (polyacrylic acid - PAA, polyethylene glycol - PEG, polyvinylpyrrolidone - PVP), administered at relevant environmental concentrations (0.001, 0.5 and 1 mg/L) to Danio rerio (zebrafish) embryos up to 120 h post fertilization. To assess the WSP toxicity at the molecular, cellular and organism level we used an integrated ecotoxicological approach of both biomarkers and high-throughput technology based on gel-free proteomics. The main results showed how all the three WSPs up-regulated many proteins (up to 74 in specimens exposed to 1 mg/L PVP) with a wide range of molecular functions and involved in numerous cellular pathways of exposed specimens. On the other hand, the measurement of biomarkers showed how PAA and PVP were able to activate the antioxidant machinery following an over-production of reactive oxygen species, while PEG produced no significant changes in the biomarkers measured. Based on the obtained results, the use and application of WSPs should be revised and regulated.
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Affiliation(s)
- Andrea Binelli
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| | - Lara Nigro
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy.
| | - Riccardo Sbarberi
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| | - Camilla Della Torre
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| | - Stefano Magni
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
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3
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Fujii K, Zhulyn O, Byeon GW, Genuth NR, Kerr CH, Walsh EM, Barna M. Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c. Dev Cell 2021; 56:2928-2937.e9. [PMID: 34752747 DOI: 10.1016/j.devcel.2021.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/06/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022]
Abstract
Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning. Analysis of loss-of-function eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor patched 1 (Ptch1) dosage. Genome-wide in vivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine-rich motif present in subsets of 5'-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find a transcript specific effect in Eif3c loss-of-function embryos whereby translation of Ptch1 through this pyrimidine-rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.
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Affiliation(s)
- Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.
| | - Olena Zhulyn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Naomi R Genuth
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin M Walsh
- Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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4
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Jaiswal S, Nandi S, Iquebal MA, Jasrotia RS, Patra S, Mishra G, Udit UK, Sahu DK, Angadi UB, Meher PK, Routray P, Sundaray JK, Verma DK, Das P, Jayasankar P, Rai A, Kumar D. Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing. BMC Genomics 2021; 22:685. [PMID: 34548034 PMCID: PMC8456608 DOI: 10.1186/s12864-021-08001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/26/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samiran Nandi
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunita Patra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Gayatri Mishra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Uday Kumar Udit
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Dinesh Kumar Sahu
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prem Kumar Meher
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Padmanav Routray
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | | | - Paramananda Das
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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5
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Thongkorn S, Kanlayaprasit S, Panjabud P, Saeliw T, Jantheang T, Kasitipradit K, Sarobol S, Jindatip D, Hu VW, Tencomnao T, Kikkawa T, Sato T, Osumi N, Sarachana T. Sex differences in the effects of prenatal bisphenol A exposure on autism-related genes and their relationships with the hippocampus functions. Sci Rep 2021; 11:1241. [PMID: 33441873 PMCID: PMC7806752 DOI: 10.1038/s41598-020-80390-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Our recent study has shown that prenatal exposure to bisphenol A (BPA) altered the expression of genes associated with autism spectrum disorder (ASD). In this study, we further investigated the effects of prenatal BPA exposure on ASD-related genes known to regulate neuronal viability, neuritogenesis, and learning/memory, and assessed these functions in the offspring of exposed pregnant rats. We found that prenatal BPA exposure increased neurite length, the number of primary neurites, and the number of neurite branches, but reduced the size of the hippocampal cell body in both sexes of the offspring. However, in utero exposure to BPA decreased the neuronal viability and the neuronal density in the hippocampus and impaired learning/memory only in the male offspring while the females were not affected. Interestingly, the expression of several ASD-related genes (e.g. Mief2, Eif3h, Cux1, and Atp8a1) in the hippocampus were dysregulated and showed a sex-specific correlation with neuronal viability, neuritogenesis, and/or learning/memory. The findings from this study suggest that prenatal BPA exposure disrupts ASD-related genes involved in neuronal viability, neuritogenesis, and learning/memory in a sex-dependent manner, and these genes may play an important role in the risk and the higher prevalence of ASD in males subjected to prenatal BPA exposure.
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Affiliation(s)
- Surangrat Thongkorn
- grid.7922.e0000 0001 0244 7875The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Songphon Kanlayaprasit
- grid.7922.e0000 0001 0244 7875The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pawinee Panjabud
- grid.7922.e0000 0001 0244 7875The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thanit Saeliw
- grid.7922.e0000 0001 0244 7875The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thanawin Jantheang
- grid.7922.e0000 0001 0244 7875The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kasidit Kasitipradit
- grid.7922.e0000 0001 0244 7875The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Suthathip Sarobol
- grid.411628.80000 0000 9758 8584Specimen Center, Department of Laboratory Medicine, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Depicha Jindatip
- grid.7922.e0000 0001 0244 7875Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie W. Hu
- grid.253615.60000 0004 1936 9510Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, The George Washington University, Washington, DC USA
| | - Tewin Tencomnao
- grid.7922.e0000 0001 0244 7875Age-Related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Takako Kikkawa
- grid.69566.3a0000 0001 2248 6943Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Miyagi Japan
| | - Tatsuya Sato
- grid.412754.10000 0000 9956 3487Department of Healthcare Management, Faculty of Health Sciences, Tohoku Fukushi University, Sendai, Miyagi Japan
| | - Noriko Osumi
- grid.69566.3a0000 0001 2248 6943Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Miyagi Japan
| | - Tewarit Sarachana
- grid.7922.e0000 0001 0244 7875SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Age-Related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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6
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Lin L, Cao J, Du A, An Q, Chen X, Yuan S, Batool W, Shabbir A, Zhang D, Wang Z, Norvienyeku J. eIF3k Domain-Containing Protein Regulates Conidiogenesis, Appressorium Turgor, Virulence, Stress Tolerance, and Physiological and Pathogenic Development of Magnaporthe oryzae Oryzae. FRONTIERS IN PLANT SCIENCE 2021; 12:748120. [PMID: 34733303 PMCID: PMC8558559 DOI: 10.3389/fpls.2021.748120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/22/2021] [Indexed: 05/05/2023]
Abstract
The eukaryotic translation initiation factor 3 (eIF3) complex consists of essential and non-essential sub-complexes. Non-essential eIF3 complex subunits, such as eIF3e, eIF3j, eIF3k, and eIF3l, modulate stress tolerance and enhance the lifespan of Neurospora crassa and Caenorhabditis elegans. However, there is limited knowledge of the role of the non-essential eIF3 sub-complex in the pathophysiological development of plant fungal pathogens. Here, we deployed genetic and biochemical techniques to explore the influence of a hypothetical protein containing eIF3k domain in Magnaporthe oryzae Oryzae (MoOeIF3k) on reproduction, hyphae morphogenesis, stress tolerance, and pathogenesis. Also, the targeted disruption of MoOeIF3k suppressed vegetative growth and asexual sporulation in ΔMoOeif3k strains significantly. We demonstrated that MoOeIF3k promotes the initiation and development of the rice blast disease by positively regulating the mobilization and degradation of glycogen, appressorium integrity, host penetration, and colonization during host-pathogen interaction. For the first time, we demonstrated that the eIF3k subunit supports the survival of the blast fungus by suppressing vegetative growth and possibly regulating the conversions and utilization of stored cellular energy reserves under starvation conditions. We also observed that the deletion of MoOeIF3k accelerated ribosomal RNA (rRNA) generation in the ΔMoOeif3k strains with a corresponding increase in total protein output. In summary, this study unravels the pathophysiological significance of eIF3k filamentous fungi. The findings also underscored the need to systematically evaluate the individual subunits of the non-essential eIF3 sub-complex during host-pathogen interaction. Further studies are required to unravel the influence of synergetic coordination between translation and transcriptional regulatory machinery on the pathogenesis of filamentous fungi pathogens.
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Affiliation(s)
- Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaying Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anqiang Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiuli An
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuangshuang Yuan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wajjiha Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ammarah Shabbir
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Zonghua Wang,
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
- *Correspondence: Justice Norvienyeku,
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7
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Zebrafish embryogenesis – A framework to study regulatory RNA elements in development and disease. Dev Biol 2020; 457:172-180. [DOI: 10.1016/j.ydbio.2019.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/26/2022]
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8
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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9
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Docquier A, Pavlin L, Raibon A, Bertrand‐Gaday C, Sar C, Leibovitch S, Candau R, Bernardi H. eIF3f depletion impedes mouse embryonic development, reduces adult skeletal muscle mass and amplifies muscle loss during disuse. J Physiol 2019; 597:3107-3131. [DOI: 10.1113/jp277841] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/24/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Aurélie Docquier
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Laura Pavlin
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Audrey Raibon
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | | | - Chamroeun Sar
- Institut National de la Santé et de la Recherche Médicale, U‐583Institut des Neurosciences de MontpellierHôpital Saint Eloi Montpellier France
| | - Serge Leibovitch
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Robin Candau
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Henri Bernardi
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
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10
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Shen Y, Shen Y, Liu J, Shi JM, Ding J. Significance of expression of EIF3h, MMP-10 and MMP-11 in colonic adenocarcinoma. Shijie Huaren Xiaohua Zazhi 2018; 26:834-841. [DOI: 10.11569/wcjd.v26.i14.834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To detect the expression of eukaryotic translation initiation factor 3h (EIF3h), matrix metallopeptidase 10 (MMP-10), and matrix metallopeptidase 11 (MMP-11) in colonic adenocarcinoma and to analyze their clinical significance.
METHODS One hundred and ten colonic adenocarcinoma tissues, 43 high-grade colorectal intraepithelial neoplasia tissues, 43 low-grade colorectal intraepithelial neoplasia tissues, and 43 normal colonic mucosal tissues were collected. The expression of EIF3h, MMP-10, and MMP-11 in the above tissues was detected by immunohistochemistry.
RESULTS The expression of EIF3h, MMP-10, and MMP-11 differed significantly among the four groups. Expression of EIF3h, MMP-10, and MMP-11 was correlated with lymph node metastasis. Expression of EIF3h was correlated with tumor size, differentiation, proliferation index, and TNM stage. Expression of MMP-10 and MMP-11 was correlated with vascular invasion. There was a positive correlation between MMP-10 and MMP-11 expression in colonic adenocarcinoma.
CONCLUSION High expression and synergy of EIF3h, MMP-10, and MMP-11 can promote tumor formation and progression in colonic adenocarcinoma. EIF3h may be associated with the prognosis of colonic adenocarcinoma.
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Affiliation(s)
- Yuan Shen
- Department of Internal Medicine, Huzhou Sixth Hospital, Huzhou 313000, Zhejiang Province, China
| | - Ying Shen
- Department of Internal Medicine, Huzhou Sixth Hospital, Huzhou 313000, Zhejiang Province, China
| | - Jiang Liu
- Department of Gastroenterology, Huzhou Central Hospital, Huzhou 313000, Zhejiang Province, China
| | - Jie-Min Shi
- Department of Gastroenterology, Huzhou Central Hospital, Huzhou 313000, Zhejiang Province, China
| | - Jian Ding
- Department of Gastroenterology, Huzhou Central Hospital, Huzhou 313000, Zhejiang Province, China
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11
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Abstract
In this issue of Cell Reports, Shah et al. present evidence that a subcomplex of the eIF3 translation initiation factor regulates translation of mRNAs encoding components of the mitochondrial electron transport chain and glycolytic enzymes, thus linking translational control with energy metabolism.
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12
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Cattie DJ, Richardson CE, Reddy KC, Ness-Cohn EM, Droste R, Thompson MK, Gilbert WV, Kim DH. Mutations in Nonessential eIF3k and eIF3l Genes Confer Lifespan Extension and Enhanced Resistance to ER Stress in Caenorhabditis elegans. PLoS Genet 2016; 12:e1006326. [PMID: 27690135 PMCID: PMC5045169 DOI: 10.1371/journal.pgen.1006326] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/26/2016] [Indexed: 11/18/2022] Open
Abstract
The translation initiation factor eIF3 is a multi-subunit protein complex that coordinates the assembly of the 43S pre-initiation complex in eukaryotes. Prior studies have demonstrated that not all subunits of eIF3 are essential for the initiation of translation, suggesting that some subunits may serve regulatory roles. Here, we show that loss-of-function mutations in the genes encoding the conserved eIF3k and eIF3l subunits of the translation initiation complex eIF3 result in a 40% extension in lifespan and enhanced resistance to endoplasmic reticulum (ER) stress in Caenorhabditis elegans. In contrast to previously described mutations in genes encoding translation initiation components that confer lifespan extension in C. elegans, loss-of-function mutations in eif-3.K or eif-3.L are viable, and mutants show normal rates of growth and development, and have wild-type levels of bulk protein synthesis. Lifespan extension resulting from EIF-3.K or EIF-3.L deficiency is suppressed by a mutation in the Forkhead family transcription factor DAF-16. Mutations in eif-3.K or eif-3.L also confer enhanced resistance to ER stress, independent of IRE-1-XBP-1, ATF-6, and PEK-1, and independent of DAF-16. Our data suggest a pivotal functional role for conserved eIF3k and eIF3l accessory subunits of eIF3 in the regulation of cellular and organismal responses to ER stress and aging.
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Affiliation(s)
- Douglas J. Cattie
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Claire E. Richardson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kirthi C. Reddy
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Elan M. Ness-Cohn
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rita Droste
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mary K. Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Wendy V. Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dennis H. Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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13
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Abstract
The RNA-binding protein Elavl1 (also known as HuR) regulates gene expression at the posttranscriptional level. Early embryonic lethality of the mouse knockout challenges investigation into hematopoietic functions for Elavl1. We identified 2 zebrafish elavl1 genes, designated elavl1a (the predominant isoform during embryogenesis) and elavl1b. Knockdown of Elavl1a using specific morpholinos resulted in a striking loss of primitive embryonic erythropoiesis. Transcript levels for early hematopoietic regulatory genes including lmo2 and scl are unaltered, but levels of gata1 transcripts, encoding a key erythroid transcription factor, are significantly reduced in elavl1a morphants. Other mesoderm markers are mostly unchanged by depletion of Elav1a. The 3'-untranslated region (UTR) of gata1 contains putative Elavl1a-binding sites that support robust expression levels when fused to a transfected luciferase reporter gene, and Elavl1a binds the gata1 3'-UTR sequences in a manner dependent on these sites. Moreover, expression of a transgenic reporter specifically in developing embryonic erythroid cells is enhanced by addition of the gata1 3'UTR with intact Elavl1-binding sites. Injection of gata1 messenger RNA partially rescues the erythropoiesis defect caused by Elavl1 knockdown. Our study reveals a posttranscriptional regulatory mechanism by which RNA-binding protein Elavl1a regulates embryonic erythropoiesis by maintaining appropriate levels of gata1 expression.
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14
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Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis. Proc Natl Acad Sci U S A 2013; 110:9818-23. [PMID: 23716667 DOI: 10.1073/pnas.1302934110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic translation initiation factor 3 (eIF3) plays a central role in translation initiation and consists of five core (conserved) subunits present in both budding yeast and higher eukaryotes. Higher eukaryotic eIF3 contains additional (noncore or nonconserved) subunits of poorly defined function, including sub-unit h (eIF3h), which in zebrafish is encoded by two distinct genes (eif3ha and eif3hb). Previously we showed that eif3ha encodes the predominant isoform during zebrafish embryogenesis and that depletion of this factor causes defects in the development of the brain and eyes. To investigate the molecular mechanism governing this regulation, we developed a genome-wide polysome-profiling strategy using stage-matched WT and eif3ha morphant zebrafish embryos. This strategy identified a large set of predominantly neural-associated translationally regulated mRNAs. A striking finding was a cohort of lens-associated crystallin isoform mRNAs lost from the eif3ha morphant polysomes, revealing a mechanism by which lens development is translationally controlled. We show that both UTR sequences of a targeted crystallin transcript are necessary but not sufficient for translational regulation by eif3ha. Therefore, our study reveals the role of a noncore eIF3 subunit in modulating a specific developmental program by regulating translation of defined transcripts and highlights the potential of the zebrafish system to identify translational regulatory mechanisms controlling vertebrate development.
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15
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A forward genetic screen identifies eukaryotic translation initiation factor 3, subunit H (eIF3h), as an enhancer of variegation in the mouse. G3-GENES GENOMES GENETICS 2012; 2:1393-6. [PMID: 23173090 PMCID: PMC3484669 DOI: 10.1534/g3.112.004036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 09/10/2012] [Indexed: 12/25/2022]
Abstract
We have used a forward genetic screen to identify genes required for transgene silencing in the mouse. Previously these genes were found using candidate-based sequencing, a slow and labor-intensive process. Recently, whole-exome deep sequencing has accelerated our ability to find the causative point mutations, resulting in the discovery of novel and sometimes unexpected genes. Here we report the identification of translation initiation factor 3, subunit H (eIF3h) in two modifier of murine metastable epialleles (Mommes) lines. Mice carrying mutations in this gene have not been reported previously, and a possible involvement of eIF3h in transcription or epigenetic regulation has not been considered.
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16
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Janowski D, Salilew-Wondim D, Torner H, Tesfaye D, Ghanem N, Tomek W, El-Sayed A, Schellander K, Hölker M. Incidence of apoptosis and transcript abundance in bovine follicular cells is associated with the quality of the enclosed oocyte. Theriogenology 2012; 78:656-69.e1-5. [PMID: 22578626 DOI: 10.1016/j.theriogenology.2012.03.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/01/2012] [Accepted: 03/04/2012] [Indexed: 12/01/2022]
Abstract
The close contact and interaction between the oocyte and the follicular environment influence the establishment of oocyte developmental competence. Moreover, it is assumed that apoptosis in the follicular cells has a beneficial influence on the developmental competence of oocytes. The aim of this study was to investigate whether bovine oocytes with varied developmental competence show differences in the degree of apoptosis and gene expression pattern in their surrounding follicular cells (cumulus and granulosa cells). Oocytes and follicular cells from follicles of 3 to 5 mm in diameter were grouped as brilliant cresyl blue (BCB)+ and BCB- based on glucose-6-phosphate dehydrogenase (G6PDH) activity in the ooplasm by BCB staining. In the follicular cells initial, early and late apoptotic events were assessed by analyzing caspase-3 activity, annexin-V and TUNEL, respectively. Global gene expression was investigated in immature oocytes and corresponding follicular cells. BCB+ oocytes resulted in a higher blastocyst rate (19.3%) compared to the BCB- group (7.4%, P < 0.05). Moreover, the analysis of apoptosis showed a higher caspase-3 activity in the follicular cells and an increased degree of late apoptotic events in granulosa cells in the BCB+ compared with the BCB- group. Additionally, the global gene expression profile revealed a total of 34 and 37 differentially expressed genes between BCB+ and BCB- cumulus cells and granulosa cells, respectively, whereas 207 genes showed an altered transcript abundance between BCB+ and BCB- oocytes. Among these, EIF3F, RARRES2, RNF34, ACTA1, GSTA1, EIF3A, VIM and CS gene transcripts were most highly enriched in the BCB+ oocytes, whereas OLFM1, LINGO1, ALDH1A3, PTHLH, BTN3A3, MRPS2 and PPM1K were most significantly reduced in these cells. Therefore, the follicular cells enclosing developmentally competent oocytes show a higher level of apoptosis and a different pattern of gene expression compared to follicular cells enclosing non-competent bovine oocytes.
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Affiliation(s)
- D Janowski
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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17
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Peixeiro I, Inácio Â, Barbosa C, Silva AL, Liebhaber SA, Romão L. Interaction of PABPC1 with the translation initiation complex is critical to the NMD resistance of AUG-proximal nonsense mutations. Nucleic Acids Res 2011; 40:1160-73. [PMID: 21989405 PMCID: PMC3273812 DOI: 10.1093/nar/gkr820] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and rapidly degrades mRNAs containing premature termination codons (PTC). The strength of the NMD response appears to reflect multiple determinants on a target mRNA. We have previously reported that mRNAs containing PTCs in close proximity to the translation initiation codon (AUG-proximal PTCs) can substantially evade NMD. Here, we explore the mechanistic basis for this NMD resistance. We demonstrate that translation termination at an AUG-proximal PTC lacks the ribosome stalling that is evident in an NMD-sensitive PTC. This difference is associated with demonstrated interactions of the cytoplasmic poly(A)-binding protein 1, PABPC1, with the cap-binding complex subunit, eIF4G and the 40S recruitment factor eIF3 as well as the ribosome release factor, eRF3. These interactions, in combination, underlie critical 3′–5′ linkage of translation initiation with efficient termination at the AUG-proximal PTC and contribute to an NMD-resistant PTC definition at an early phase of translation elongation.
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Affiliation(s)
- Isabel Peixeiro
- Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
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