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Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [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: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
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Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
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2
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Huang X, Wang C, Zhang T, Li R, Chen L, Leung KL, Lakso M, Zhou Q, Zhang H, Wong G. PIWI-interacting RNA expression regulates pathogenesis in a Caenorhabditis elegans model of Lewy body disease. Nat Commun 2023; 14:6137. [PMID: 37783675 PMCID: PMC10545829 DOI: 10.1038/s41467-023-41881-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that regulate gene expression, yet their molecular functions in neurobiology are unclear. While investigating neurodegeneration mechanisms using human α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg pan-neuronal overexpressing strains, we unexpectedly observed dysregulation of piRNAs. RNAi screening revealed that knock down of piRNA biogenesis genes improved thrashing behavior; further, a tofu-1 gene deletion ameliorated phenotypic deficits in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg transgenic strains. piRNA expression was extensively downregulated and H3K9me3 marks were decreased after tofu-1 deletion in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg strains. Dysregulated piRNAs targeted protein degradation genes suggesting that a decrease of piRNA expression leads to an increase of degradation ability in C. elegans. Finally, we interrogated piRNA expression in brain samples from PD patients. piRNAs were observed to be widely overexpressed at late motor stage. In this work, our results provide evidence that piRNAs are mediators in pathogenesis of Lewy body diseases and suggest a molecular mechanism for neurodegeneration in these and related disorders.
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Affiliation(s)
- Xiaobing Huang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, China
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Changliang Wang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, 510799, China
| | - Tianjiao Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Rongzhen Li
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, 515063, China
| | - Ka Lai Leung
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Merja Lakso
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Qinghua Zhou
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, China
| | - Hongjie Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Garry Wong
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China.
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Soutschek M, Schratt G. Non-coding RNA in the wiring and remodeling of neural circuits. Neuron 2023:S0896-6273(23)00341-0. [PMID: 37230080 DOI: 10.1016/j.neuron.2023.04.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023]
Abstract
The brain constantly adapts to changes in the environment, a capability that underlies memory and behavior. Long-term adaptations require the remodeling of neural circuits that are mediated by activity-dependent alterations in gene expression. Over the last two decades, it has been shown that the expression of protein-coding genes is significantly regulated by a complex layer of non-coding RNA (ncRNA) interactions. The aim of this review is to summarize recent discoveries regarding the functional involvement of ncRNAs during different stages of neural circuit development, activity-dependent circuit remodeling, and circuit maladapations underlying neurological and neuropsychiatric disorders. In addition to the intensively studied microRNA (miRNA) family, we focus on more recently added ncRNA classes, such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs), and discuss the complex regulatory interactions between these different RNAs. We conclude by discussing the potential relevance of ncRNAs for cell-type and -state-specific regulation in the context of memory formation, the evolution of human cognitive abilities, and the development of new diagnostic and therapeutic tools in brain disorders.
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Affiliation(s)
- Michael Soutschek
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, 8057 Zurich, Switzerland
| | - Gerhard Schratt
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, 8057 Zurich, Switzerland.
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4
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Zhao P, Mondal S, Martin C, DuPlissis A, Chizari S, Ma KY, Maiya R, Messing RO, Jiang N, Ben-Yakar A. Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing. Nat Methods 2023; 20:590-599. [PMID: 36928074 DOI: 10.1038/s41592-023-01804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/26/2023] [Indexed: 03/18/2023]
Abstract
Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single-neuron resolution in model organisms such as Caenorhabditis elegans. Existing cell isolation techniques cannot isolate neurons with specific regeneration phenotypes from C. elegans. We present femtosecond laser microdissection (fs-LM), a single-cell isolation method that dissects specific cells directly from living tissue by leveraging the micrometer-scale precision of fs-laser ablation. We show that fs-LM facilitates sensitive and specific gene expression profiling by single-cell RNA sequencing (scRNA-seq), while mitigating the stress-related transcriptional artifacts induced by tissue dissociation. scRNA-seq of fs-LM isolated regenerating neurons revealed transcriptional programs that are correlated with either successful or failed regeneration in wild-type and dlk-1 (0) animals, respectively. This method also allowed studying heterogeneity displayed by the same type of neuron and found gene modules with expression patterns correlated with axon regrowth rate. Our results establish fs-LM as a spatially resolved single-cell isolation method for phenotype-to-genotype mapping.
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Affiliation(s)
- Peisen Zhao
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Sudip Mondal
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chris Martin
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Andrew DuPlissis
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Shahab Chizari
- Deparment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Ke-Yue Ma
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Rajani Maiya
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Institute of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Department of Physiology, LSU Health Sciences Center, New Orleans, LA, USA
| | - Robert O Messing
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Institute of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Ning Jiang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Deparment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Adela Ben-Yakar
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute of Neuroscience, The University of Texas at Austin, Austin, TX, USA.
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Shi C, Murphy CT. piRNAs regulate a Hedgehog germline-to-soma pro-aging signal. NATURE AGING 2023; 3:47-63. [PMID: 37118518 PMCID: PMC10154208 DOI: 10.1038/s43587-022-00329-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2022] [Indexed: 04/30/2023]
Abstract
The reproductive system regulates somatic aging through competing anti- and pro-aging signals. Germline removal extends somatic lifespan through conserved pathways including insulin and mammalian target-of-rapamycin signaling, while germline hyperactivity shortens lifespan through unknown mechanisms. Here we show that mating-induced germline hyperactivity downregulates piRNAs, in turn desilencing their targets, including the Hedgehog-like ligand-encoding genes wrt-1 and wrt-10, ultimately causing somatic collapse and death. Germline-produced Hedgehog signals require PTR-6 and PTR-16 receptors for mating-induced shrinking and death. Our results reveal an unconventional role of the piRNA pathway in transcriptional regulation of Hedgehog signaling and a new role of Hedgehog signaling in the regulation of longevity and somatic maintenance: Hedgehog signaling is controlled by the tunable piRNA pathway to encode the previously unknown germline-to-soma pro-aging signal. Mating-induced piRNA downregulation in the germline and subsequent Hedgehog signaling to the soma enable the animal to tune somatic resource allocation to germline needs, optimizing reproductive timing and survival.
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Affiliation(s)
- Cheng Shi
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA.
| | - Coleen T Murphy
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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Zhan L, Chen M, Pang T, Li X, Long L, Liang D, Peng L, Sun W, Xu E. Attenuation of Piwil2 induced by hypoxic postconditioning prevents cerebral ischemic injury by inhibiting CREB2 promoter methylation. Brain Pathol 2022; 33:e13109. [PMID: 35794855 PMCID: PMC9836370 DOI: 10.1111/bpa.13109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/24/2022] [Indexed: 01/24/2023] Open
Abstract
Epigenetic modification contributes to the pathogenesis of cerebral ischemia. Piwil2 belongs to the PIWI proteins subfamily and has a key role in the regulation of gene transcription through epigenetics. However, the roles of Piwil2 in cerebral ischemia have not been investigated. In this study, we aim to elucidate the roles and the underlying molecular mechanisms of Piwil2 in ischemic tolerance induced by hypoxic postconditioning (HPC) against transient global cerebral ischemia (tGCI). We found that the expression of Piwil2 in CA1 was downregulated by HPC after tGCI. Silencing Piwil2 with antisense oligodeoxynucleotide (AS-ODN) in CA1 after tGCI decreased the expression of apoptosis-related proteins and exerted neuroprotective effects. Opposite results were observed after overexpression of Piwil2 induced by administration of Piwil2-carried lentivirus. Furthermore, we revealed differentially expressed Piwil2-interacting piRNAs in CA1 between HPC and tGCI groups by RNA binding protein immunoprecipitation (RIP) assay. Moreover, downregulating Piwil2 induced by HPC or AS-ODN after tGCI caused a marked reduction of DNA methyltransferase 3A (DNMT3A), which in turn abolished the tGCI-induced increase in the DNA methylation of cyclic AMP response element-binding 2 (CREB2), thus increasing mRNA and protein of CREB2. Finally, downregulating Piwil2 restored dendritic complexity and length, prevented the loss of dentritic spines, thereby improving cognitive function after tGCI. These data firstly reveal that Piwil2 plays an important part in HPC-mediated neuroprotection against cerebral ischemia through epigenetic regulation of CREB2.
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Affiliation(s)
- Lixuan Zhan
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Meiyan Chen
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Taoyan Pang
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Xinyu Li
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Long Long
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Donghai Liang
- Department of Environmental Health Sciences, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
| | - Linhui Peng
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Weiwen Sun
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - En Xu
- Institute of Neurosciences and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
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7
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Zhang T, Chen L, Li R, Liu N, Huang X, Wong G. PIWI-interacting RNAs in human diseases: databases and computational models. Brief Bioinform 2022; 23:6603448. [PMID: 35667080 DOI: 10.1093/bib/bbac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
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Affiliation(s)
- Tianjiao Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Liang Chen
- Department of Computer Science, School of Engineering, Shantou University, Shantou, China
| | - Rongzhen Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Ning Liu
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Xiaobing Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
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8
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Yin C, Wang C, Wang C. Aberrantly Expressed Small Noncoding RNAome in Keloid Skin Tissue. Front Genet 2022; 13:803083. [PMID: 35495137 PMCID: PMC9045488 DOI: 10.3389/fgene.2022.803083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/17/2022] [Indexed: 11/29/2022] Open
Abstract
The skin is an organ that protects against injury and infection but can be damaged easily. Wound healing is a subtle balance which, if broken, can lead to keloid formation. Small noncoding (nc) RNAs can be of “housekeeping,” for example, ribosomal RNAs and transfer RNAs, or “regulatory,” for example, microRNAs (miRNAs or miRs), small nucleolar RNAs (snoRNAs), and P-element–induced Wimpy testis (PIWI)-interacting RNA (piRNA) types. We examined five types of small ncRNAs [miR, piRNA, snoRNA, small nuclear (sn) RNA, and repeat-associated small interfering RNA (rasiRNA)] in keloid skin tissue (KST) using sequencing and real-time reverse transcription-quantitative polymerase chain reaction. All comparisons were made in relation to expression in normal skin tissue (obtained by abdominoplasty). The expression of three piRNAs was upregulated, and the expression of six piRNAs was downregulated in KST. The expression of 12 snoRNAs was upregulated, and the expression of two snoRNAs was downregulated in KST. The expression of two snRNAs was downregulated in KST. The expression of 18 miRs was upregulated, and the expression of three miRNAs was downregulated in KST. The expression of one rasiRNA was upregulated, and the expression of one rasiRNA was downregulated in KST. We revealed the differential expression of small ncRNAs in KST, which may aid the development of new treatment for keloids.
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Affiliation(s)
- Chuang Yin
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Chen Wang, ; Chuandong Wang,
| | - Chen Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Chen Wang, ; Chuandong Wang,
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9
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Wang H, Jiang F, Liu X, Liu Q, Fu Y, Li R, Hou L, Zhang J, He J, Kang L. Piwi/piRNAs control food intake by promoting neuropeptide F expression in locusts. EMBO Rep 2022; 23:e50851. [PMID: 34985794 PMCID: PMC8892266 DOI: 10.15252/embr.202050851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Animal feeding, which directly affects growth and metabolism, is an important physiological process. However, the contribution of PIWI proteins and PIWI‐interacting RNAs (piRNAs) to the regulatory mechanism of animal feeding is unknown. Here, we report a novel function of Piwi and piRNAs in regulating food intake in locusts. Our study shows that the locust can serve as a representative species for determining PIWI function in insects. Knockdown of Piwi1 expression suppresses anabolic processes and reduces food consumption and body weight. The reduction in food intake by knockdown of Piwi1 expression results from decreased expression of neuropeptide NPF1 in a piRNA‐dependent manner. Mechanistically, intronic piRNAs might enhance RNA splicing of NPF1 by preventing hairpin formation at the branch point sites. These results suggest a novel nuclear PIWI/piRNA‐mediated mechanism that controls food intake in the locust nervous system.
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Affiliation(s)
- Huimin Wang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Feng Jiang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qing Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- Sino‐Danish College University of Chinese Academy of Sciences Beijing China
| | - Yunyun Fu
- College of Life Science Hebei University Baoding China
| | - Ran Li
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jie Zhang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
| | - Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Le Kang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science Hebei University Baoding China
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10
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Dysregulation of Human Somatic piRNA Expression in Parkinson's Disease Subtypes and Stages. Int J Mol Sci 2022; 23:ijms23052469. [PMID: 35269612 PMCID: PMC8910154 DOI: 10.3390/ijms23052469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Piwi interacting RNAs (piRNAs) are small non-coding single-stranded RNA species 20–31 nucleotides in size generated from distinct loci. In germline tissues, piRNAs are amplified via a “ping-pong cycle” to produce secondary piRNAs, which act in transposon silencing. In contrast, the role of somatic-derived piRNAs remains obscure. Here, we investigated the identity and distribution of piRNAs in human somatic tissues to determine their function and potential role in Parkinson’s disease (PD). Human datasets were curated from the Gene Expression Omnibus (GEO) database and a workflow was developed to identify piRNAs, which revealed 902 somatic piRNAs of which 527 were expressed in the brain. These were mainly derived from chromosomes 1, 11, and 19 compared to the germline tissues, which were from 15 and 19. Approximately 20% of somatic piRNAs mapped to transposon 3′ untranslated regions (UTRs), but a large proportion were sensed to the transcript in contrast to germline piRNAs. Gene set enrichment analysis suggested that somatic piRNAs function in neurodegenerative disease. piRNAs undergo dysregulation in different PD subtypes (PD and Parkinson’s disease dementia (PDD)) and stages (premotor and motor). piR-has-92056, piR-hsa-150797, piR-hsa-347751, piR-hsa-1909905, piR-hsa-2476630, and piR-hsa-2834636 from blood small extracellular vesicles were identified as novel biomarkers for PD diagnosis using a sparse partial least square discriminant analysis (sPLS-DA) (accuracy: 92%, AUC = 0.89). This study highlights a role for piRNAs in PD and provides tools for novel biomarker development.
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Tsuji J, Thomson T, Brown C, Ghosh S, Theurkauf WE, Weng Z, Schwartz LM. Somatic piRNAs and Transposons are Differentially Expressed Coincident with Skeletal Muscle Atrophy and Programmed Cell Death. Front Genet 2022; 12:775369. [PMID: 35003216 PMCID: PMC8730325 DOI: 10.3389/fgene.2021.775369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/30/2021] [Indexed: 12/02/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small single-stranded RNAs that can repress transposon expression via epigenetic silencing and transcript degradation. They have been identified predominantly in the ovary and testis, where they serve essential roles in transposon silencing in order to protect the integrity of the genome in the germline. The potential expression of piRNAs in somatic cells has been controversial. In the present study we demonstrate the expression of piRNAs derived from both genic and transposon RNAs in the intersegmental muscles (ISMs) from the tobacco hawkmoth Manduca sexta. These piRNAs are abundantly expressed, ∼27 nt long, map antisense to transposons, are oxidation resistant, exhibit a 5’ uridine bias, and amplify via the canonical ping-pong pathway. An RNA-seq analysis demonstrated that 19 piRNA pathway genes are expressed in the ISMs and are developmentally regulated. The abundance of piRNAs does not change when the muscles initiate developmentally-regulated atrophy, but are repressed coincident with the commitment of the muscles undergo programmed cell death at the end of metamorphosis. This change in piRNA expression is correlated with the repression of several retrotransposons and the induction of specific DNA transposons. The developmentally-regulated changes in the expression of piRNAs, piRNA pathway genes, and transposons are all regulated by 20-hydroxyecdysone, the steroid hormone that controls the timing of ISM death. Taken together, these data provide compelling evidence for the existence of piRNA in somatic tissues and suggest that they may play roles in developmental processes such as programmed cell death.
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Affiliation(s)
- Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Travis Thomson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.,Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Christine Brown
- Department of Biology, University of Massachusetts, Amherst, MA, United States
| | - Subhanita Ghosh
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, United States
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Lawrence M Schwartz
- Department of Biology, University of Massachusetts, Amherst, MA, United States
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12
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Penning A, Tosoni G, Abiega O, Bielefeld P, Gasperini C, De Pietri Tonelli D, Fitzsimons CP, Salta E. Adult Neural Stem Cell Regulation by Small Non-coding RNAs: Physiological Significance and Pathological Implications. Front Cell Neurosci 2022; 15:781434. [PMID: 35058752 PMCID: PMC8764185 DOI: 10.3389/fncel.2021.781434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/09/2021] [Indexed: 01/11/2023] Open
Abstract
The adult neurogenic niches are complex multicellular systems, receiving regulatory input from a multitude of intracellular, juxtacrine, and paracrine signals and biological pathways. Within the niches, adult neural stem cells (aNSCs) generate astrocytic and neuronal progeny, with the latter predominating in physiological conditions. The new neurons generated from this neurogenic process are functionally linked to memory, cognition, and mood regulation, while much less is known about the functional contribution of aNSC-derived newborn astrocytes and adult-born oligodendrocytes. Accumulating evidence suggests that the deregulation of aNSCs and their progeny can impact, or can be impacted by, aging and several brain pathologies, including neurodevelopmental and mood disorders, neurodegenerative diseases, and also by insults, such as epileptic seizures, stroke, or traumatic brain injury. Hence, understanding the regulatory underpinnings of aNSC activation, differentiation, and fate commitment could help identify novel therapeutic avenues for a series of pathological conditions. Over the last two decades, small non-coding RNAs (sncRNAs) have emerged as key regulators of NSC fate determination in the adult neurogenic niches. In this review, we synthesize prior knowledge on how sncRNAs, such as microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), may impact NSC fate determination in the adult brain and we critically assess the functional significance of these events. We discuss the concepts that emerge from these examples and how they could be used to provide a framework for considering aNSC (de)regulation in the pathogenesis and treatment of neurological diseases.
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Affiliation(s)
- Amber Penning
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
| | - Giorgia Tosoni
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
| | - Oihane Abiega
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Pascal Bielefeld
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Caterina Gasperini
- Neurobiology of miRNAs Lab, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Carlos P. Fitzsimons
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Carlos Fitzsimons Evgenia Salta
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
- *Correspondence: Carlos Fitzsimons Evgenia Salta
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13
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Mesquita-Ribeiro R, Fort RS, Rathbone A, Farias J, Lucci C, James V, Sotelo-Silveira J, Duhagon MA, Dajas-Bailador F. Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. RNA Biol 2021; 18:832-855. [PMID: 34882524 PMCID: PMC8782166 DOI: 10.1080/15476286.2021.2000792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neurons have highlighted the needs for decentralized gene expression and specific RNA function in somato-dendritic and axonal compartments, as well as in intercellular communication via extracellular vesicles (EVs). Despite advances in miRNA biology, the identity and regulatory capacity of other small non-coding RNAs (sncRNAs) in neuronal models and local subdomains has been largely unexplored.We identified a highly complex and differentially localized content of sncRNAs in axons and EVs during early neuronal development of cortical primary neurons and in adult axons in vivo. This content goes far beyond miRNAs and includes most known sncRNAs and precisely processed fragments from tRNAs, sno/snRNAs, Y RNAs and vtRNAs. Although miRNAs are the major sncRNA biotype in whole-cell samples, their relative abundance is significantly decreased in axons and neuronal EVs, where specific tRNA fragments (tRFs and tRHs/tiRNAs) mainly derived from tRNAs Gly-GCC, Val-CAC and Val-AAC predominate. Notably, although 5'-tRHs compose the great majority of tRNA-derived fragments observed in vitro, a shift to 3'-tRNAs is observed in mature axons in vivo.The existence of these complex sncRNA populations that are specific to distinct neuronal subdomains and selectively incorporated into EVs, equip neurons with key molecular tools for spatiotemporal functional control and cell-to-cell communication.
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Affiliation(s)
| | - Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alex Rathbone
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.,Polo de Desarrollo Universitario "Espacio de Biología Vegetal del Noreste", Centro Universitario Regional Noreste, UdelaR, Uruguay
| | - Cristiano Lucci
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jose Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Maria Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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14
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Huang S, Yoshitake K, Asakawa S. A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans. Int J Mol Sci 2021; 22:ijms222011166. [PMID: 34681826 PMCID: PMC8538981 DOI: 10.3390/ijms222011166] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.
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Affiliation(s)
- Songqian Huang
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
| | | | - Shuichi Asakawa
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
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15
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Fonseca Cabral G, Schaan AP, Cavalcante GC, Sena-dos-Santos C, de Souza TP, Souza Port’s NM, dos Santos Pinheiro JA, Ribeiro-dos-Santos Â, Vidal AF. Nuclear and Mitochondrial Genome, Epigenome and Gut Microbiome: Emerging Molecular Biomarkers for Parkinson's Disease. Int J Mol Sci 2021; 22:9839. [PMID: 34576000 PMCID: PMC8471599 DOI: 10.3390/ijms22189839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is currently the second most common neurodegenerative disorder, burdening about 10 million elderly individuals worldwide. The multifactorial nature of PD poses a difficult obstacle for understanding the mechanisms involved in its onset and progression. Currently, diagnosis depends on the appearance of clinical signs, some of which are shared among various neurologic disorders, hindering early diagnosis. There are no effective tools to prevent PD onset, detect the disease in early stages or accurately report the risk of disease progression. Hence, there is an increasing demand for biomarkers that may identify disease onset and progression, as treatment-based medicine may not be the best approach for PD. Over the last few decades, the search for molecular markers to predict susceptibility, aid in accurate diagnosis and evaluate the progress of PD have intensified, but strategies aimed to improve individualized patient care have not yet been established. CONCLUSIONS Genomic variation, regulation by epigenomic mechanisms, as well as the influence of the host gut microbiome seem to have a crucial role in the onset and progress of PD, thus are considered potential biomarkers. As such, the human nuclear and mitochondrial genome, epigenome, and the host gut microbiome might be the key elements to the rise of personalized medicine for PD patients.
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Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ana Paula Schaan
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Giovanna C. Cavalcante
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Natacha M. Souza Port’s
- Laboratório de Neurofarmacologia Molecular, Universidade de São Paulo, São Paulo 05508-000, Brazil;
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará–R. dos Mundurucus, Belém 66073-000, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
| | - Amanda F. Vidal
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
- ITVDS—Instituto Tecnológico Vale Desenvolvimento Sustentável–R. Boaventura da Silva, Belém 66055-090, Brazil
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16
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Lite C, Sridhar VV, Sriram S, Juliet M, Arshad A, Arockiaraj J. Functional role of piRNAs in animal models and its prospects in aquaculture. REVIEWS IN AQUACULTURE 2021; 13:2038-2052. [DOI: 10.1111/raq.12557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/01/2021] [Indexed: 10/16/2023]
Abstract
AbstractThe recent advances in the field of aquaculture over the last decade has helped the cultured‐fish industry production sector to identify problems and choose the best approaches to achieve high‐volume production. Understanding the emerging roles of non‐coding RNA (ncRNA) in the regulation of fish physiology and health will assist in gaining knowledge on the possible applications of ncRNAs for the advancement of aquaculture. There is information available on the practical considerations of epigenetic mechanisms like DNA methylation, histone modification and ncRNAs, such as microRNA in aquaculture, for both fish and shellfish. Among the non‐coding RNAs, PIWI‐interacting RNA (piRNA) is 24–31 bp long transcripts, which is primarily involved in silencing the germline transposons. Besides, the burgeoning reports and studies establish piRNAs' role in various aspects of biology. Till date, there are no reviews that summarize the recent findings available on piRNAs in animal models, especially on piRNAs biogenesis and biological action. To gain a better understanding and get an overview on the process of piRNA genesis among the different animals, this work reviews the literature available on the processes of piRNA biogenesis in animal models with special reference to aquatic animal model zebrafish. This review also presents a short discussion and prospects of piRNA’s application in relevance to the aquaculture industry.
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Affiliation(s)
- Christy Lite
- Endocrine and Exposome (E2) Laboratory Department of Zoology Madras Christian College Chennai India
| | - Vasisht Varsh Sridhar
- Department of Biotechnology School of Bioengineering SRM Institute of Science and Technology Chennai India
| | - Swati Sriram
- Department of Biotechnology School of Bioengineering SRM Institute of Science and Technology Chennai India
| | - Melita Juliet
- Department of Oral and Maxillofacial Surgery SRM Dental College and Hospital, SRM Institute of Science and Technology Chennai India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
- Department of Aquaculture Faculty of Agriculture Universiti Putra Malaysia Serdang Malaysia
| | - Jesu Arockiaraj
- SRM Research Institute SRM Institute of Science and Technology Chennai India
- Department of Biotechnology, Faculty of Science and Humanities SRM Institute of Science and Technology Chennai India
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17
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Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are regulatory small non-coding RNAs that participate in transposon inactivation, chromatin regulation, and endogenous gene regulation. Numerous genetic and epigenetic factors regulate cell proliferation and tumor metastasis. PIWI proteins and piRNAs have been revealed to function in regulating upstream or downstream of oncogenes or tumor-suppressor genes in cancer tissues. In the present review, we summarize major recent findings in uncovering the regulation and role of PIWI proteins and piRNAs in tumorigenesis and highlight some of the promising applications of specific piRNAs in cancer therapeutics and as cancer biomarkers.
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18
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Ow MC, Nichitean AM, Hall SE. Somatic aging pathways regulate reproductive plasticity in Caenorhabditis elegans. eLife 2021; 10:61459. [PMID: 34236316 PMCID: PMC8291976 DOI: 10.7554/elife.61459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 06/26/2021] [Indexed: 01/21/2023] Open
Abstract
In animals, early-life stress can result in programmed changes in gene expression that can affect their adult phenotype. In C. elegans nematodes, starvation during the first larval stage promotes entry into a stress-resistant dauer stage until environmental conditions improve. Adults that have experienced dauer (postdauers) retain a memory of early-life starvation that results in gene expression changes and reduced fecundity. Here, we show that the endocrine pathways attributed to the regulation of somatic aging in C. elegans adults lacking a functional germline also regulate the reproductive phenotypes of postdauer adults that experienced early-life starvation. We demonstrate that postdauer adults reallocate fat to benefit progeny at the expense of the parental somatic fat reservoir and exhibit increased longevity compared to controls. Our results also show that the modification of somatic fat stores due to parental starvation memory is inherited in the F1 generation and may be the result of crosstalk between somatic and reproductive tissues mediated by the germline nuclear RNAi pathway.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, United States
| | | | - Sarah E Hall
- Department of Biology, Syracuse University, Syracuse, United States
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19
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Ow MC, Hall SE. piRNAs and endo-siRNAs: Small molecules with large roles in the nervous system. Neurochem Int 2021; 148:105086. [PMID: 34082061 DOI: 10.1016/j.neuint.2021.105086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/23/2021] [Accepted: 05/26/2021] [Indexed: 01/02/2023]
Abstract
Since their discovery, small non-coding RNAs have emerged as powerhouses in the regulation of numerous cellular processes. In addition to guarding the integrity of the reproductive system, small non-coding RNAs play critical roles in the maintenance of the soma. Accumulating evidence indicates that small non-coding RNAs perform vital functions in the animal nervous system such as restricting the activity of deleterious transposable elements, regulating nerve regeneration, and mediating learning and memory. In this review, we provide an overview of the current understanding of the contribution of two major classes of small non-coding RNAs, piRNAs and endo-siRNAs, to the nervous system development and function, and present highlights on how the dysregulation of small non-coding RNA pathways can assist in understanding the neuropathology of human neurological disorders.
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Affiliation(s)
- Maria C Ow
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| | - Sarah E Hall
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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20
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Kärkkäinen E, Heikkinen S, Tengström M, Kosma VM, Mannermaa A, Hartikainen JM. The debatable presence of PIWI-interacting RNAs in invasive breast cancer. Cancer Med 2021; 10:3593-3603. [PMID: 33960684 PMCID: PMC8178507 DOI: 10.1002/cam4.3915] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/16/2020] [Accepted: 03/29/2021] [Indexed: 01/27/2023] Open
Abstract
Numerous factors influence breast cancer (BC) prognosis, thus complicating the prediction of outcome. By identifying biomarkers that would distinguish the cases with poorer response to therapy already at the time of diagnosis, the rate of survival could be improved. Lately, Piwi-interacting RNAs (piRNAs) have been introduced as potential cancer biomarkers, however, due to the recently raised challenges in piRNA annotations, further evaluation of piRNAs' involvement in cancer is required. We performed small RNA sequencing in 227 fresh-frozen breast tissue samples from the Eastern Finnish Kuopio Breast Cancer Project material to study the presence of piRNAs in BC and their associations with the clinicopathological features and outcome of BC patients. We observed the presence of three small RNAs annotated as piRNA database entries (DQ596932, DQ570994, and DQ571955) in our samples. The actual species of these RNAs however remain uncertain. All three small RNAs were upregulated in grade III tumors and DQ596932 additionally in estrogen receptor negative tumors. Furthermore, patients with estrogen receptor positive BC and higher DQ571955 had shorter relapse-free survival and poorer BC-specific survival, thus indicating DQ571955 as a candidate predictive marker for radiotherapy response in estrogen receptor positive BC. DQ596932 showed possible prognostic value in BC, whereas DQ570994 was identified as a candidate predictive marker for tamoxifen and chemotherapy response. These three small RNAs appear as candidate biomarkers for BC, which could after further investigation provide novel approaches for the treatment of therapy resistant BC. Overall, our results indicate that the prevalence of piRNAs in cancer is most likely not as comprehensive as has been previously thought.
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Affiliation(s)
- Emmi Kärkkäinen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| | - Sami Heikkinen
- School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Maria Tengström
- School of Medicine, Institute of Clinical Medicine, Oncology, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland.,Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland.,Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
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21
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Hale AT, Bastarache L, Morales DM, Wellons JC, Limbrick DD, Gamazon ER. Multi-omic analysis elucidates the genetic basis of hydrocephalus. Cell Rep 2021; 35:109085. [PMID: 33951428 PMCID: PMC8124085 DOI: 10.1016/j.celrep.2021.109085] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/01/2019] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
We conducted PrediXcan analysis of hydrocephalus risk in ten neurological tissues and whole blood. Decreased expression of MAEL in the brain was significantly associated (Bonferroni-adjusted p < 0.05) with hydrocephalus. PrediXcan analysis of brain imaging and genomics data in the independent UK Biobank (N = 8,428) revealed that MAEL expression in the frontal cortex is associated with white matter and total brain volumes. Among the top differentially expressed genes in brain, we observed a significant enrichment for gene-level associations with these structural phenotypes, suggesting an effect on disease risk through regulation of brain structure and integrity. We found additional support for these genes through analysis of the choroid plexus transcriptome of a murine model of hydrocephalus. Finally, differential protein expression analysis in patient cerebrospinal fluid recapitulated disease-associated expression changes in neurological tissues, but not in whole blood. Our findings provide convergent evidence highlighting the importance of tissue-specific pathways and mechanisms in the pathophysiology of hydrocephalus. Hale et al. present an integrated omics approach to characterize the genetic basis of hydrocephalus. They reveal tissue-specific genetic associations and enrichment of genes associated with human brain structure phenotypes. Validation of hydrocephalus-associated genes in mouse choroid plexus and human cerebrospinal fluid supports polygenic contributions to hydrocephalus risk.
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Affiliation(s)
- Andrew T Hale
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN 37232, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Lisa Bastarache
- Department of Bioinformatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Diego M Morales
- Division of Pediatric Neurosurgery, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - John C Wellons
- Division of Pediatric Neurosurgery, Monroe Carell Jr. Children's Hospital of Vanderbilt University, Nashville, TN 37232, USA
| | - David D Limbrick
- Division of Pediatric Neurosurgery, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Data Science Institute, Vanderbilt University, Nashville, TN 37232, USA; Clare Hall, University of Cambridge, Cambridge CB3 9AL, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge CB3 9AL, UK.
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22
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Abstract
Memories encoded in the parent's brain should not be able to transfer to the progeny. This assumption, which is compatible with the tenets of modern neuroscience and genetics, is challenged by new insights regarding inheritance of transgenerational epigenetic responses. Here we reflect on new discoveries regarding "molecular memories" in light of older and scandalous work on "Memory transfer" spearheaded by James V. McConnell and Georges Ungar. While the history of this field is filled with controversies, mechanisms for transmission of information across generations are being elucidated in different organisms. Most strikingly, it is now clear that in Caenorhabditis elegans nematodes, somatic responses can control gene activity in descendants via heritable small RNA molecules, and that this type of inheritance is tightly regulated by dedicated machinery. In this perspective we will focus mostly on studies conducted using C. elegans, and examine recent work on the connection between small RNAs in the nervous system and germline. We will discuss the evidence for the inheritance of brain-orchestrated behavior, and its possible significance.
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Affiliation(s)
- Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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23
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Huang X, Wong G. An old weapon with a new function: PIWI-interacting RNAs in neurodegenerative diseases. Transl Neurodegener 2021; 10:9. [PMID: 33685517 PMCID: PMC7938595 DOI: 10.1186/s40035-021-00233-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding transcripts that are highly conserved across species and regulate gene expression through pre- and post-transcriptional processes. piRNAs were originally discovered in germline cells and protect against transposable element expression to promote and maintain genome stability. In the recent decade, emerging roles of piRNAs have been revealed, including the roles in sterility, tumorigenesis, metabolic homeostasis, neurodevelopment, and neurodegenerative diseases. In this review, we summarize piRNA biogenesis in C. elegans, Drosophila, and mice, and further elaborate upon how piRNAs mitigate the harmful effects of transposons. Lastly, the most recent findings on piRNA participation in neurological diseases are highlighted. We speculate on the mechanisms of piRNA action in the development and progression of neurodegenerative diseases. Understanding the roles of piRNAs in neurological diseases may facilitate their applications in diagnostic and therapeutic practice.
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Affiliation(s)
- Xiaobing Huang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, 999078, S.A.R., China
| | - Garry Wong
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, 999078, S.A.R., China.
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24
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Shen L, Wang C, Chen L, Wong G. Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson's Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1. Front Neurosci 2021; 15:600462. [PMID: 33762903 PMCID: PMC7982545 DOI: 10.3389/fnins.2021.600462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) regulate gene expression and biological processes through specific genetic and epigenetic mechanisms. Recent studies have described a dysregulation of small non-coding RNAs in Parkinson’s disease (PD) tissues but have been limited in scope. Here, we extend these studies by comparing the dysregulation of both miRNAs and piRNAs from transgenic Caenorhabditis elegans (C. elegans) nematodes overexpressing pan-neuronally human α-synuclein wild-type (WT) (HASNWT OX) or mutant (HASNA53T OX). We observed 32 miRNAs and 112 piRNAs dysregulated in HASNA53T OX compared with WT. Genetic crosses of HASNA53T OX PD animal models with tdp-1 null mutants, the C. elegans ortholog of TDP-43, an RNA-binding protein aggregated in frontal temporal lobar degeneration, improved their behavioral deficits and changed the number of dysregulated miRNAs to 11 and piRNAs to none. Neuronal function-related genes T28F4.5, C34F6.1, C05C10.3, camt-1, and F54D10.3 were predicted to be targeted by cel-miR-1018, cel-miR-355-5p (C34F6.1 and C05C10.3), cel-miR-800-3p, and 21ur-1581 accordingly. This study provides a molecular landscape of small non-coding RNA dysregulation in an animal model that provides insight into the epigenetic changes, molecular processes, and interactions that occur during PD-associated neurodegenerative disorders.
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Affiliation(s)
- Linjing Shen
- Centre for Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| | - Changliang Wang
- Centre for Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, China.,Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University, Shantou, China
| | - Garry Wong
- Centre for Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
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25
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Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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26
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Kim IV, Riedelbauch S, Kuhn CD. The piRNA pathway in planarian flatworms: new model, new insights. Biol Chem 2020; 401:1123-1141. [DOI: 10.1515/hsz-2019-0445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/12/2020] [Indexed: 12/22/2022]
Abstract
AbstractPIWI-interacting RNAs (piRNAs) are small regulatory RNAs that associate with members of the PIWI clade of the Argonaute superfamily of proteins. piRNAs are predominantly found in animal gonads. There they silence transposable elements (TEs), regulate gene expression and participate in DNA methylation, thus orchestrating proper germline development. Furthermore, PIWI proteins are also indispensable for the maintenance and differentiation capabilities of pluripotent stem cells in free-living invertebrate species with regenerative potential. Thus, PIWI proteins and piRNAs seem to constitute an essential molecular feature of somatic pluripotent stem cells and the germline. In keeping with this hypothesis, both PIWI proteins and piRNAs are enriched in neoblasts, the adult stem cells of planarian flatworms, and their presence is a prerequisite for the proper regeneration and perpetual tissue homeostasis of these animals. The piRNA pathway is required to maintain the unique biology of planarians because, in analogy to the animal germline, planarian piRNAs silence TEs and ensure stable genome inheritance. Moreover, planarian piRNAs also contribute to the degradation of numerous protein-coding transcripts, a function that may be critical for neoblast differentiation. This review gives an overview of the planarian piRNA pathway and of its crucial function in neoblast biology.
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Affiliation(s)
- Iana V. Kim
- Gene regulation by Non-coding RNA, Elite Network of Bavaria and University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Sebastian Riedelbauch
- Gene regulation by Non-coding RNA, Elite Network of Bavaria and University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Claus-D. Kuhn
- Gene regulation by Non-coding RNA, Elite Network of Bavaria and University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
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27
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Kulkarni A, Lopez DH, Extavour CG. Shared Cell Biological Functions May Underlie Pleiotropy of Molecular Interactions in the Germ Lines and Nervous Systems of Animals. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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28
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Zeng C, Weng C, Wang X, Yan YH, Li WJ, Xu D, Hong M, Liao S, Dong MQ, Feng X, Xu C, Guang S. Functional Proteomics Identifies a PICS Complex Required for piRNA Maturation and Chromosome Segregation. Cell Rep 2020; 27:3561-3572.e3. [PMID: 31216475 DOI: 10.1016/j.celrep.2019.05.076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/08/2019] [Accepted: 05/20/2019] [Indexed: 01/19/2023] Open
Abstract
piRNAs play significant roles in suppressing transposons and nonself nucleic acids, maintaining genome integrity, and defending against viral infections. In C. elegans, piRNA precursors are transcribed in the nucleus and are subjected to a number of processing and maturation steps. The biogenesis of piRNAs is not fully understood. We use functional proteomics in C. elegans and identify a piRNA biogenesis and chromosome segregation (PICS) complex. The PICS complex contains TOFU-6, PID-1, PICS-1, TOST-1, and ERH-2, which exhibit dynamic localization among different subcellular compartments. In the germlines, the PICS complex contains TOFU-6/PICS-1/ERH-2/PID-1, is largely concentrated at the perinuclear granule zone, and engages in piRNA processing. During embryogenesis, the TOFU-6/PICS-1/ERH-2/TOST-1 complex accumulates in the nucleus and plays essential roles in chromosome segregation. The functions of these factors in mediating chromosome segregation are independent of piRNA production. We speculate that differential compositions of PICS factors may help cells coordinate distinct cellular processes.
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Affiliation(s)
- Chenming Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Chenchun Weng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xiaoyang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Jun Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Demin Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Minjie Hong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.
| | - Chao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui 230027, P.R. China.
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29
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Pinto P, da Silva MB, Moreira FC, Bouth RC, Gobbo AR, Sandoval TV, Ribeiro-Dos-Santos AM, Vidal AF, Barreto JG, Santos S, Spencer JS, Salgado CG, Ribeiro-Dos-Santos Â. Leprosy piRnome: exploring new possibilities for an old disease. Sci Rep 2020; 10:12648. [PMID: 32724108 PMCID: PMC7387468 DOI: 10.1038/s41598-020-69355-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
Leprosy, which is caused by the human pathogen Mycobacterium leprae, causes nerve damage, deformity and disability in over 200,000 people every year. Because of the long doubling time of M. leprae (13 days) and the delayed onset of detectable symptoms, which is estimated to be approximately 3-7 years after infection, there is always a large percentage of subclinically infected individuals in the population who will eventually develop the disease, mainly in endemic countries. piRNAs comprise the largest group of small noncoding RNAs found in humans, and they are distinct from microRNAs (miRNAs) and small interfering RNAs (siRNAs). piRNAs function in transposon silencing, epigenetic regulation, and germline development. The functional role of piRNAs and their associated PIWI proteins have started to emerge in the development of human cancers and viral infections, but their relevance to bacterial diseases has not been investigated. The present study reports the piRNome of human skin, revealing that all but one of the piRNAs examined are downregulated in leprosy skin lesions. Considering that one of the best characterized functions of piRNAs in humans is posttranscriptional mRNA silencing, their functions are similar to what we have described for miRNAs, including acting on apoptosis, M. leprae recognition and engulfment, Schwann cell (SC) demyelination, epithelial-mesenchymal transition (EMT), loss of sensation and neuropathic pain. In addition to new findings on leprosy physiopathology, the discovery of relevant piRNAs involved in disease processes in human skin may provide new clues for therapeutic targets, specifically to control nerve damage, a prominent feature of leprosy that has no currently available pharmaceutical treatment.
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Affiliation(s)
- Pablo Pinto
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
- Oncology Research Center (NPO), UFPA, Belém, 66075110, Brazil
| | - Moisés Batista da Silva
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil
| | | | - Raquel Carvalho Bouth
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil
| | - Angélica Rita Gobbo
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil
| | - Tatiana Vinasco Sandoval
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
| | | | - Amanda Ferreira Vidal
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
| | | | - Sidney Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
- Oncology Research Center (NPO), UFPA, Belém, 66075110, Brazil
| | - John Stewart Spencer
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, 80523-1601, USA
| | - Claudio Guedes Salgado
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil.
| | - Ândrea Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil.
- Oncology Research Center (NPO), UFPA, Belém, 66075110, Brazil.
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30
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Abstract
Nictation is a behaviour in which a nematode stands on its tail and waves its head in three dimensions. This activity promotes dispersal of dauer larvae by allowing them to attach to other organisms and travel on them to a new niche. In this review, we describe our understanding of nictation, including its diversity in nematode species, how it is induced by environmental factors, and neurogenetic factors that regulate nictation. We also highlight the known cellular and signalling factors that affect nictation, for example, IL2 neurons, insulin/IGF-1 signalling, TGF-β signalling, FLP neuropeptides and piRNAs. Elucidation of the mechanism of nictation will contribute to increased understanding of the conserved dispersal strategies in animals.
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Affiliation(s)
- Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Bo Yun Lee
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, South Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
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31
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Wu WS, Brown JS, Chen TT, Chu YH, Huang WC, Tu S, Lee HC. piRTarBase: a database of piRNA targeting sites and their roles in gene regulation. Nucleic Acids Res 2020; 47:D181-D187. [PMID: 30357353 PMCID: PMC6323935 DOI: 10.1093/nar/gky956] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small noncoding RNAs that guard animal genomes against mutation by silencing transposons. In addition, recent studies have reported that piRNAs silence various endogenous genes. Tens of thousands of distinct piRNAs made in animals do not pair well to transposons and currently the functions and targets of piRNAs are largely unexplored. piRTarBase provides a user-friendly interface to access both predicted and experimentally identified piRNA targeting sites in Caenorhabditis elegans. The user can input genes of interest and retrieve a list of piRNA targeting sites on the input genes. Alternatively, the user can input a piRNA and retrieve a list of its mRNA targets. Additionally, piRTarBase integrates published mRNA and small RNA sequencing data, which will help users identify biologically relevant targeting events. Importantly, our analyses suggest that the piRNA sites found by both predictive and experimental approaches are more likely to exhibit silencing effects on their targets than each method alone. Taken together, piRTarBase offers an integrative platform that will help users to identify functional piRNA target sites by evaluating various information. piRTarBase is freely available for academic use at http://cosbi6.ee.ncku.edu.tw/piRTarBase/.
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Affiliation(s)
- Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Jordan S Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tsung-Te Chen
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Han Chu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Che Huang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Shikui Tu
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Heng-Chi Lee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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32
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Liu HH, Jan YN. Mechanisms of neurite repair. Curr Opin Neurobiol 2020; 63:53-58. [PMID: 32278210 DOI: 10.1016/j.conb.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
Upon receiving injury signals, neurons can activate various pathways to reduce harm, initiate neuroprotection, and repair damaged neurite without cell death. Here, we review recent progresses in the study of neurite repair focusing on neuronal cell-autonomous mechanisms, including new findings on ion channels that serve as key regulators to initiate neurite repair and intrinsic signaling pathways and transcriptional and post-transcriptional factors that facilitate neurite repair. We also touch upon reports on how dendrites may be affected upon axotomy and how the regeneration potential in injured neurites might be maximized.
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Affiliation(s)
- Han-Hsuan Liu
- Howard Hughes Medical Institute, Department of Physiology, University of California, San Francisco, CA 94158, USA
| | - Yuh-Nung Jan
- Howard Hughes Medical Institute, Department of Physiology, University of California, San Francisco, CA 94158, USA.
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33
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Abstract
In this issue, Moore et al. and Posner et al., provide evidence for how the activity of the nervous system in C. elegans results in gene expression changes in the germline to pass on parental experiences and learned behavior to their progeny.
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Affiliation(s)
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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34
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Tang NH, Kim KW, Xu S, Blazie SM, Yee BA, Yeo GW, Jin Y, Chisholm AD. The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics. Curr Biol 2020; 30:865-876.e7. [PMID: 31983639 DOI: 10.1016/j.cub.2019.12.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/26/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
Abstract
mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for translational repression and mRNA degradation. How mRNA decay pathways regulate cellular function in vivo with specificity is poorly understood. Here, we show that C. elegans mRNA decay factors, including the translational repressors CAR-1/LSM14 and CGH-1/DDX6, and the decapping enzymes DCAP-1/DCP1, function in neurons to differentially regulate axon development, maintenance, and regrowth following injury. In neuronal cell bodies, CAR-1 fully colocalizes with CGH-1 and partially colocalizes with DCAP-1, suggesting that mRNA decay components form at least two types of cytoplasmic granules. Following axon injury in adult neurons, loss of CAR-1 or CGH-1 results in increased axon regrowth and growth cone formation, whereas loss of DCAP-1 or DCAP-2 results in reduced regrowth. To determine how CAR-1 inhibits regrowth, we analyzed mRNAs bound to pan-neuronally expressed GFP::CAR-1 using a crosslinking and immunoprecipitation-based approach. Among the putative mRNA targets of CAR-1, we characterized the roles of micu-1, a regulator of the mitochondrial calcium uniporter MCU-1, in axon injury. We show that loss of car-1 results increased MICU-1 protein levels, and that enhanced axon regrowth in car-1 mutants is dependent on micu-1 and mcu-1. Moreover, axon injury induces transient calcium influx into axonal mitochondria, dependent on MCU-1. In car-1 loss-of-function mutants and in micu-1 overexpressing animals, the axonal mitochondrial calcium influx is more sustained, which likely underlies enhanced axon regrowth. Our data uncover a novel pathway that controls axon regrowth through axonal mitochondrial calcium uptake.
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Affiliation(s)
- Ngang Heok Tang
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyung Won Kim
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Suhong Xu
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen M Blazie
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrew D Chisholm
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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35
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Site-Specific Expression Pattern of PIWI-Interacting RNA in Skin and Oral Mucosal Wound Healing. Int J Mol Sci 2020; 21:ijms21020521. [PMID: 31947648 PMCID: PMC7013508 DOI: 10.3390/ijms21020521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/02/2020] [Accepted: 01/11/2020] [Indexed: 12/24/2022] Open
Abstract
The oral mucosa exhibits exceptional healing capability when compared to skin. Recent studies suggest that intrinsic differences in coding genes and regulatory small non-coding RNA (sncRNA) genes (e.g., microRNAs) may underlie the exceptional healing that occurs in the oral mucosa. Here, we investigate the role of a novel class of sncRNA-Piwi-interacting RNA (piRNA)-in the tissue-specific differential response to injury. An abundance of piRNAs was detected in both skin and oral mucosal epithelium during wound healing. The expression of PIWI genes (the obligate binding partners of piRNAs) was also detected in skin and oral wound healing. This data suggested that PIWI-piRNA machinery may serve an unknown function in the highly orchestrated wound healing process. Furthermore, unique tissue-specific piRNA profiles were obtained in the skin and oral mucosal epithelium, and substantially more changes in piRNA expression were observed during skin wound healing than oral mucosal wound healing. Thus, we present the first clue suggesting a role of piRNA in wound healing, and provide the first site-specific piRNA profile of skin and oral mucosal wound healing. These results serve as a foundation for the future investigation of the functional contribution(s) of piRNA in wound repair and tissue regeneration.
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36
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Kim KW. PIWI Proteins and piRNAs in the Nervous System. Mol Cells 2019; 42:828-835. [PMID: 31838836 PMCID: PMC6939654 DOI: 10.14348/molcells.2019.0241] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/29/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
PIWI Argonaute proteins and Piwi-interacting RNAs (piRNAs) are expressed in all animal species and play a critical role in cellular defense by inhibiting the activation of transposable elements in the germline. Recently, new evidence suggests that PIWI proteins and piRNAs also play important roles in various somatic tissues, including neurons. This review summarizes the neuronal functions of the PIWI-piRNA pathway in multiple animal species, including their involvement in axon regeneration, behavior, memory formation, and transgenerational epigenetic inheritance of adaptive memory. This review also discusses the consequences of dysregulation of neuronal PIWI-piRNA pathways in certain neurological disorders, including neurodevelopmental and neurodegenerative diseases. A full understanding of neuronal PIWI-piRNA pathways will ultimately provide novel insights into small RNA biology and could potentially provide precise targets for therapeutic applications.
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Affiliation(s)
- Kyung Won Kim
- Convergence Program of Material Science for Medicine and Pharmaceutics, Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252,
Korea
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37
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Suvorov A, Naumov V, Shtratnikova V, Logacheva M, Shershebnev A, Wu H, Gerasimov E, Zheludkevich A, Pilsner JR, Sergeyev O. Rat liver epigenome programing by perinatal exposure to 2,2',4'4'-tetrabromodiphenyl ether. Epigenomics 2019; 12:235-249. [PMID: 31833787 DOI: 10.2217/epi-2019-0315] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Perinatal exposures to polybrominated diphenyl ethers permanently reprogram liver metabolism and induce a nonalcoholic fatty liver disease-like phenotype and insulin resistance in rodents. Aim: To test if these changes are associated with altered liver epigenome. Materials & methods: Expression of small RNA and changes in DNA methylation in livers of adult rats were analyzed following perinatal exposure to 2,2',4,4'-tetrabromodiphenyl ether, the polybrominated diphenyl ether congener most prevalent in human tissues. Results: We identified 33 differentially methylated DNA regions and 15 differentially expressed miRNAs. These changes were enriched for terms related to lipid and carbohydrate metabolism, insulin signaling, Type-2 diabetes and nonalcoholic fatty liver disease. Conclusion: Changes in the liver epigenome are a likely candidate mechanism of long-term maintenance of an aberrant metabolic phenotype.
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Affiliation(s)
- Alexander Suvorov
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA.,A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia
| | - Vladimir Naumov
- Kulakov National Medical Research Center of Obstetrics, Gynecology & Perinatology, Ministry of Health of the Russian Federation, Oparina 4, 117997, Moscow, Russia
| | - Victoria Shtratnikova
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia.,Center for Data-Intensive Biomedicine & Biotechnology, Skolkovo Institute of Science & Technology, 143028, Moscow, Russia
| | - Maria Logacheva
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia.,Center for Data-Intensive Biomedicine & Biotechnology, Skolkovo Institute of Science & Technology, 143028, Moscow, Russia
| | - Alex Shershebnev
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA.,Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 W 168th St, New York, NY 10032, USA
| | - Evgeny Gerasimov
- E.I. Martsinovsky Institute of Medical Parasitology & Tropical Medicine, I.M. Sechenov First Moscow State Medical University, 20 Malaya Pirogovskaya, 119435, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | | | - Jonathan R Pilsner
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA
| | - Oleg Sergeyev
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia.,Chapaevsk Medical Association, 3a Meditsinskaya St., Samara region, 446100, Chapaevsk, Russia
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38
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Laredo F, Plebanski J, Tedeschi A. Pericytes: Problems and Promises for CNS Repair. Front Cell Neurosci 2019; 13:546. [PMID: 31866833 PMCID: PMC6908836 DOI: 10.3389/fncel.2019.00546] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Microvascular complications are often associated with slow and progressive damage of various organs. Pericytes are multi-functional mural cells of the microcirculation that control blood flow, vascular permeability and homeostasis. Whereas accumulating evidence suggests that these cells are also implicated in a variety of diseases, pericytes represent promising targets that can be manipulated for therapeutic gain. Here, we review the role of pericytes in angiogenesis, blood-brain barrier (BBB) function, neuroinflammation, tissue fibrosis, axon regeneration failure, and neurodegeneration. In addition, we outline strategies altering pericyte behavior to point out problems and promises for axon regeneration and central nervous system (CNS) repair following injury or disease.
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Affiliation(s)
- Fabio Laredo
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, United States.,Department of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Julia Plebanski
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Andrea Tedeschi
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, United States.,Discovery Theme on Chronic Brain Injury, The Ohio State University, Columbus, OH, United States
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39
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Sohn EJ, Jo YR, Park HT. Downregulation MIWI-piRNA regulates the migration of Schwann cells in peripheral nerve injury. Biochem Biophys Res Commun 2019; 519:605-612. [PMID: 31540693 DOI: 10.1016/j.bbrc.2019.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 11/26/2022]
Abstract
Although MIWI (PIWI in humans) regulates spermatogenesis and translation machinery, its role in peripheral nerve injury is poorly understood. In this study, we characterized the expression profiles of MIWI after sciatic nerve injury. The results revealed that MIWI was downregulated after sciatic nerve injury. MIWI was colocalized with S100 (a Schwan cell marker), and TOM20 (a mitochondrial marker) on uncut nerves, while some MIWI was also colocalized with myelin protein zero (a myelin marker) on injured nerves. Immunofluorescence revealed that some MIWI was colocalized with SOX10 in the nuclear compartment following nerve injury. MIWI depletion by MIWI siRNA resulted in the reduction of EGR2. To characterize the expression of PIWI interacting RNA (piRNA) during sciatic nerve injury, microarray-based piRNA was conducted. The results revealed that 3447 piRNAs were upregulated, while 4117 piRNAs were downregulated after nerve transection. Interestingly, piR 009614 downregulated the mRNA level of MBP and enhanced the migration of RT-4 Schwann cells. Together, our results suggest that the MIWI-piRNA complex may play a role in Schwann cell responses to nerve injury.
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Affiliation(s)
- Eun Jung Sohn
- Peripheral Neuropathy Research Center, Department of Molecular Neuroscience, College of Medicine, Dong-A University, Dongdaesin-Dong, Seo-Gu, Busan, 602-714, South Korea.
| | - Young Rae Jo
- Peripheral Neuropathy Research Center, Department of Molecular Neuroscience, College of Medicine, Dong-A University, Dongdaesin-Dong, Seo-Gu, Busan, 602-714, South Korea
| | - Hwan Tae Park
- Peripheral Neuropathy Research Center, Department of Molecular Neuroscience, College of Medicine, Dong-A University, Dongdaesin-Dong, Seo-Gu, Busan, 602-714, South Korea
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40
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Nance J, Frøkjær-Jensen C. The Caenorhabditis elegans Transgenic Toolbox. Genetics 2019; 212:959-990. [PMID: 31405997 PMCID: PMC6707460 DOI: 10.1534/genetics.119.301506] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/01/2019] [Indexed: 12/30/2022] Open
Abstract
The power of any genetic model organism is derived, in part, from the ease with which gene expression can be manipulated. The short generation time and invariant developmental lineage have made Caenorhabditis elegans very useful for understanding, e.g., developmental programs, basic cell biology, neurobiology, and aging. Over the last decade, the C. elegans transgenic toolbox has expanded considerably, with the addition of a variety of methods to control expression and modify genes with unprecedented resolution. Here, we provide a comprehensive overview of transgenic methods in C. elegans, with an emphasis on recent advances in transposon-mediated transgenesis, CRISPR/Cas9 gene editing, conditional gene and protein inactivation, and bipartite systems for temporal and spatial control of expression.
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Affiliation(s)
- Jeremy Nance
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York 10016
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal 23955-6900, Saudi Arabia
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41
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Abstract
While PIWI-interacting RNAs (piRNAs) are primarily recognized as guardians of genome integrity, new functions of these small non-coding RNAs are emerging. In this issue, Kim et al. (2018) describe a piRNA-based mechanism that limits axon regeneration in C. elegans.
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Affiliation(s)
- Cláudio Gouveia Roque
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Ulrich Hengst
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
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42
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Using Nanobodies to Study Protein Function in Developing Organisms. Antibodies (Basel) 2019; 8:antib8010016. [PMID: 31544822 PMCID: PMC6640693 DOI: 10.3390/antib8010016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 12/28/2022] Open
Abstract
Polyclonal and monoclonal antibodies have been invaluable tools to study proteins over the past decades. While indispensable for most biological studies including developmental biology, antibodies have been used mostly in fixed tissues or as binding reagents in the extracellular milieu. For functional studies and for clinical applications, antibodies have been functionalized by covalently fusing them to heterologous partners (i.e., chemicals, proteins or other moieties). Such functionalized antibodies have been less widely used in developmental biology studies. In the past few years, the discovery and application of small functional binding fragments derived from single-chain antibodies, so-called nanobodies, has resulted in novel approaches to study proteins during the development of multicellular animals in vivo. Expression of functionalized nanobody fusions from integrated transgenes allows manipulating proteins of interest in the extracellular and the intracellular milieu in a tissue- and time-dependent manner in an unprecedented manner. Here, we describe how nanobodies have been used in the field of developmental biology and look into the future to imagine how else nanobody-based reagents could be further developed to study the proteome in living organisms.
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43
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Weng C, Kosalka J, Berkyurek AC, Stempor P, Feng X, Mao H, Zeng C, Li WJ, Yan YH, Dong MQ, Morero NR, Zuliani C, Barabas O, Ahringer J, Guang S, Miska EA. The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans. Genes Dev 2019; 33:90-102. [PMID: 30567997 PMCID: PMC6317315 DOI: 10.1101/gad.319293.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/19/2018] [Indexed: 01/15/2023]
Abstract
Piwi-interacting RNAs (piRNAs) engage Piwi proteins to suppress transposons and nonself nucleic acids and maintain genome integrity and are essential for fertility in a variety of organisms. In Caenorhabditis elegans, most piRNA precursors are transcribed from two genomic clusters that contain thousands of individual piRNA transcription units. While a few genes have been shown to be required for piRNA biogenesis, the mechanism of piRNA transcription remains elusive. Here we used functional proteomics approaches to identify an upstream sequence transcription complex (USTC) that is essential for piRNA biogenesis. The USTC contains piRNA silencing-defective 1 (PRDE-1), SNPC-4, twenty-one-U fouled-up 4 (TOFU-4), and TOFU-5. The USTC forms unique piRNA foci in germline nuclei and coats the piRNA cluster genomic loci. USTC factors associate with the Ruby motif just upstream of type I piRNA genes. USTC factors are also mutually dependent for binding to the piRNA clusters and forming the piRNA foci. Interestingly, USTC components bind differentially to piRNAs in the clusters and other noncoding RNA genes. These results reveal the USTC as a striking example of the repurposing of a general transcription factor complex to aid in genome defense against transposons.
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Affiliation(s)
- Chenchun Weng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Joanna Kosalka
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Ahmet C Berkyurek
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Przemyslaw Stempor
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Hui Mao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chenming Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wen-Jun Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Natalia Rosalía Morero
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Julie Ahringer
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Eric A Miska
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
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44
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Kim KW, Tang NH, Piggott CA, Andrusiak MG, Park S, Zhu M, Kurup N, Cherra SJ, Wu Z, Chisholm AD, Jin Y. Expanded genetic screening in Caenorhabditis elegans identifies new regulators and an inhibitory role for NAD + in axon regeneration. eLife 2018; 7:39756. [PMID: 30461420 PMCID: PMC6281318 DOI: 10.7554/elife.39756] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
The mechanisms underlying axon regeneration in mature neurons are relevant to the understanding of normal nervous system maintenance and for developing therapeutic strategies for injury. Here, we report novel pathways in axon regeneration, identified by extending our previous function-based screen using the C. elegans mechanosensory neuron axotomy model. We identify an unexpected role of the nicotinamide adenine dinucleotide (NAD+) synthesizing enzyme, NMAT-2/NMNAT, in axon regeneration. NMAT-2 inhibits axon regrowth via cell-autonomous and non-autonomous mechanisms. NMAT-2 enzymatic activity is required to repress regrowth. Further, we find differential requirements for proteins in membrane contact site, components and regulators of the extracellular matrix, membrane trafficking, microtubule and actin cytoskeleton, the conserved Kelch-domain protein IVNS-1, and the orphan transporter MFSD-6 in axon regrowth. Identification of these new pathways expands our understanding of the molecular basis of axonal injury response and regeneration.
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Affiliation(s)
- Kyung Won Kim
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Ngang Heok Tang
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Christopher A Piggott
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Matthew G Andrusiak
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Seungmee Park
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Ming Zhu
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Naina Kurup
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Salvatore J Cherra
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Zilu Wu
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Andrew D Chisholm
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, United States
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45
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Rojas-Ríos P, Simonelig M. piRNAs and PIWI proteins: regulators of gene expression in development and stem cells. Development 2018; 145:145/17/dev161786. [PMID: 30194260 DOI: 10.1242/dev.161786] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PIWI proteins and Piwi-interacting RNAs (piRNAs) have established and conserved roles in repressing transposable elements (TEs) in the germline of animals. However, in several biological contexts, a large proportion of piRNAs are not related to TE sequences and, accordingly, functions for piRNAs and PIWI proteins that are independent of TE regulation have been identified. This aspect of piRNA biology is expanding rapidly. Indeed, recent reports have revealed the role of piRNAs in the regulation of endogenous gene expression programs in germ cells, as well as in somatic tissues, challenging dogma in the piRNA field. In this Review, we focus on recent data addressing the biological and developmental functions of piRNAs, highlighting their roles in embryonic patterning, germ cell specification, stem cell biology, neuronal activity and metabolism.
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Affiliation(s)
- Patricia Rojas-Ríos
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
| | - Martine Simonelig
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
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46
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Abstract
piRNAs are known to silence transposable elements, but not all piRNAs match transposon sequences. Recent studies from Shen et al. (2018) and Zhang et al. (2018) identify rules for piRNA target recognition in Caenorhabditis elegans. Permissive pairing rules allow targeting of essentially all germline mRNAs, while protective mechanisms prevent silencing self-genes.
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Affiliation(s)
- Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
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