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Bao N, Wang Z, Fu J, Dong H, Jin Y. RNA structure in alternative splicing regulation: from mechanism to therapy. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034824 DOI: 10.3724/abbs.2024119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.
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Hamid R, Ghorbanzadeh Z, Jacob F, Nekouei MK, Zeinalabedini M, Mardi M, Sadeghi A, Ghaffari MR. Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation. BMC PLANT BIOLOGY 2024; 24:468. [PMID: 38811873 PMCID: PMC11134665 DOI: 10.1186/s12870-024-05172-8] [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: 01/20/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. RESULTS In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. CONCLUSIONS This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | | | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Akram Sadeghi
- Department of Microbial Biotechnology and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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Libri D. Memories of a young student: the early days of splicing regulation with François Gros. C R Biol 2024; 346:55-57. [PMID: 38234147 DOI: 10.5802/crbiol.138] [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: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 01/19/2024]
Abstract
I joined the laboratory of François Gros as a young student in the mid-1980s and worked on the characterization of the β -tropomyosin gene in chicken and the regulation of alternative splicing of its transcript, under the supervision of Marc Fiszman. In particular, I was interested in how secondary structures of the RNA influence the recognition of exons specifically used in muscle cells. I will recall a few memories on how interacting with François on this project shaped my perception of the scientific process and of the relationships between models and data. Later I worked on many aspects of RNA biology, from transcription to mRNP biogenesis and non-coding RNAs.
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Dong H, Li J, Wu Q, Jin Y. Confluence and convergence of Dscam and Pcdh cell-recognition codes. Trends Biochem Sci 2023; 48:1044-1057. [PMID: 37839971 DOI: 10.1016/j.tibs.2023.09.001] [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: 07/19/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 10/17/2023]
Abstract
The ability of neurites of the same neuron to avoid each other (self-avoidance) is a conserved feature in both invertebrates and vertebrates. The key to self-avoidance is the generation of a unique subset of cell-surface proteins in individual neurons engaging in isoform-specific homophilic interactions that drive neurite repulsion rather than adhesion. Among these cell-surface proteins are fly Dscam1 and vertebrate clustered protocadherins (cPcdhs), as well as the recently characterized shortened Dscam (sDscam) in the Chelicerata. Herein, we review recent advances in our understanding of how cPcdh, Dscam, and sDscam cell-surface recognition codes are expressed and translated into cellular functions essential for neural wiring.
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Affiliation(s)
- Haiyang Dong
- The First Affiliated Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, China; MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Jinhuan Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yongfeng Jin
- The First Affiliated Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, China; MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China.
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5
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Chen Y, Luo K, Zhang B, Lu Z, Wang F. Shrimp MANF maintains hemocyte viability via interaction with a tyrosine kinase Abl. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 143:104675. [PMID: 36863646 DOI: 10.1016/j.dci.2023.104675] [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: 11/03/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a highly conserved cell protective protein. In this study, we explored its functions in shrimp hemocytes. Our results indicated that LvMANF knockdown could cause a decrease in total hemocyte count (THC) and an increase in caspase3/7 activity. To further explore its working mechanism, transcriptomic analyses were performed with wild-type and LvMANF-knockdown hemocytes. Three upregulated genes from transcriptomic data, including FAS-associated factor 2, rho-associated protein kinase 1, and serine/threonine-protein kinase WNK4 were validated with qPCR. Further experiments showed that LvMANF knockdown and tyrosine kinase LvAbl knockdown could decrease tyrosine phosphorylation in shrimp hemocytes. In addition, the interaction between LvMANF and LvAbl was validated with immunoprecipitation. The knockdown of LvMANF would decrease ERK phosphorylation and increase LvAbl expression. Our results suggest intracellular LvMANF may maintain shrimp hemocyte viability by interacting with LvAbl.
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Affiliation(s)
- Yaohui Chen
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Kaiwen Luo
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Baoyuan Zhang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Zhiyao Lu
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Fan Wang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China; Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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6
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Dong H, Xu B, Guo P, Zhang J, Yang X, Li L, Fu Y, Shi J, Zhang S, Zhu Y, Shi Y, Zhou F, Bian L, You W, Shi F, Yang X, Huang J, He H, Jin Y. Hidden RNA pairings counteract the "first-come, first-served" splicing principle to drive stochastic choice in Dscam1 splice variants. SCIENCE ADVANCES 2022; 8:eabm1763. [PMID: 35080968 PMCID: PMC8791459 DOI: 10.1126/sciadv.abm1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drosophila melanogaster Dscam1 encodes 38,016 isoforms via mutually exclusive splicing; however, the regulatory mechanism behind this is not fully understood. Here, we found a set of hidden RNA secondary structures that balance the stochastic choice of Dscam1 splice variants (designated balancer RNA secondary structures). In vivo mutational analyses revealed the dual function of these balancer interactions in driving the stochastic choice of splice variants, through enhancement of the inclusion of distal exon 6s by cooperating with docking site–selector pairing to form a stronger multidomain pre-mRNA structure and through simultaneous repression of the inclusion of proximal exon 6s by antagonizing their docking site–selector pairings. Thus, we provide an elegant molecular model based on competition and cooperation between two sets of docking site–selector and balancer pairings, which counteracts the “first-come, first-served” principle. Our findings provide conceptual and mechanistic insight into the dynamics and functions of long-range RNA secondary structures.
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Affiliation(s)
- Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pengjuan Guo
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xi Yang
- Department of Neurosurgery and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fengyan Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lina Bian
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wendong You
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Yang
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Haihuai He
- Department of Neurosurgery and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
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7
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Williams DL, Sikora VM, Hammer MA, Amin S, Brinjikji T, Brumley EK, Burrows CJ, Carrillo PM, Cromer K, Edwards SJ, Emri O, Fergle D, Jenkins MJ, Kaushik K, Maydan DD, Woodard W, Clowney EJ. May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression. Front Cell Dev Biol 2022; 9:720798. [PMID: 35087825 PMCID: PMC8787164 DOI: 10.3389/fcell.2021.720798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.
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Affiliation(s)
- Donnell L. Williams
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Veronica Maria Sikora
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Max A. Hammer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Sayali Amin
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Taema Brinjikji
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Emily K. Brumley
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Connor J. Burrows
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Paola Michelle Carrillo
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Kirin Cromer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Summer J. Edwards
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Olivia Emri
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Fergle
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - M. Jamal Jenkins
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Krishangi Kaushik
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniella D. Maydan
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Wrenn Woodard
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
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8
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Liberti A, Natarajan O, Atkinson CGF, Dishaw LJ. Secreted immunoglobulin domain effector molecules of invertebrates and management of gut microbial ecology. Immunogenetics 2022; 74:99-109. [PMID: 34988622 DOI: 10.1007/s00251-021-01237-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 02/01/2023]
Abstract
The origins of a "pass-through" gut in early bilaterians facilitated the exploration of new habitats, motivated the innovation of feeding styles and behaviors, and helped drive the evolution of more complex organisms. The gastrointestinal tract has evolved to consist of a series of interwoven exchanges between nutrients, host immunity, and an often microbe-rich environmental interface. Not surprisingly, animals have expanded their immune repertoires to include soluble effectors that can be secreted into luminal spaces, e.g., in the gut, facilitating interactions with microbes in ways that influence their settlement dynamics, virulence, and their interaction with other microbes. The immunoglobulin (Ig) domain, which is also found in some non-immune molecules, is recognized as one of the most versatile recognition domains lying at the interface of innate and adaptive immunity; among vertebrates, secreted Igs are known to play crucial roles in the management of gut microbial communities. In this mini-review, we will focus on secreted immune effectors possessing Ig-like domains in invertebrates, such as the fibrinogen-related effector proteins first described in the gastropod Biomphalaria glabrata, the Down syndrome cellular adhesion molecule first described in the arthropod, Drosophila melanogaster, and the variable region-containing chitin-binding proteins of the protochordates. We will highlight our current understanding of their function and their potential role, if not yet recognized, in the establishment and maintenance of host-microbial interfaces and argue that these Igs are likely also essential to microbiome management.
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Affiliation(s)
- Assunta Liberti
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Ojas Natarajan
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA
| | - Celine Grace F Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA.,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA
| | - Larry J Dishaw
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA. .,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA.
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9
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Hong W, Zhang J, Dong H, Shi Y, Ma H, Zhou F, Xu B, Fu Y, Zhang S, Hou S, Li G, Wu Y, Chen S, Zhu X, You W, Shi F, Yang X, Gong Z, Huang J, Jin Y. Intron-targeted mutagenesis reveals roles for Dscam1 RNA pairing architecture-driven splicing bias in neuronal wiring. Cell Rep 2021; 36:109373. [PMID: 34260933 DOI: 10.1016/j.celrep.2021.109373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/05/2021] [Accepted: 06/18/2021] [Indexed: 12/28/2022] Open
Abstract
Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam1) can generate 38,016 different isoforms through largely stochastic, yet highly biased, alternative splicing. These isoforms are required for nervous functions. However, the functional significance of splicing bias remains unknown. Here, we provide evidence that Dscam1 splicing bias is required for mushroom body (MB) axonal wiring. We generate mutant flies with normal overall protein levels and an identical number but global changes in exon 4 and 9 isoform bias (DscamΔ4D-/- and DscamΔ9D-/-), respectively. In contrast to DscamΔ4D-/-, DscamΔ9D-/- exhibits remarkable MB defects, suggesting a variable domain-specific requirement for isoform bias. Importantly, changes in isoform bias cause axonal defects but do not influence the self-avoidance of axonal branches. We conclude that, in contrast to the isoform number that provides the molecular basis for neurite self-avoidance, isoform bias may play a role in MB axonal wiring by influencing non-repulsive signaling.
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Affiliation(s)
- Weiling Hong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Hongru Ma
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Fengyan Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shouqing Hou
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Guo Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yandan Wu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shuo Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Xiaohua Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Wendong You
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Xiaofeng Yang
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Zhefeng Gong
- Department of Neuroscience, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China; Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China.
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10
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Dong H, Li L, Zhu X, Shi J, Fu Y, Zhang S, Shi Y, Xu B, Zhang J, Shi F, Jin Y. Complex RNA Secondary Structures Mediate Mutually Exclusive Splicing of Coleoptera Dscam1. Front Genet 2021; 12:644238. [PMID: 33859670 PMCID: PMC8042237 DOI: 10.3389/fgene.2021.644238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Mutually exclusive splicing is an important mechanism for expanding protein diversity. An extreme example is the Down syndrome cell adhesion molecular (Dscam1) gene of insects, containing four clusters of variable exons (exons 4, 6, 9, and 17), which potentially generates tens of thousands of protein isoforms through mutually exclusive splicing, of which regulatory mechanisms are still elusive. Here, we systematically analyzed the variable exon 4, 6, and 9 clusters of Dscam1 in Coleoptera species. Through comparative genomics and RNA secondary structure prediction, we found apparent evidence that the evolutionarily conserved RNA base pairing mediates mutually exclusive splicing in the Dscam1 exon 4 cluster. In contrast to the fly exon 6, most exon 6 selector sequences in Coleoptera species are partially located in the variable exon region. Besides, bidirectional RNA–RNA interactions are predicted to regulate the mutually exclusive splicing of variable exon 9 of Dscam1. Although the docking sites in exon 4 and 9 clusters are clade specific, the docking sites-selector base pairing is conserved in secondary structure level. In short, our result provided a mechanistic framework for the application of long-range RNA base pairings in regulating the mutually exclusive splicing of Coleoptera Dscam1.
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Affiliation(s)
- Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaohua Zhu
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
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11
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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12
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Hong W, Shi Y, Xu B, Jin Y. RNA secondary structures in Dscam1 mutually exclusive splicing: unique evolutionary signature from the midge. RNA (NEW YORK, N.Y.) 2020; 26:1086-1093. [PMID: 32471818 PMCID: PMC7430681 DOI: 10.1261/rna.075259.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/27/2020] [Indexed: 05/12/2023]
Abstract
The Drosophila melanogaster gene Dscam1 potentially generates 38,016 distinct isoforms via mutually exclusive splicing, which are required for both nervous and immune functions. However, the mechanism underlying splicing regulation remains obscure. Here we show apparent evolutionary signatures characteristic of competing RNA secondary structures in exon clusters 6 and 9 of Dscam1 in the two midge species (Belgica antarctica and Clunio marinus). Surprisingly, midge Dscam1 encodes only ∼6000 different isoforms through mutually exclusive splicing. Strikingly, the docking site of the exon 6 cluster is conserved in almost all insects and crustaceans but is specific in the midge; however, the docking site-selector base-pairings are conserved. Moreover, the docking site is complementary to all predicted selector sequences downstream from every variable exon 9 of the midge Dscam1, which is in accordance with the broad spectrum of their isoform expression. This suggests that these cis-elements mainly function through the formation of long-range base-pairings. This study provides a vital insight into the evolution and mechanism of Dscam1 alternative splicing.
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Affiliation(s)
- Weiling Hong
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
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13
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Taylor K, Sobczak K. Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control. Int J Mol Sci 2020; 21:ijms21145161. [PMID: 32708277 PMCID: PMC7404189 DOI: 10.3390/ijms21145161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.
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14
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Ng TH, Kurtz J. Dscam in immunity: A question of diversity in insects and crustaceans. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 105:103539. [PMID: 31734281 DOI: 10.1016/j.dci.2019.103539] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
In insects and crustaceans, thousands of Down syndrome cell adhesion molecules (Dscam) can be generated by alternative splicing of variable exons from a single-locus gene, Dscam-hv. This extraordinarily versatile gene (38,016 protein isoforms produced in Drosophila) was first proposed to be involved in exon guidance and subsequently implicated in immunity as a hypervariable immune molecule. Almost 20 y after discovery of Dscam-hv, there have been many studies in insects and crustaceans regarding roles of Dscam in immunity, with many similarities and concurrently, many differences. Here, we review the current status of Dscam-hv, presented as a comparison of similarities and differences in insects and crustaceans and discuss hypotheses of Dscam functions in immunity.
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Affiliation(s)
- Tze Hann Ng
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany.
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15
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Abstract
The composition of insect hemolymph can change depending on many factors, e.g. access to nutrients, stress conditions, and current needs of the insect. In this chapter, insect immune-related polypeptides, which can be permanently or occasionally present in the hemolymph, are described. Their division into peptides or low-molecular weight proteins is not always determined by the length or secondary structure of a given molecule but also depends on the mode of action in insect immunity and, therefore, it is rather arbitrary. Antimicrobial peptides (AMPs) with their role in immunity, modes of action, and classification are presented in the chapter, followed by a short description of some examples: cecropins, moricins, defensins, proline- and glycine-rich peptides. Further, we will describe selected immune-related proteins that may participate in immune recognition, may possess direct antimicrobial properties, or can be involved in the modulation of insect immunity by both abiotic and biotic factors. We briefly cover Fibrinogen-Related Proteins (FREPs), Down Syndrome Cell Adhesion Molecules (Dscam), Hemolin, Lipophorins, Lysozyme, Insect Metalloproteinase Inhibitor (IMPI), and Heat Shock Proteins. The reader will obtain a partial picture presenting molecules participating in one of the most efficient immune strategies found in the animal world, which allow insects to inhabit all ecological land niches in the world.
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Affiliation(s)
- Iwona Wojda
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Małgorzata Cytryńska
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Agnieszka Zdybicka-Barabas
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jakub Kordaczuk
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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16
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Baralle FE, Singh RN, Stamm S. RNA structure and splicing regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194448. [PMID: 31730825 DOI: 10.1016/j.bbagrm.2019.194448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Francisco E Baralle
- Italian Liver Disease Foundation (FIF), Building Q AREA Science Park, Basovizza Campus ss14, Km 163,5, 34149 Trieste, Italy
| | - Ravindra N Singh
- Iowa State University, Department of Biomedical Science, 2034 Veterinary Medicine, Ames, IA 50011, United States.
| | - Stefan Stamm
- University of Kentucky, Department of Molecular and Cellular Biochemistry, College of Medicine, B159 Biomedical Biological Sciences Research Bldg. 741 South Limestone, Lexington, KY 40536, United States
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