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Munaron L, Chinigò G, Scarpellino G, Ruffinatti FA. The fallacy of functional nomenclature in the kingdom of biological multifunctionality: physiological and evolutionary considerations on ion channels. J Physiol 2024; 602:2367-2381. [PMID: 37635695 DOI: 10.1113/jp284422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Living organisms are multiscale complex systems that have evolved high degrees of multifunctionality and redundancy in the structure-function relationship. A number of factors, only in part determined genetically, affect the jobs of proteins. The overall structural organization confers unique molecular properties that provide the potential to perform a pattern of activities, some of which are co-opted by specific environments. The variety of multifunctional proteins is expanding, but most cases are handled individually and according to the still dominant 'one structure-one function' approach, which relies on the attribution of canonical names typically referring to the first task identified for a given protein. The present topical review focuses on the multifunctionality of ion channels as a paradigmatic example. Mounting evidence reports the ability of many ion channels (including members of voltage-dependent, ligand-gated and transient receptor potential families) to exert biological effects independently of their ion conductivity. 'Functionally based' nomenclature (the practice of naming a protein or family of proteins based on a single purpose) is a conceptual bias for three main reasons: (i) it increases the amount of ambiguity, deceiving our understanding of the multiple contributions of biomolecules that is the heart of the complexity; (ii) it is in stark contrast to protein evolution dynamics, largely based on multidomain arrangement; and (iii) it overlooks the crucial role played by the microenvironment in adjusting the actions of cell structures and in tuning protein isoform diversity to accomplish adaptational requirements. Biological information in protein physiology is distributed among different entwined layers working as the primary 'locus' of natural selection and of evolutionary constraints.
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Affiliation(s)
- Luca Munaron
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Chinigò
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Scarpellino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Chen Y, Gao Y, Huang X, Li S, Zhang Z, Zhan A. Incorporating adaptive genomic variation into predictive models for invasion risk assessment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 18:100299. [PMID: 37701243 PMCID: PMC10494315 DOI: 10.1016/j.ese.2023.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Global climate change is expected to accelerate biological invasions, necessitating accurate risk forecasting and management strategies. However, current invasion risk assessments often overlook adaptive genomic variation, which plays a significant role in the persistence and expansion of invasive populations. Here we used Molgula manhattensis, a highly invasive ascidian, as a model to assess its invasion risks along Chinese coasts under climate change. Through population genomics analyses, we identified two genetic clusters, the north and south clusters, based on geographic distributions. To predict invasion risks, we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability, respectively. These approaches yielded distinct predictions: the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster (i.e., lower invasion risks), while the species distribution model indicated higher future habitat suitability for the same cluster (i.e, higher invasion risks). By integrating these models, we found that the south cluster exhibited minor genome-niche disruptions in the future, indicating higher invasion risks. Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change. Moreover, incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yangchun Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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Chen Y, Ni P, Fu R, Murphy KJ, Wyeth RC, Bishop CD, Huang X, Li S, Zhan A. (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2772. [PMID: 36316814 DOI: 10.1002/eap.2772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kieran J Murphy
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Cory D Bishop
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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Huang X, Li H, Zhan A. Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians. Int J Mol Sci 2023; 24:14921. [PMID: 37834365 PMCID: PMC10573349 DOI: 10.3390/ijms241914921] [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: 08/30/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative splicing (AS), a pivotal biological process contributing to phenotypic plasticity, creates a bridge linking genotypes with phenotypes. Despite its importance, the AS mechanisms underlying environmental response and adaptation have not been well studied, and more importantly, the cis- and trans-acting factors influencing AS variation remain unclear. Using the model invasive congeneric ascidians, Ciona robusta, and Ciona savignyi, we compared their AS responses to environmental changes and explored the potential determinants. Our findings unveiled swift and dynamic AS changes in response to environmental challenges, and differentially alternative spliced genes (DASGs) were functionally enriched in transmembrane transport processes. Interestingly, both the prevalence and level of AS in C. robusta were lower than those observed in C. savignyi. Furthermore, these two indices were higher under temperature stresses compared to salinity stresses in C. savignyi. All the observed patterns underscore the species-specific and environmental context-dependent AS responses to environmental challenges. The dissimilarities in genomic structure and exon/intron size distributions between these two species likely contributed to the observed AS variation. Moreover, we identified a total of 11 and 9 serine/arginine-rich splicing factors (SRSFs) with conserved domains and gene structures in the genomes of C. robusta and C. savignyi, respectively. Intriguingly, our analysis revealed that all detected SRSFs did not exhibit prevalent AS regulations. Instead, we observed AS control over a set of genes related to splicing factors and spliceosome components. Altogether, our results elucidate species-specific and environmental challenge-dependent AS response patterns in closely related invasive ascidians. The identified splicing factors and spliceosome components under AS control offer promising candidates for further investigations into AS-mediated rapid responses to environmental challenges complementary to SRSFs.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; (X.H.); (H.L.)
| | - Hanxi Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; (X.H.); (H.L.)
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; (X.H.); (H.L.)
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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Zhang X, Zhang X, Yuan J, Li F. The Responses of Alternative Splicing during Heat Stress in the Pacific White Shrimp Litopenaeus vannamei. Genes (Basel) 2023; 14:1473. [PMID: 37510377 PMCID: PMC10379218 DOI: 10.3390/genes14071473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Heat tolerance is increasingly becoming a crucial trait for aquaculture species in the face of rapidly changing climate conditions. Alternative splicing (AS) is a vital mechanism within cells that modulates gene abundance and functional diversity, enabling organisms to effectively respond to diverse stressful conditions, including thermal stress. However, it is still uncertain whether AS contributes to heat tolerance in shrimp. In this study, we conducted an extensive transcriptome analysis on the Pacific white shrimp, Litopenaeus vannamei, revealing a total of 1267, 987, and 130 differential AS events (DAS) in the gill, hepatopancreas, and muscle, respectively, following exposure to heat stress. Among all of the DAS events, exon skipping (ES) was the predominant form of splicing modification observed. Interestingly, a minor portion of DAS genes exhibited overlap across the three tissues, implying that heat stress exerts unique effects on various tissue types. Moreover, the functional enrichment analysis demonstrated that commonly identified DAS genes were primarily associated with the "spliceosome" pathway, indicating that the AS of splicing-related genes played a crucial role in the response to heat stress. Our findings also revealed that heat stress tended to induce longer mRNA isoforms through differential alternative 3' splice site (A3SS) events. Notably, A3SS events exhibited the highest proportion of maintained open reading frames (ORFs) under heat stress. Interestingly, we observed a limited overlap between the genes exhibiting DAS and those showing differential gene expression (DEG), indicating that AS may function as a distinct regulatory mechanism independent of transcriptional regulation in response to heat stress. This is the first comprehensive study on AS in crustacea species under heat stress, which broadens our understanding of the regulatory mechanisms governing the crustaceans' response to environmental stress, providing valuable insights for the aquaculture breeding of shrimp and other aquatic animals.
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Affiliation(s)
- Xiaoxi Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaojun Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianbo Yuan
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fuhua Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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Huang X, Li H, Shenkar N, Zhan A. Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions. RNA (NEW YORK, N.Y.) 2023; 29:675-690. [PMID: 36810233 PMCID: PMC10159005 DOI: 10.1261/rna.079319.122] [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: 06/16/2022] [Accepted: 02/01/2023] [Indexed: 05/06/2023]
Abstract
Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or posttranscriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hyposalinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their nonredundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acids under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by up-regulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
| | - Hanxi Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801 Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel-Aviv, Israel
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
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Li C, Wang Y, Wei M, Wang X. The involvement of a novel calmodulin-like protein isoform from oyster Crassostrea gigas in transcription factor regulation provides new insight into acclimation to ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 257:106423. [PMID: 36822075 DOI: 10.1016/j.aquatox.2023.106423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Marine organisms need to adapt to improve organismal fitness under ocean acidification (OA). Recent studies have shown that marine calcifiers can achieve acclimation by stimulating calcium binding/signaling pathways. Here, a CaM-like gene (CgCaLP-2) from oyster Crassostrea gigas which typically responded to long-term CO2 exposure (two months) rather than short-term exposure (one week) was characterized. The cloned cDNA was 678 bp and was shorter than the retrieved sequence from NCBI (1125 bp). The two sequences, designated as CgCaLP-2-v1 and CgCaLP-2-v2, were demonstrated to be different splice variants by the genome sequence analysis. Western blotting analysis revealed two bands of 23 kD and 43 kD in mantle and hemocytes, corresponding to predicted molecular weight of CgCaLP-2-v1 and CgCaLP-2-v2, respectively. The isoform CgCaLP-2-v1 (the 23 kD band) was highly stimulated in response to long-term CO2 exposure (42-day and 56-day treatment) in hemocytes and mantle tissue. The fluorescence signal of CgCaLP-2 in mantle and hemocytes became more intensive after long-term CO2 exposure. Besides, in hemocytes, CgCaLP-2 presented a higher localization on the nuclear membrane after long-term CO2 exposure (56 d). The target gene network of CgCaLP-2 was predicted, and a transcription factor (TF) gene annotated as Homeobox protein SIX4 (CgSIX4) showed a similar expressive trend to CgCaLP-2 during CO2 exposure. Suppression of CgCaLP-2 via RNA interference significantly reduced the mRNA expression of CgSIX4. The results suggested that CgCaLP-2 might mediate the Ca2+-CaLP-TF signal transduction pathway under long-term CO2 exposure. This study serves as an example to reveal that alternative splicing is an important mechanism for generation multiple protein isoforms and thus shape the plastic responses under CO2 exposure, providing new insight into the potential acclimation ability of marine calcifiers to future OA.
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Affiliation(s)
- Changmei Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yilin Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Manman Wei
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiudan Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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Chen Z, Huang X, Fu R, Zhan A. Neighbours matter: Effects of genomic organization on gene expression plasticity in response to environmental stresses during biological invasions. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100992. [PMID: 35504120 DOI: 10.1016/j.cbd.2022.100992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/07/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Gene expression regulation has been widely recognized as an important molecular mechanism underlying phenotypic plasticity in environmental adaptation. However, it remains largely unexplored on the effects of genomic organization on gene expression plasticity under environmental stresses during biological invasions. Here, we use an invasive model ascidian, Ciona robusta, to investigate how genomic organization affects gene expression in response to salinity stresses during range expansions. Our study showed that neighboring genes were co-expressed and approximately 30% of stress responsive genes were physically clustered on chromosomes. Such coordinated expression was substantially affected by the physical distance and orientation of genes. Interestingly, the overall expression correlation of neighboring genes was significantly decreased under high salinity stresses, illustrating that the co-expression regulation could be disrupted by salinity challenges. Furthermore, the clustering of genes was associated with their function constraints and expression patterns - operon genes enriched in gene expression machinery had the highest transcriptional activity and expression stability. Notably, our analyses showed that the tail-to-tail genes, mainly involved in biological functions related to phosphorylation, homeostatic process, and ion transport, exhibited higher intrinsic expression variability and greater response to salinity challenges. Altogether, the results obtained here provide new insights into the effects of gene organization on gene expression plasticity under environmental challenges, hence improving our knowledge on mechanisms of rapid environmental adaptation during biological invasions.
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Affiliation(s)
- Zaohuang Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China.
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Wei L, Liu Y, Zhang H, Ma Y, Lu Z, Gu Z, Ding C. TMPO-AS1, a Novel E2F1-Regulated lncRNA, Contributes to the Proliferation of Lung Adenocarcinoma Cells via Modulating miR-326/SOX12 Axis. Cancer Manag Res 2020; 12:12403-12414. [PMID: 33293866 PMCID: PMC7719338 DOI: 10.2147/cmar.s269269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background TMPO-AS1, an antisense lncRNA located at human chromosome 12p23.1, has been identified as an oncogene involved in cell proliferation in various cancers, including LUAD. In this study, we aimed to explore the novel molecular mechanism of TMPO-AS1 underlying LUAD growth. Materials and Methods The transcription levels of TMPO-AS1, miR-326, and SOX12 in LUAD tissues and cell lines were detected by quantitative real-time PCR (qRT-PCR). The cell proliferation ability was evaluatect 3d by cell counting kit-8 (CCK-8) assay. Cell cycle and apoptosis analysis was assessed by flow cytometry. The target relationship among TMPO-AS1, miR-326, and SOX12 and promoter activity of TMPO-AS1 was measured using dual-luciferase reporter assay. The protein levels of SOX12 in LUAD cells were determined by Western blot. ChIP-qPCR assay was performed to validate the direct binding between E2F1 and TMPO-AS1 promoter. Results TMPO-AS1 was up-regulated in LUAD tissues as well as cell lines. Boosted TMPO-AS1 expression was positively correlated with poor prognosis and pathological stage in LUAD. Down-regulation of TMPO-AS1 could restrain the proliferation of LUAD cells through arresting the cell cycle at G0/G1 phase and inducing apoptosis in vitro. Mechanically, we demonstrated that TMPO-AS1 could modulate the proliferation of LUAD cells through increasing SOX12 expression level via sponging miR-326 in accordance with bioinformatics analysis and experimental validation. Furthermore, we identified that TMPO-AS1 could be activated by E2F transcription factor 1 (E2F1) as a novel target gene. Conclusion TMPO-AS1 can modulate LUAD cell proliferation through E2F1/miR-326/SOX12 pathway.
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Affiliation(s)
- Lin Wei
- Department of Thoracic Surgery, Xi'an Chest Hospital, Xi'an 710100, People's Republic of China
| | - Yugang Liu
- Department of Thoracic Surgery, Xi'an Chest Hospital, Xi'an 710100, People's Republic of China
| | - Huijun Zhang
- Department of Thoracic Surgery, Xi'an Chest Hospital, Xi'an 710100, People's Republic of China
| | - Yuefeng Ma
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an 710004, People's Republic of China
| | - Zenghui Lu
- Department of Thoracic Surgery, Xi'an Chest Hospital, Xi'an 710100, People's Republic of China
| | - Zhenning Gu
- Department of Thoracic Surgery, Xi'an Chest Hospital, Xi'an 710100, People's Republic of China
| | - Chao Ding
- Department of Thoracic Surgery, Xi'an Chest Hospital, Xi'an 710100, People's Republic of China
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