1
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Guo C, Wang X, Ren H. Databases and computational methods for the identification of piRNA-related molecules: A survey. Comput Struct Biotechnol J 2024; 23:813-833. [PMID: 38328006 PMCID: PMC10847878 DOI: 10.1016/j.csbj.2024.01.011] [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: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.
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Affiliation(s)
- Chang Guo
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Han Ren
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
- Laboratory of Language and Artificial Intelligence, Guangdong University of Foreign Studies, Guangzhou 510420, China
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2
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Li B, Wang K, Cheng W, Fang B, Li YH, Yang SM, Zhang MH, Wang YH, Wang K. Recent advances of PIWI-interacting RNA in cardiovascular diseases. Clin Transl Med 2024; 14:e1770. [PMID: 39083321 PMCID: PMC11290350 DOI: 10.1002/ctm2.1770] [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: 02/04/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The relationship between noncoding RNAs (ncRNAs) and human diseases has been a hot topic of research, but the study of ncRNAs in cardiovascular diseases (CVDs) is still in its infancy. PIWI-interacting RNA (piRNA), a small ncRNA that binds to the PIWI protein to maintain genome stability by silencing transposons, was widely studied in germ lines and stem cells. In recent years, piRNA has been shown to be involved in key events of multiple CVDs through various epigenetic modifications, revealing the potential value of piRNA as a new biomarker or therapeutic target. CONCLUSION This review explores origin, degradation, function, mechanism and important role of piRNA in CVDs, and the promising therapeutic targets of piRNA were summarized. This review provide a new strategy for the treatment of CVDs and lay a theoretical foundation for future research. KEY POINTS piRNA can be used as a potential therapeutic target and biomaker in CVDs. piRNA influences apoptosis, inflammation and angiogenesis by regulating epigenetic modificaions. Critical knowledge gaps remain in the unifying piRNA nomenclature and PIWI-independent function.
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Affiliation(s)
- Bo Li
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Kai Wang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Wei Cheng
- Department of Cardiovascular SurgeryBeijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Bo Fang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Ying Hui Li
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Su Min Yang
- Department of Cardiovascular SurgeryThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Mei Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
| | - Yun Hong Wang
- Hypertension CenterBeijing Anzhen HospitalCapital Medical UniversityBeijingChina
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
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3
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Karpagavalli M, Sivagurunathan S, Panda TS, Srikakulam N, Arora R, Dohadwala L, Tiwary BK, Sadras SR, Arunachalam JP, Pandi G, Chidambaram S. piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress. Mol Omics 2024; 20:248-264. [PMID: 38314503 DOI: 10.1039/d3mo00122a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Long considered active only in the germline, the PIWI/piRNA pathway is now known to play a significant role in somatic cells, especially neurons. In this study, piRNAs were profiled in the human retina and retinal pigment epithelium (RPE). Furthermore, RNA immunoprecipitation with HIWI2 (PIWIL4) in ARPE19 cells yielded 261 piRNAs, and the expression of selective piRNAs in donor eyes was assessed by qRT-PCR. Intriguingly, computational analysis revealed complete and partial seed sequence similarity between piR-hsa-26131 and the sensory organ specific miR-183/96/182 cluster. Furthermore, the expression of retina-enriched piR-hsa-26131 was positively correlated with miR-182 in HIWI2-silenced Y79 cells. In addition, the lnc-ZNF169 sequence matched with two miRNAs of the let-7 family, and piRNAs, piR-hsa-11361 and piR-hsa-11360, which could modulate the regulatory network of retinal differentiation. Interestingly, we annotated four enriched motifs among the piRNAs and found that the piRNAs containing CACAATG and CTCATCAKYG motifs were snoRNA-derived piRNAs, which are significantly associated with developmental functions. However, piRNAs consisting of ACCACTANACCAC and AKCACGYTCSC motifs were mainly tRNA-derived fragments linked to stress response and sensory perception. Additionally, co-expression network analysis revealed cell cycle control, intracellular transport and stress response as the important biological functions regulated by piRNAs in the retina. Moreover, loss of piRNAs in HIWI2 knockdown ARPE19 confirmed altered expression of targets implicated in intracellular transport, circadian clock, and retinal degeneration. Moreover, piRNAs were dysregulated under oxidative stress conditions, indicating their potential role in retinal pathology. Therefore, we postulate that piRNAs, miRNAs, and lncRNAs might have a functional interplay during retinal development and functions to regulate retinal homeostasis.
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Affiliation(s)
| | - Suganya Sivagurunathan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India
| | - T Sayamsmruti Panda
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Reety Arora
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | | | - Basant K Tiwary
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
| | - Jayamuruga Pandian Arunachalam
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry-607402, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Subbulakshmi Chidambaram
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
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4
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Corell-Sierra J, Marquez-Molins J, Marqués MC, Hernandez-Azurdia AG, Montagud-Martínez R, Cebriá-Mendoza M, Cuevas JM, Albert E, Navarro D, Rodrigo G, Gómez G. SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity. NPJ Syst Biol Appl 2024; 10:41. [PMID: 38632240 PMCID: PMC11024147 DOI: 10.1038/s41540-024-00367-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.
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Affiliation(s)
- Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - María-Carmen Marqués
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | | | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010, Valencia, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Gustavo Gómez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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5
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Tang L, Swedlund B, Dupont S, Harland C, Costa Monteiro Moreira G, Durkin K, Artesi M, Mullaart E, Sartelet A, Karim L, Coppieters W, Georges M, Charlier C. GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle. Nat Commun 2024; 15:2154. [PMID: 38461177 PMCID: PMC10924933 DOI: 10.1038/s41467-024-46434-1] [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: 06/29/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024] Open
Abstract
Five to ten percent of mammalian genomes is occupied by multiple clades of endogenous retroviruses (ERVs), that may count thousands of members. New ERV clades arise by retroviral infection of the germline followed by expansion by reinfection and/or retrotransposition. ERV mobilization is a source of deleterious variation, driving the emergence of ERV silencing mechanisms, leaving "DNA fossils". Here we show that the ERVK[2-1-LTR] clade is still active in the bovine and a source of disease-causing alleles. We develop a method to measure the rate of ERVK[2-1-LTR] mobilization, finding an average of 1 per ~150 sperm cells, with >10-fold difference between animals. We perform a genome-wide association study and identify eight loci affecting ERVK[2-1-LTR] mobilization. We provide evidence that polymorphic ERVK[2-1-LTR] elements in four of these loci cause the association. We generate a catalogue of full length ERVK[2-1-LTR] elements, and show that it comprises 15% of C-type autonomous elements, and 85% of D-type non-autonomous elements lacking functional genes. We show that >25% of the variance of mobilization rate is determined by the number of C-type elements, yet that de novo insertions are dominated by D-type elements. We propose that D-type elements act as parasite-of-parasite gene drives that may contribute to the observed demise of ERV elements.
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Affiliation(s)
- Lijing Tang
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Benjamin Swedlund
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sébastien Dupont
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Chad Harland
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Livestock Improvement Corporation, Hamilton, New Zealand
| | | | - Keith Durkin
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory of Human Genetics, GIGA & Faculty of Medicine, University of Liège, Liège, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory of Human Genetics, GIGA & Faculty of Medicine, University of Liège, Liège, Belgium
| | | | - Arnaud Sartelet
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Comparative Veterinary Medicine, FARAH & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Genomics core facility, GIGA, University of Liège, Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Genomics core facility, GIGA, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Carole Charlier
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
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6
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Jehn J, Trudzinski F, Horos R, Schenz J, Uhle F, Weigand MA, Frank M, Kahraman M, Heuvelman M, Sikosek T, Rajakumar T, Gerwing J, Skottke J, Daniel-Moreno A, Rudolf C, Hinkfoth F, Tikk K, Christopoulos P, Klotz LV, Winter H, Kreuter M, Steinkraus BR. miR-Blood - a small RNA atlas of human blood components. Sci Data 2024; 11:164. [PMID: 38307869 PMCID: PMC10837159 DOI: 10.1038/s41597-024-02976-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
miR-Blood is a high-quality, small RNA expression atlas for the major components of human peripheral blood (plasma, erythrocytes, thrombocytes, monocytes, neutrophils, eosinophils, basophils, natural killer cells, CD4+ T cells, CD8+ T cells, and B cells). Based on the purified blood components from 52 individuals, the dataset provides a comprehensive repository for the expression of 4971 small RNAs from eight non-coding RNA classes.
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Affiliation(s)
- Julia Jehn
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Franziska Trudzinski
- Center for Interstitial and Rare Lung Diseases, Thoraxklinik, University of Heidelberg, and German Center for Lung Research (DZL), Heidelberg, Germany
| | - Rastislav Horos
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Judith Schenz
- Department of Anesthesiology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Florian Uhle
- Department of Anesthesiology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Maurice Frank
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Mustafa Kahraman
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Marco Heuvelman
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Tobias Sikosek
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Timothy Rajakumar
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Jennifer Gerwing
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Jasmin Skottke
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | | | - Christina Rudolf
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Franziska Hinkfoth
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Kaja Tikk
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center Heidelberg (TLRC-H), and German Center for Lung Research (DZL), Heidelberg, Germany
| | - Laura V Klotz
- Department of Thoracic Surgery, Thoraxklinik, University of Heidelberg, Translational Lung Research Center Heidelberg (TLRC-H), and German Center for Lung Research (DZL), Heidelberg, Germany
| | - Hauke Winter
- Department of Thoracic Surgery, Thoraxklinik, University of Heidelberg, Translational Lung Research Center Heidelberg (TLRC-H), and German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michael Kreuter
- Center for Interstitial and Rare Lung Diseases, Thoraxklinik, University of Heidelberg, and German Center for Lung Research (DZL), Heidelberg, Germany
| | - Bruno R Steinkraus
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany.
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7
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Aharon-Yariv A, Wang Y, Ahmed A, Delgado-Olguín P. Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart. BMC Genomics 2023; 24:709. [PMID: 37996818 PMCID: PMC10668469 DOI: 10.1186/s12864-023-09801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases in a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome-wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. RESULTS Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis demonstrated that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progressed. Moreover, we found that downregulated targets of upregulated miRNAs, including hsa-let-7b, miR-1-3p, miR-133a-3p, miR-143-3p, miR-499a-5p, and miR-30a-5p predominantly control cell cycle progression. In contrast, upregulated targets of downregulated miRNAs, including hsa-miR-1276, miR-183-5p, miR-1229-3p, miR-615-3p, miR-421, miR-200b-3p and miR-18a-3p, are linked to energy sensing and oxidative metabolism. Furthermore, integrating miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets and their associated metabolites mediate fatty acid oxidation and are enriched as the heart develops. CONCLUSIONS This study presents the first comprehensive analysis of the small RNAome of the maturing human fetal heart. Our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart. Our results provide novel insights into the molecular control of metabolic maturation of the human fetal heart.
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Affiliation(s)
- Adar Aharon-Yariv
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yaxu Wang
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Abdalla Ahmed
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul Delgado-Olguín
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada.
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Heart & Stroke, Richard Lewar Centre of Excellence, Toronto, Ontario, Canada.
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8
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Gupta P, Das G, Chattopadhyay T, Ghosh Z, Mallick B. TarpiD, a database of putative and validated targets of piRNAs. Mol Omics 2023; 19:706-713. [PMID: 37427797 DOI: 10.1039/d3mo00098b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a novel class of 18-36 nts long small non-coding single-stranded RNAs that play crucial roles in a wide array of critical biological activities besides maintaining genome integrity by transposon silencing. piRNAs influence biological processes and pathways by regulating gene expression at transcriptional and post-transcriptional level. Studies have reported that piRNAs silence various endogenous genes post-transcriptionally by binding to respective mRNAs through interaction with the PIWI proteins. Several thousands of piRNAs have been discovered in animals, but their functions remain largely undiscovered owing to a lack of proper guiding principles of piRNA targeting or diversity in targeting patterns amongst piRNAs from the same or different species. Identification of piRNA targets is essential for deciphering their functions. There are a few tools and databases on piRNAs, but there are no systematic and exclusive repositories to obtain information on target genes regulated by piRNAs and other related information. Hence, we developed a user-friendly database named TarpiD (Targets of piRNA Database) that offers comprehensive information on piRNA and its targets, including their expression, methodologies (high-throughput or low-throughput) for target identification/validation, cells/tissue types, diseases, target gene regulation types, target binding regions, and key functions driven by piRNAs through target gene interactions. The contents of TarpiD are curated from the published literature and enable users to search and download the targets of a particular piRNA or the piRNAs that target a specific gene for use in their research. This database harbours 28 682 entries of piRNA-target interactions supported by 15 methodologies reported in hundreds of cell types/tissues from 9 species. TarpiD will be a valuable resource for a better understanding of the functions and gene-regulatory mechanisms mediated by piRNAs. TarpiD is freely accessible for academic use at https://tarpid.nitrkl.ac.in/tarpid_db/.
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Affiliation(s)
- Pooja Gupta
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela-769008, Odisha, India.
| | - Gourab Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela-769008, Odisha, India.
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela-769008, Odisha, India.
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9
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Reshi QUA, Godakumara K, Ord J, Dissanayake K, Hasan MM, Andronowska A, Heath P, Fazeli A. Spermatozoa, acts as an external cue and alters the cargo and production of the extracellular vesicles derived from oviductal epithelial cells in vitro. J Cell Commun Signal 2023; 17:737-755. [PMID: 36469292 PMCID: PMC10409707 DOI: 10.1007/s12079-022-00715-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/23/2022] [Indexed: 12/09/2022] Open
Abstract
The oviduct provides optimum physiological and biochemical milieu essential for successful fertilization, early embryo development and facilitates functional maturation of spermatozoa. A study has revealed that spermatozoa alters the gene expression in bovine oviductal epithelial cells (BOECs) remotely via bio-active particles, thus acting as a cue to the oviduct prior to their arrival. However, very little attention has been paid to the question of whether spermatozoa could alter the cargo of extracellular vesicles (EVs) derived from BOECs. Therefore, the aim of this study was to investigate the alterations in small non-coding RNAs in EVs cargo derived from BOECs when incubated with spermatozoa in contact and non-contact co-culture models. After 4 h of incubation the EVs were isolated from the conditioned media, followed by small non-coding sequencing of the BOEC derived EVs. Our results revealed that EVs from both co-culture models contained distinct cargo in form of miRNA, fragmented mRNA versus control. The pathway enrichment analysis revealed that EV miRNA from direct co-culture were involved in the biological processes associated with phagocytosis, macroautophagy, placenta development, cellular responses to TNF and FGF. The mRNA fragments also varied within the different groups and mapped to the exonic regions of the transcriptome providing vital insights regarding the changes in cellular transcriptome on the arrival of spermatozoa. The findings of this study suggest that spermatozoa, in contact as well as remotely, alter the EV cargo of female reproductive tract epithelial cells which might be playing an essential role in pre and post-fertilization events.
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Affiliation(s)
- Qurat Ul Ain Reshi
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, 50411, Tartu, Estonia
| | - Kasun Godakumara
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, 50411, Tartu, Estonia
| | - James Ord
- Institute for Fish and Wildlife Health, University of Bern, Längassstrasse 122, 3012, Bern, Switzerland
| | - Keerthie Dissanayake
- Department of Anatomy, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Mohammad Mehedi Hasan
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, 50411, Tartu, Estonia
- Institute for Women's Health, Maternal and Fetal Medicine Department, University College London, 86-96 Chenies Mews, London, WC1N 1EH, UK
| | - Aneta Andronowska
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima St. 10, 10-748, Olsztyn, Poland
| | - Paul Heath
- Sheffield Institute for Translational Neuroscience SITraN, University of Sheffield, 385a Glossop Rd, Sheffield, S10 2HQ, UK
| | - Alireza Fazeli
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006, Tartu, Estonia.
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, 50411, Tartu, Estonia.
- Academic Unit of Reproductive and Developmental Medicine, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, S10 2SF, UK.
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10
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Wyse BA, Salehi R, Russell SJ, Sangaralingam M, Jahangiri S, Tsang BK, Librach CL. Obesity and PCOS radically alters the snRNA composition of follicular fluid extracellular vesicles. Front Endocrinol (Lausanne) 2023; 14:1205385. [PMID: 37404312 PMCID: PMC10315679 DOI: 10.3389/fendo.2023.1205385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/29/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction The ovarian follicle consists of the oocyte, somatic cells, and follicular fluid (FF). Proper signalling between these compartments is required for optimal folliculogenesis. The association between polycystic ovarian syndrome (PCOS) and extracellular vesicular small non-coding RNAs (snRNAs) signatures in follicular fluid (FF) and how this relates to adiposity is unknown. The purpose of this study was to determine whether FF extracellular vesicle (FFEV)-derived snRNAs are differentially expressed (DE) between PCOS and non-PCOS subjects; and if these differences are vesicle-specific and/or adiposity-dependent. Methods FF and granulosa cells (GC) were collected from 35 patients matched by demographic and stimulation parameters. FFEVs were isolated and snRNA libraries were constructed, sequenced, and analyzed. Results miRNAs were the most abundant biotype present, with specific enrichment in exosomes (EX), whereas in GCs long non-coding RNAs were the most abundant biotype. In obese PCOS vs. lean PCOS, pathway analysis revealed target genes involved in cell survival and apoptosis, leukocyte differentiation and migration, JAK/STAT, and MAPK signalling. In obese PCOS FFEVs were selectively enriched (FFEVs vs. GCs) for miRNAs targeting p53 signalling, cell survival and apoptosis, FOXO, Hippo, TNF, and MAPK signalling. Discussion We provide comprehensive profiling of snRNAs in FFEVs and GCs of PCOS and non-PCOS patients, highlighting the effect of adiposity on these findings. We hypothesize that the selective packaging and release of miRNAs specifically targeting anti-apoptotic genes into the FF may be an attempt by the follicle to reduce the apoptotic pressure of the GCs and stave off premature apoptosis of the follicle observed in PCOS.
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Affiliation(s)
- Brandon A. Wyse
- Research Department, CReATe Fertility Centre, Toronto, ON, Canada
| | - Reza Salehi
- Research Department, CReATe Fertility Centre, Toronto, ON, Canada
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Departments of Obstetrics and Gynecology & Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | | | - Sahar Jahangiri
- Research Department, CReATe Fertility Centre, Toronto, ON, Canada
- CReATe Biobank, Toronto, ON, Canada
| | - Benjamin K. Tsang
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Departments of Obstetrics and Gynecology & Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Clifford L. Librach
- Research Department, CReATe Fertility Centre, Toronto, ON, Canada
- CReATe Biobank, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Biological Sciences, DAN Women & Babies Research Program, Sunnybrook Research Institute, Toronto, ON, Canada
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11
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Yao Y, Li Y, Zhu X, Zhao C, Yang L, Huang X, Wang L. The emerging role of the piRNA/PIWI complex in respiratory tract diseases. Respir Res 2023; 24:76. [PMID: 36915129 PMCID: PMC10010017 DOI: 10.1186/s12931-023-02367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
PIWI-interacting RNA (piRNA) is a class of recently discovered small non-coding RNA molecules with a length of 18-33 nt that interacts with the PIWI protein to form the piRNA/PIWI complex. The PIWI family is a subfamily of Argonaute (AGO) proteins that also contain the AGO family which bind to microRNA (miRNA). Recently studies indicate that piRNAs are not specific to in the mammalian germline, they are also expressed in a tissue-specific manner in a variety of human tissues and participated in various of diseases, such as cardiovascular, neurological, and urinary tract diseases, and are especially prevalent in malignant tumors in these systems. However, the functions and abnormal expression of piRNAs in respiratory tract diseases and their underlying mechanisms remain incompletely understood. In this review, we discuss current studies summarizing the biogenetic processes, functions, and emerging roles of piRNAs in respiratory tract diseases, providing a reference value for future piRNA research.
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Affiliation(s)
- Yizhu Yao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yaozhe Li
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Xiayan Zhu
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Chengguang Zhao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.,School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lehe Yang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Xiaoying Huang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Liangxing Wang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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12
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Zhu Q, Jiang F, Song Y, Lu L, He F, Huang S, Huang Z, Yao J, Lei N, Huang J, Lu S. Small noncoding RNA dysregulation is implicated in manganism in a rat model of methylcyclopentadienyl manganese tricarbonyl-induced unrepaired striatum damage. J Toxicol Sci 2023; 48:535-546. [PMID: 37778982 DOI: 10.2131/jts.48.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The accumulation of excessively high manganese levels within the brain can contribute to a series of Parkinsonian symptoms referred to as manganism. The gasoline antiknock additive Methylcyclopentadienyl Manganese Tricarbonyl (MMT) is an environmental source of manganese exposure and can induce manganism in rats. While some prior reports have demonstrated the differential expression of small noncoding RNAs (sncRNAs) in patients with Parkinson's disease (PD), the degree of sncRNA dysfunction in manganism has yet to be clearly documented. As sncRNAs such as transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) exhibit high levels of modifications such as 3' terminal 3'-phosphate and 2',3'-cyclic phosphate modifications that disrupt the process of adapter ligation and m1A, m3C, m1G, and m22G RNA methylation, these transcripts are not detected in traditional small RNA-sequencing studies. Here, differential sncRNA expression was analyzed by comparing a rat model of MMT-induced unrepaired striatum damage to appropriate control samples via PANDORA-Seq, which can detect highly modified sncRNAs. Following the removal of sncRNA modifications, this approach identified 599 sncRNAs that were differentially expressed in the striatum of MMT-exposed rats relative to controls, as well as 1155 sncRNAs that were differentially expressed in Mn-treated and control rats. Additional functional analyses were performed to predict the putative targets of these sncRNAs, implicating a role for such sncRNA dysregulation in the pathogenesis of manganism in this rat model system.
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Affiliation(s)
- Qifeng Zhu
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Fan Jiang
- Department of Rehabilitation medicine, the First Institute of Clinical Medicine Guangxi Medical University, China
| | - Yuanbo Song
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Lili Lu
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Fajian He
- RnD Department, Wilking Biotechnology Co., Ltd, China
| | - Shuqi Huang
- RnD Department, Wilking Biotechnology Co., Ltd, China
| | - Zhaoying Huang
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Jing Yao
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Ningning Lei
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Jianmin Huang
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Shijin Lu
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
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13
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Di R, Zhang R, Mwacharo JM, Wang X, He X, Liu Y, Zhang J, Gong Y, Zhang X, Chu M. Characteristics of piRNAs and their comparative profiling in testes of sheep with different fertility. Front Genet 2022; 13:1078049. [PMID: 36568364 PMCID: PMC9768229 DOI: 10.3389/fgene.2022.1078049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
As a novel class of small RNAs, piRNAs are highly expressed in the animal gonads and their main known role is to inhibit transposon activity for ensuring the correctness and integrity of genome. In order to explore the characteristics of piRNAs in sheep testis and their possible regulatory roles on male reproduction, deep sequencing technology was used to sequence small RNAs and identify piRNAs in testes of sheep. The length of piRNAs in sheep testes showed a unimodal distribution between 26 and 31 nt, with a peak at 29 nt. These piRNAs exhibited obvious ping-pong signature and strand specificity. In the genome, they were mainly aligned to CDS, intron, repetitive sequence regions and unannotated regions. Furthermore, in transposon analysis, piRNAs were aligned predominantly to LINE, SINE, and LTR types of retrotransposon in sheep testes, and the piRNAs derived from each type showed obvious ping-pong signature. The piRNA clusters identified in sheep testes were mainly distributed on chromosomes 3, 7, 15, 17, 18 and 20. The results combining semen determination with pathway enrichment analysis implied that differentially expressed piRNAs between the testes of rams with different fertility might participate in spermatogenesis by regulating multiple pathways closely related to stabilization of blood-testis barrier and renewal and differentiation of spermatogonial stem cell. Taken together, the study provided new insights into the characteristics, origin and expression patterns of piRNAs in sheep testes tissue, which would help us better understand the role of piRNAs in sheep reproduction.
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Affiliation(s)
- Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,School of Advanced Agricultural Sciences, Yiyang Vocational & Technical College, Yiyang, China
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia,Institute of Animal and Veterinary Sciences, SRUC and Center for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yiming Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China,*Correspondence: Xiaosheng Zhang, ; Mingxing Chu,
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xiaosheng Zhang, ; Mingxing Chu,
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14
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PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences. Curr Environ Health Rep 2022; 9:650-660. [PMID: 35917009 DOI: 10.1007/s40572-022-00372-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW: The epigenome modulates gene expression in response to environmental stimuli. Modifications to the epigenome are potentially reversible, making them a promising therapeutic approach to mitigate environmental exposure effects on human health. This review details currently available genome and epigenome editing technologies and highlights ncRNA, including piRNA, as potential tools for targeted epigenome editing. RECENT FINDINGS: Zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) associated nuclease (CRISPR/Cas) research has significantly advanced genome editing technology, with broad promise in genetic research and targeted therapies. Initial epigenome-directed therapies relied on global modification and suffered from limited specificity. Adapted from current genome editing tools, zinc finger protein (ZFP), TALE, and CRISPR/nuclease-deactivated Cas (dCas) systems now confer locus-specific epigenome editing, with promising applicability in the field of environmental health sciences. However, high incidence of off-target effects and time taken for screening limit their use. FUTURE DEVELOPMENT: ncRNA serve as a versatile biomarker with well-characterized regulatory mechanisms that can easily be adapted to edit the epigenome. For instance, the transposon silencing mechanism of germline PIWI-interacting RNAs (piRNA) could be engineered to specifically methylate a given gene, overcoming pitfalls of current global modifiers. Future developments in epigenome editing technologies will inform risk assessment through mechanistic investigation and serve as potential modes of intervention to mitigate environmentally induced adverse health outcomes later in life.
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15
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Hamilton M, Russell S, Menezes K, Moskovtsev SI, Librach C. Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males. Sci Rep 2022; 12:20010. [PMID: 36411317 PMCID: PMC9678953 DOI: 10.1038/s41598-022-24568-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Clinical testing strategies for diagnosing male factor infertility are limited. A deeper analysis of spermatozoa-derived factors could potentially diagnose some cases of 'unexplained infertility'. Spermatozoa carry a rich and dynamic profile of small RNAs, which have demonstrated potential developmental importance and association with fertility status. We used next-generation sequencing to correlate sperm small RNA profiles of normozoospermic males (n = 54) with differing blastocyst development rates, when using young donor oocytes. While ribosomal RNAs accounted for the highest number of sequencing reads, transfer RNA fragments of tRNAGly/GCC and tRNAVal-CAC were the most abundant sequences across all sperm samples. A total of 324 small RNAs were differentially expressed between samples with high (n = 18) and low (n = 14) blastocyst rates (p-adj < 0.05). Ninety three miRNAs were differentially expressed between these groups (p-adj < 0.05). Differentially expressed transfer RNA fragments included: 5'-tRF-Asp-GTC; 5'-tRF-Phe-GAA; and 3'-tRF-Ser-GCA. Differentially expressed miRNAs included: let-7f-2-5p; miR-4755-3p; and miR-92a-3p. This study provides the foundation on which to validate a clinical panel of fertility-related sperm small RNAs, as well as to pursue potential mechanisms through which they alter blastocyst development.
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Affiliation(s)
| | | | - Karen Menezes
- grid.490031.fCReATe Fertility Centre, Toronto, ON Canada
| | - Sergey I. Moskovtsev
- grid.490031.fCReATe Fertility Centre, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Clifford Librach
- grid.490031.fCReATe Fertility Centre, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Physiology and Institute of Medical Sciences, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada
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16
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Li C, Zhang R, Zhang Z, Ren C, Wang X, He X, Mwacharo JM, Zhang X, Zhang J, Di R, Chu M. Expression characteristics of piRNAs in ovine luteal phase and follicular phase ovaries. Front Vet Sci 2022; 9:921868. [PMID: 36157184 PMCID: PMC9493120 DOI: 10.3389/fvets.2022.921868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs), as a novel class of small non-coding RNAs that have been shown to be indispensable in germline integrity and stem cell development. However, the expressed characteristics and regulatory roles of piRNAs during different reproductive phases of animals remain unknown. In this study, we investigated the piRNAs expression profiles in ovaries of sheep during the luteal phase (LP) and follicular phase (FP) using the Solexa sequencing technique. A total of 85,219 and 1,27,156 piRNAs tags were identified in ovine ovaries across the two phases. Most expressed piRNAs start with uracil. piRNAs with a length of 24 nt or 27–29 nts accounted for the largest proportion. The obvious ping-pong signature appeared in the FP ovary. The piRNA clusters in the sheep ovary were unevenly distributed on the chromosomes, with high density on Chr 3 and 1. For genome distribution, piRNAs in sheep ovary were mainly derived from intron, CDS, and repeat sequence regions. Compared to the LP ovary, a greater number of expressed piRNA clusters were detected in the FP ovary. Simultaneously, we identified 271 differentially expressed (DE) piRNAs between LP and FP ovaries, with 96 piRNAs upregulated and 175 piRNAs downregulated, respectively. Functional enrichment analysis (GO and KEGG) indicated that their target genes were enriched in reproduction-related pathways including oocyte meiosis, PI3K-Akt, Wnt, and TGF-β signaling pathways. Together, our results highlighted the sequence and expression characteristics of the piRNAs in the sheep ovary, which will help us understand the roles of piRNAs in the ovine estrus cycle.
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Affiliation(s)
- Chunyan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
- Institute of Animal and Veterinary Sciences, Animal and Veterinary Sciences, SRUC and Center for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | | | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Ran Di
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Mingxing Chu
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17
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Zhang W, Hou J, Liu B. iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank. PLoS Comput Biol 2022; 18:e1010404. [PMID: 35969645 PMCID: PMC9410559 DOI: 10.1371/journal.pcbi.1010404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/25/2022] [Accepted: 07/18/2022] [Indexed: 12/01/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are regarded as drug targets and biomarkers for the diagnosis and therapy of diseases. However, biological experiments cost substantial time and resources, and the existing computational methods only focus on identifying missing associations between known piRNAs and diseases. With the fast development of biological experiments, more and more piRNAs are detected. Therefore, the identification of piRNA-disease associations of newly detected piRNAs has significant theoretical value and practical significance on pathogenesis of diseases. In this study, the iPiDA-LTR predictor is proposed to identify associations between piRNAs and diseases based on Learning to Rank. The iPiDA-LTR predictor not only identifies the missing associations between known piRNAs and diseases, but also detects diseases associated with newly detected piRNAs. Experimental results demonstrate that iPiDA-LTR effectively predicts piRNA-disease associations outperforming the other related methods.
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Affiliation(s)
- Wenxiang Zhang
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Jialu Hou
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
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18
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Werry N, Russell SJ, Gillis DJ, Miller S, Hickey K, Larmer S, Lohuis M, Librach C, LaMarre J. Characteristics of miRNAs Present in Bovine Sperm and Associations With Differences in Fertility. Front Endocrinol (Lausanne) 2022; 13:874371. [PMID: 35663333 PMCID: PMC9160602 DOI: 10.3389/fendo.2022.874371] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/14/2022] [Indexed: 12/23/2022] Open
Abstract
Small non-coding RNAs have been linked to different phenotypes in bovine sperm, however attempts to identify sperm-borne molecular biomarkers of male fertility have thus far failed to identify a robust profile of expressed miRNAs related to fertility. We hypothesized that some differences in bull fertility may be reflected in the levels of different miRNAs in sperm. To explore such differences in fertility that are not due to differences in visible metrics of sperm quality, we employed Next Generation Sequencing to compare the miRNA populations in Bos taurus sperm from bulls with comparable motility and morphology but varying Sire Conception Rates. We identified the most abundant miRNAs in both populations (miRs -34b-3p; -100-5p; -191-5p; -30d-4p; -21-5p) and evaluated differences in the overall levels and specific patterns of isomiR expression. We also explored correlations between specific pairs of miRNAs in each population and identified 10 distinct pairs of miRNAs that were positively correlated in bulls with higher fertility and negatively correlated in comparatively less fertile individuals. Furthermore, 8 additional miRNA pairs demonstrated the opposite trend; negatively correlated in high fertility animals and positively correlated in less fertile bulls. Finally, we performed pathway analysis to identify potential roles of miRNAs present in bull sperm in the regulation of specific genes that impact spermatogenesis and embryo development. Together, these results present a comprehensive picture of the bovine sperm miRNAome that suggests multiple potential roles in fertility.
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Affiliation(s)
- Nicholas Werry
- Department of Biomedical Sciences, The University of Guelph, Guelph, ON, Canada
| | | | - Daniel J. Gillis
- School of Computer Science, The University of Guelph, Guelph, ON, Canada
| | | | | | | | | | - Clifford Librach
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, The University of Guelph, Guelph, ON, Canada
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19
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Crisóstomo L, Bourgery M, Rato L, Raposo JF, Batterham RL, Kotaja N, Alves MG. Testicular "Inherited Metabolic Memory" of Ancestral High-Fat Diet Is Associated with Sperm sncRNA Content. Biomedicines 2022; 10:909. [PMID: 35453658 PMCID: PMC9027117 DOI: 10.3390/biomedicines10040909] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023] Open
Abstract
Excessive adiposity caused by high-fat diets (HFDs) is associated with testicular metabolic and functional abnormalities up to grand-offspring, but the mechanisms of this epigenetic inheritance are unclear. Here we describe an association of sperm small non-coding RNA (sncRNA) with testicular "inherited metabolic memory" of ancestral HFD, using a transgenerational rodent model. Male founders were fed a standard chow for 200 days (CTRL), HFD for 200 days (HFD), or standard chow for 60 days followed by HFD for 140 days (HFDt). The male offspring and grand-offspring were fed standard chow for 200 days. The sncRNA sequencing from epidydimal spermatozoa revealed signatures associated with testicular metabolic plasticity in HFD-exposed mice and in the unexposed progeny. Sperm tRNA-derived RNA (tsRNA) and repeat-derived small RNA (repRNA) content were specially affected by HFDt and in the offspring of HFD and HFDt mice. The grand-offspring of HFD and HFDt mice showed lower sperm counts than CTRL descendants, whereas the sperm miRNA content was affected. Although the causality between sperm sncRNAs content and transgenerational epigenetic inheritance of HFD-related traits remains elusive, our results suggest that sperm sncRNA content is influenced by ancestral exposure to HFD, contributing to the sperm epigenome up to the grand-offspring.
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Affiliation(s)
- Luís Crisóstomo
- Departamento de Anatomia, e UMIB—Unidade Multidisciplinar de Investigação em Biomedicina, ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal;
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, 4050-600 Porto, Portugal
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (M.B.); (N.K.)
| | - Matthieu Bourgery
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (M.B.); (N.K.)
| | - Luís Rato
- Polytechnic Institute of Guarda, School of Health, 6300-035 Guarda, Portugal;
- Faculty of Health Sciences, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - João F. Raposo
- NOVA Medical School, New University Lisbon, 1250-189 Lisbon, Portugal;
- Associação Protetora dos Diabéticos de Portugal (APDP), 1250-189 Lisbon, Portugal
| | - Rachel L. Batterham
- Centre for Obesity Research, Department of Medicine, University College London (UCL), London WC1E 6JF, UK;
- National Institute for Health Research, Biomedical Research Centre, University College London Hospital (UCLH), London W1T 7DN, UK
| | - Noora Kotaja
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (M.B.); (N.K.)
| | - Marco G. Alves
- Departamento de Anatomia, e UMIB—Unidade Multidisciplinar de Investigação em Biomedicina, ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal;
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, 4050-600 Porto, Portugal
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, 17003 Girona, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, 17003 Girona, Spain
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20
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Ali SD, Tayara H, Chong KT. Identification of piRNA disease associations using deep learning. Comput Struct Biotechnol J 2022; 20:1208-1217. [PMID: 35317234 PMCID: PMC8908038 DOI: 10.1016/j.csbj.2022.02.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/09/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a pivotal role in maintaining genome integrity by repression of transposable elements, gene stability, and association with various disease progressions. Cost-efficient computational methods for the identification of piRNA disease associations promote the efficacy of disease-specific drug development. In this regard, we developed a simple, robust, and efficient deep learning method for identifying the piRNA disease associations known as piRDA. The proposed architecture extracts the most significant and abstract information from raw sequences represented in a simplicated piRNA disease pair without any involvement of features engineering. Two-step positive unlabeled learning and bootstrapping technique are utilized to abstain from the false-negative and biased predictions dealing with positive unlabeled data. The performance of proposed method piRDA is evaluated using k-fold cross-validation. The piRDA is significantly improved in all the performance evaluation measures for the identification of piRNA disease associations in comparison to state-of-the-art method. Moreover, it is thus projected conclusively that the proposed computational method could play a significant role as a supportive and practical tool for primitive disease mechanisms and pharmaceutical research such as in academia and drug design. Eventually, the proposed model can be accessed using publicly available and user-friendly web tool athttp://nsclbio.jbnu.ac.kr/tools/piRDA/.
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Affiliation(s)
- Syed Danish Ali
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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21
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Doke M, Kashanchi F, Khan MA, Samikkannu T. HIV-1 Tat and cocaine coexposure impacts piRNAs to affect astrocyte energy metabolism. Epigenomics 2022; 14:261-278. [PMID: 35170353 PMCID: PMC8892230 DOI: 10.2217/epi-2021-0252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Aim: To understand the effect of HIV infection and cocaine exposure on piRNA expression in human primary astrocytes. Materials & methods: We used small RNA sequencing analysis to investigate the impacts of HIV-1 Tat and cocaine coexposure on the expression of piRNAs in human primary astrocytes. Results: We identified 27,700 piRNAs and analyzed them by small RNA next-generation sequencing. A total of 239 piRNAs were significantly altered by HIV-1 Tat and cocaine coexposure. We also identified PIWIL1, PIWIL2, PIWIL3 and PIWIL4 as interacting partners of piRNAs that were affected by cocaine and HIV-1 Tat coexposure. Epigenetic changes in the expression levels of these piRNA targets were associated with Kyoto Encyclopedia of Genes and Genomes pathways of energy metabolism and neurodegeneration. Conclusion: These findings provide evidence that cocaine exposure and HIV infection affect the expression levels of piRNA, PIWIL1, PIWIL2, PIWIL3 and PIWIL4.
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Affiliation(s)
- Mayur Doke
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University Health Science Center, Kingsville, TX 78363, USA
| | - Fatah Kashanchi
- National Center for Biodefense & Infectious Disease, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110, USA
| | - Mansoor A Khan
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University Health Science Center, Kingsville, TX 78363, USA
| | - Thangavel Samikkannu
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University Health Science Center, Kingsville, TX 78363, USA,Author for correspondence: Tel.: +1 361 221 0750;
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22
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Hanusek K, Poletajew S, Kryst P, Piekiełko-Witkowska A, Bogusławska J. piRNAs and PIWI Proteins as Diagnostic and Prognostic Markers of Genitourinary Cancers. Biomolecules 2022; 12:biom12020186. [PMID: 35204687 PMCID: PMC8869487 DOI: 10.3390/biom12020186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
piRNAs (PIWI-interacting RNAs) are small non-coding RNAs capable of regulation of transposon and gene expression. piRNAs utilise multiple mechanisms to affect gene expression, which makes them potentially more powerful regulators than microRNAs. The mechanisms by which piRNAs regulate transposon and gene expression include DNA methylation, histone modifications, and mRNA degradation. Genitourinary cancers (GC) are a large group of neoplasms that differ by their incidence, clinical course, biology, and prognosis for patients. Regardless of the GC type, metastatic disease remains a key therapeutic challenge, largely affecting patients’ survival rates. Recent studies indicate that piRNAs could serve as potentially useful biomarkers allowing for early cancer detection and therapeutic interventions at the stage of non-advanced tumour, improving patient’s outcomes. Furthermore, studies in prostate cancer show that piRNAs contribute to cancer progression by affecting key oncogenic pathways such as PI3K/AKT. Here, we discuss recent findings on biogenesis, mechanisms of action and the role of piRNAs and the associated PIWI proteins in GC. We also present tools that may be useful for studies on the functioning of piRNAs in cancers.
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Affiliation(s)
- Karolina Hanusek
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
| | - Sławomir Poletajew
- Centre of Postgraduate Medical Education, II Department of Urology, 01-813 Warsaw, Poland; (S.P.); (P.K.)
| | - Piotr Kryst
- Centre of Postgraduate Medical Education, II Department of Urology, 01-813 Warsaw, Poland; (S.P.); (P.K.)
| | - Agnieszka Piekiełko-Witkowska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
- Correspondence: (A.P.-W.); (J.B.)
| | - Joanna Bogusławska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
- Correspondence: (A.P.-W.); (J.B.)
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23
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Ghosh B, Sarkar A, Mondal S, Bhattacharya N, Khatua S, Ghosh Z. piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species. RNA Biol 2021; 19:12-25. [PMID: 34965192 PMCID: PMC8786328 DOI: 10.1080/15476286.2021.2010960] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2.
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Affiliation(s)
- Byapti Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Arijita Sarkar
- Division of Bioinformatics, Bose Institute, Kolkata, India.,Present Affiliation: Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Namrata Bhattacharya
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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24
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Merkerova MD, Krejcik Z. Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review). Int J Oncol 2021; 59:105. [PMID: 34779490 DOI: 10.3892/ijo.2021.5285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022] Open
Abstract
Our current understanding of hematopoietic stem cell differentiation and the abnormalities that lead to leukemogenesis originates from the accumulation of knowledge regarding protein‑coding genes. However, the possible impact of transposable element (TE) mobilization and the expression of P‑element‑induced WImpy testis‑interacting RNAs (piRNAs) on leukemogenesis has been beyond the scope of scientific interest to date. The expression profiles of these molecules and their importance for human health have only been characterized recently due to the rapid progress of high‑throughput sequencing technology development. In the present review, current knowledge on the expression profile and function of TEs and piRNAs was summarized, with specific focus on their reported involvement in leukemogenesis and pathogenesis of myelodysplastic syndrome.
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Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, 128 20 Prague, Czech Republic
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25
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Zhou Y, Fang Y, Dai C, Wang Y. PiRNA pathway in the cardiovascular system: a novel regulator of cardiac differentiation, repair and regeneration. J Mol Med (Berl) 2021; 99:1681-1690. [PMID: 34533602 DOI: 10.1007/s00109-021-02132-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 07/18/2021] [Accepted: 08/20/2021] [Indexed: 11/25/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a novel group of small non-coding RNA molecules with lengths of 21-35 nucleotides, first identified from the germline. PiRNAs and their associated PIWI clade Argonaute proteins constitute a key part of the piRNA pathway, with the best-known biological function to silence transposable elements in germ cells. The piRNA pathway, in fact, is not exclusive to the germline. Somatic functions of piRNAs have been recorded since their first discovery. To date, involvement of the piRNA pathway has been identified within the biological functions of genome rearrangement, epigenetic regulation, protein regulation in the germline and/or the soma transcriptionally or post-transcriptionally. Emerging evidence has shown that the piRNA pathway is essential for the normal function of the cardiovascular system and that its abnormal expression is correlated with cardiovascular dysfunction, although comprehensive roles of the piRNA pathway in the cardiovascular system and underlying mechanisms remain unclear. In this review, we discuss current findings of piRNA pathway expression in cardiac cell types and their potential functions in cardiac differentiation, repair and regeneration, thus providing new insights into cardiovascular disease development associated with the piRNA pathway.
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Affiliation(s)
- Yuling Zhou
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen Cardiovascular Hospital Xiamen University, Xiamen, China
- The School of Economics, Xiamen University, Xiamen, China
| | - Ya Fang
- School of Public Health, Key Laboratory of Health Technology Assessment of Fujian Province University, Xiamen University, Xiang'an South Road, Xiang'an District, Xiamen, 361102, Fujian, China
| | - Cuilian Dai
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen Cardiovascular Hospital Xiamen University, Xiamen, China
| | - Yan Wang
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen Cardiovascular Hospital Xiamen University, Xiamen, China.
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26
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Dhahbi JM, Chen JW, Bhupathy S, Atamna H, Cavalcante MB, Saccon TD, Nunes ADC, Mason JB, Schneider A, Masternak MM. Specific PIWI-Interacting RNAs and Related Small Noncoding RNAs Are Associated With Ovarian Aging in Ames Dwarf (df/df) Mice. J Gerontol A Biol Sci Med Sci 2021; 76:1561-1570. [PMID: 34387333 PMCID: PMC8361361 DOI: 10.1093/gerona/glab113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
The Ames dwarf (df/df) mouse is a well-established model for delayed aging. MicroRNAs (miRNAs), the most studied small noncoding RNAs (sncRNAs), may regulate ovarian aging to maintain a younger ovarian phenotype in df/df mice. In this study, we profile other types of ovarian sncRNAs, PIWI-interacting RNAs (piRNAs) and piRNA-like RNAs (piLRNAs), in young and aged df/df and normal mice. Half of the piRNAs derive from transfer RNA fragments (tRF-piRNAs). Aging and dwarfism alter the ovarian expression of these novel sncRNAs. Specific tRF-piRNAs that increased with age might target and decrease the expression of the breast cancer antiestrogen resistance protein 3 (BCAR3) gene in the ovaries of old df/df mice. A set of piLRNAs that decreased with age and map to D10Wsu102e mRNA may have trans-regulatory functions. Other piLRNAs that decreased with age potentially target and may de-repress transposable elements, leading to a beneficial impact on ovarian aging in df/df mice. These results identify unique responses in ovarian tissues with regard to aging and dwarfism. Overall, our findings highlight the complexity of the aging effects on gene expression and suggest that, in addition to miRNAs, piRNAs, piLRNAs, tRF-piRNAs, and their potential targets can be central players in the maintenance of a younger ovarian phenotype in df/df mice.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, USA
| | - Joe W Chen
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, USA
| | - Supriya Bhupathy
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, USA
| | - Hani Atamna
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, USA
| | | | - Tatiana D Saccon
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Rio Grande, Brazil
| | - Allancer D C Nunes
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, USA
| | - Jeffrey B Mason
- Department of Animal, Dairy and Veterinary Sciences, Center for Integrated BioSystems, School of Veterinary Medicine, Utah State University, Logan, USA
| | - Augusto Schneider
- Faculdade de Nutricao, Universidade Federal de Pelotas, Rio Grande, Brazil
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, USA
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, Poland
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27
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Yuan C, Qin H, Ponnusamy M, Chen Y, Lin Z. PIWI‑interacting RNA in cancer: Molecular mechanisms and possible clinical implications (Review). Oncol Rep 2021; 46:209. [PMID: 34328192 DOI: 10.3892/or.2021.8160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/05/2021] [Indexed: 11/06/2022] Open
Abstract
PIWI‑interacting RNA is a class of non‑coding small RNA that is ~30 nt long and is primarily found in mammalian germ cells from mice and humans. In cooperation with the members of PIWI protein family, this macromolecule participates in germ cell development, inhibits DNA self‑-replication and maintains genomic stability. Increasing evidence has demonstrated that PIWI‑interacting RNA (piRNAs) are abnormally expressed in various human cancers, such as liver cancer, stomach cancer, colorectal cancer, osteosarcoma, breast cancer, lung cancer, prostate cancer, etc. piRNAs abnormal expression is also associated with the occurrence and development of human cancers, such as liver cancer, stomach cancer, colorectal cancer, etc. Despite their unclear molecular mechanisms, piRNAs may act as oncogenes or tumor suppressors by interacting with multiple cancer‑related signal pathways including STAT3/Bcl‑xl or coding genes, such as heat shock transcription factor‑1. Hence, piRNAs may be potential markers and targets and provide new opportunities for cancer diagnosis, treatment or prognosis monitoring. The current review mainly aims to highlight the latest research progress made in the biological functions and regulation of piRNAs in mammals, their involvement in various cancer forms and their potential clinical applications.
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Affiliation(s)
- Chao Yuan
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Hao Qin
- Department of Public Health, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Murugavel Ponnusamy
- Department of Basic Medicine, Institute for Translational Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Yong Chen
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhijuan Lin
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
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28
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Rosenkranz D, Zischler H, Gebert D. piRNAclusterDB 2.0: update and expansion of the piRNA cluster database. Nucleic Acids Res 2021; 50:D259-D264. [PMID: 34302483 PMCID: PMC8728273 DOI: 10.1093/nar/gkab622] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/14/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically influence piRNA populations in different evolutionary lineages. We launched the initial version of the piRNA cluster database to facilitate research on regulation and evolution of piRNA-producing loci across tissues und species. In recent years the amount of small RNA sequencing data that was generated and the abundance of species that were studied has grown rapidly. To keep up with this recent progress, we have released a major update for the piRNA cluster database (https://www.smallrnagroup.uni-mainz.de/piRNAclusterDB), expanding it from 12 to a total of 51 species with hundreds of new datasets, and revised its overall structure to enable easy navigation through this large amount of data.
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Affiliation(s)
- David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany.,Senckenberg Centre for Human Genetics, Facharztzentrum Frankfurt-Nordend gGmbH, Frankfurt am Main 60314, Germany
| | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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29
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Martinez VD, Sage AP, Minatel BC, Marshall EA, Price EM, Becker-Santos DD, Robinson WP, Lam WL. Human placental piwi-interacting RNA transcriptome is characterized by expression from the DLK1-DIO3 imprinted region. Sci Rep 2021; 11:14981. [PMID: 34294738 PMCID: PMC8298716 DOI: 10.1038/s41598-021-93885-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/17/2021] [Indexed: 01/07/2023] Open
Abstract
The placenta is vital to embryonic development and requires a finely-tuned pattern of gene expression, achieved in part by its unique epigenetic landscape. Piwi-interacting RNAs (piRNAs) are a class of small-non-coding RNA with established roles as epigenetic regulators of gene expression, largely via methylation of targeted DNA sequences. The expression of piRNAs have mainly been described in germ cells, but a fraction have been shown to retain expression in adult somatic tissues. To aid in understanding the contribution of these regulators in the placenta, we provide the first description of the piRNA transcriptome in human placentas. We find 297 piRNAs to be preferentially expressed in the human placenta, a subset of which are expressed at higher levels relative to testes samples. We also observed a large proportion of placental piRNAs to be expressed from a single locus, as distinct from canonical cluster locations associated with transposable element silencing. Finally, we find that 15 of the highest-expressed placental piRNAs maps to the DLK1-DIO3 locus, suggesting a link to placental biology. Our findings suggest that piRNAs could contribute to the molecular networks defining placental function in humans, and a biological impact of piRNA expression beyond germ cells.
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Affiliation(s)
- Victor D Martinez
- British Columbia Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, Canada. .,IWK Health Centre, Halifax, NS, Canada. .,Department of Pathology, Faculty of Medicine, Dalhousie University, 5850/5980 University Avenue, Halifax, NS, B3K 6R8, Canada.
| | - Adam P Sage
- British Columbia Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, Canada
| | - Brenda C Minatel
- British Columbia Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, Canada
| | - Erin A Marshall
- British Columbia Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, Canada
| | - E Magda Price
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Wendy P Robinson
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Wan L Lam
- British Columbia Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, Canada
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30
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Tang C, Xie Y, Guo M, Yan W. AASRA: an anchor alignment-based small RNA annotation pipeline†. Biol Reprod 2021; 105:267-277. [PMID: 33787835 PMCID: PMC8256102 DOI: 10.1093/biolre/ioab062] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/02/2021] [Accepted: 03/29/2021] [Indexed: 01/31/2023] Open
Abstract
Small noncoding RNAs deep sequencing (sncRNA-Seq) has become a routine for sncRNA detection and quantification. However, the software packages currently available for sncRNA annotation can neither recognize sncRNA variants in the sequencing reads, nor annotate all known sncRNA simultaneously. Here, we report a novel anchor alignment-based small RNA annotation (AASRA) software package (https://github.com/biogramming/AASRA). AASRA represents an all-in-one sncRNA annotation pipeline, which allows for high-speed, simultaneous annotation of all known sncRNA species with the capability to distinguish mature from precursor microRNAs, and to identify novel sncRNA variants in the sncRNA-Seq sequencing reads.
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Affiliation(s)
- Chong Tang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
| | - Yeming Xie
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
| | - Mei Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
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31
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Chen S, Ben S, Xin J, Li S, Zheng R, Wang H, Fan L, Du M, Zhang Z, Wang M. The biogenesis and biological function of PIWI-interacting RNA in cancer. J Hematol Oncol 2021; 14:93. [PMID: 34118972 PMCID: PMC8199808 DOI: 10.1186/s13045-021-01104-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Small non-coding RNAs (ncRNAs) are vital regulators of biological activities, and aberrant levels of small ncRNAs are commonly found in precancerous lesions and cancer. PIWI-interacting RNAs (piRNAs) are a novel type of small ncRNA initially discovered in germ cells that have a specific length (24-31 nucleotides), bind to PIWI proteins, and show 2'-O-methyl modification at the 3'-end. Numerous studies have revealed that piRNAs can play important roles in tumorigenesis via multiple biological regulatory mechanisms, including silencing transcriptional and posttranscriptional gene processes and accelerating multiprotein interactions. piRNAs are emerging players in the malignant transformation of normal cells and participate in the regulation of cancer hallmarks. Most of the specific cancer hallmarks regulated by piRNAs are involved in sustaining proliferative signaling, resistance to cell death or apoptosis, and activation of invasion and metastasis. Additionally, piRNAs have been used as biomarkers for cancer diagnosis and prognosis and have great potential for clinical utility. However, research on the underlying mechanisms of piRNAs in cancer is limited. Here, we systematically reviewed recent advances in the biogenesis and biological functions of piRNAs and relevant bioinformatics databases with the aim of providing insights into cancer diagnosis and clinical applications. We also focused on some cancer hallmarks rarely reported to be related to piRNAs, which can promote in-depth research of piRNAs in molecular biology and facilitate their clinical translation into cancer treatment.
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Affiliation(s)
- Silu Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Zheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lulu Fan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China. .,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China.
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32
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Cuthbert JM, Russell SJ, Polejaeva IA, Meng Q, White KL, Benninghoff AD. Dynamics of small non-coding RNAs in bovine scNT embryos through the maternal-to-embryonic transition. Biol Reprod 2021; 105:918-933. [PMID: 34086842 DOI: 10.1093/biolre/ioab107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/14/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The efficiency of somatic cell nuclear transfer (scNT) for production of viable offspring is relatively low as compared to in vitro fertilization (IVF), presumably due to deficiencies in epigenetic reprogramming of the donor cell genome. Such defects may also involve the population of small non-coding RNAs (sncRNAs), which are important during early embryonic development. The objective of this study was to examine dynamic changes in relative abundance of sncRNAs during the maternal-to embryonic transition (MET) in bovine embryos produced by scNT as compared to IVF by using RNA sequencing. When comparing populations of miRNA in scNT versus IVF embryos, only miR-2340, miR-345, and miR34a were differentially expressed in morulae, though many more miRNAs were differentially expressed when comparing across developmental stages. Also of interest, distinct populations of piwi-interacting like RNAs (pilRNAs) were identified in bovine embryos prior to and during embryonic genome activation (EGA) as compared bovine embryos post EGA and differentiated cells. Overall, sncRNA sequencing analysis of preimplantation embryos revealed largely similar profiles of sncRNAs for IVF and scNT embryos at the 2-cell, 8-cell, morula and blastocyst stages of development. However, these sncRNA profiles, including miRNA, piRNA and tRNA fragments, were notably distinct prior to and after completion of the MET.
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Affiliation(s)
- Jocelyn M Cuthbert
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Stewart J Russell
- CReATe Fertility Centre, 790 Bay St. #1100, Toronto, M5G 1N8, Canada
| | - Irina A Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Qinggang Meng
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
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33
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Sellem E, Marthey S, Rau A, Jouneau L, Bonnet A, Le Danvic C, Guyonnet B, Kiefer H, Jammes H, Schibler L. Dynamics of cattle sperm sncRNAs during maturation, from testis to ejaculated sperm. Epigenetics Chromatin 2021; 14:24. [PMID: 34030709 PMCID: PMC8146655 DOI: 10.1186/s13072-021-00397-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022] Open
Abstract
Background During epididymal transit, spermatozoa go through several functional maturation steps, resulting from interactions with epididymal secretomes specific to each region. In particular, the sperm membrane is under constant remodeling, with sequential attachment and shedding of various molecules provided by the epididymal lumen fluid and epididymosomes, which also deliver sncRNA cargo to sperm. As a result, the payload of sperm sncRNAs changes during the transit from the epididymis caput to the cauda. This work was designed to study the dynamics of cattle sperm sncRNAs from spermatogenesis to final maturation. Results Comprehensive catalogues of sperm sncRNAs were obtained from testicular parenchyma, epididymal caput, corpus and cauda, as well as ejaculated semen from three Holstein bulls. The primary cattle sncRNA sperm content is markedly remodeled as sperm mature along the epididymis. Expression of piRNAs, which are abundant in testis parenchyma, decreases dramatically at epididymis. Conversely, sperm progressively acquires miRNAs, rsRNAs, and tsRNAs along epididymis, with regional specificities. For instance, miRNAs and tsRNAs are enriched in epididymis cauda and ejaculated sperm, while rsRNA expression peaks at epididymis corpus. In addition, epididymis corpus contains mainly 20 nt long piRNAs, instead of 30 nt in all other locations. Beyond the bulk differences in abundance of sncRNAs classes, K-means clustering was performed to study their spatiotemporal expression profile, highlighting differences in specific sncRNAs and providing insights into their putative biological role at each maturation stage. For instance, Gene Ontology analyses using miRNA targets highlighted enriched processes such as cell cycle regulation, response to stress and ubiquitination processes in testicular parenchyma, protein metabolism in epididymal sperm, and embryonic morphogenesis in ejaculated sperm. Conclusions Our findings confirm that the sperm sncRNAome does not simply reflect a legacy of spermatogenesis. Instead, sperm sncRNA expression shows a remarkable level of plasticity resulting probably from the combination of multiple factors such as loss of the cytoplasmic droplet, interaction with epididymosomes, and more surprisingly, the putative in situ production and/or modification of sncRNAs by sperm. Given the suggested role of sncRNA in epigenetic trans-generational inheritance, our detailed spatiotemporal analysis may pave the way for a study of sperm sncRNAs role in embryo development. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00397-5.
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Affiliation(s)
- Eli Sellem
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.
| | - Sylvain Marthey
- AgroParisTech, INRAE, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Andrea Rau
- AgroParisTech, INRAE, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,BioEcoAgro Joint Research Unit, INRAE, Université de Liège, Université de Lille, Université de Picardie Jules Verne, Estrées-Mons, France
| | - Luc Jouneau
- UVSQ, INRAE, BREED, Université Paris Saclay, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire D'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Aurelie Bonnet
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France
| | | | - Benoît Guyonnet
- R&D Department, Union Evolution, rue Eric Tabarly, 35538, Noyal-Sur-Vilaine, France
| | - Hélène Kiefer
- UVSQ, INRAE, BREED, Université Paris Saclay, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire D'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Hélène Jammes
- UVSQ, INRAE, BREED, Université Paris Saclay, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire D'Alfort, BREED, 94700, Maisons-Alfort, France
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34
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Wang K, Wang T, Gao XQ, Chen XZ, Wang F, Zhou LY. Emerging functions of piwi-interacting RNAs in diseases. J Cell Mol Med 2021; 25:4893-4901. [PMID: 33942984 PMCID: PMC8178273 DOI: 10.1111/jcmm.16466] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
PIWI‐interacting RNAs (piRNAs) are recently discovered small non‐coding RNAs consisting of 24‐35 nucleotides, usually including a characteristic 5‐terminal uridine and an adenosine at position 10. PIWI proteins can specifically bind to the unique structure of the 3′ end of piRNAs. In the past, it was thought that piRNAs existed only in the reproductive system, but recently, it was reported that piRNAs are also expressed in several other human tissues with tissue specificity. Growing evidence shows that piRNAs and PIWI proteins are abnormally expressed in various diseases, including cancers, neurodegenerative diseases and ageing, and may be potential biomarkers and therapeutic targets. This review aims to discuss the current research status regarding piRNA biogenetic processes, functions, mechanisms and emerging roles in various diseases.
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Affiliation(s)
- Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Tao Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Xiang-Qian Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Xin-Zhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu-Yu Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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35
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Wang Y, Zhou Y, Ali MA, Zhang J, Wang W, Huang Y, Luo B, Zhang H, Qin Z, Zhang Y, Zhang M, Zhou G, Zeng C. Comparative Analysis of piRNA Profiles Helps to Elucidate Cryoinjury Between Giant Panda and Boar Sperm During Cryopreservation. Front Vet Sci 2021; 8:635013. [PMID: 33969033 PMCID: PMC8100531 DOI: 10.3389/fvets.2021.635013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/17/2021] [Indexed: 12/02/2022] Open
Abstract
Cryopreservation induces sperm cryoinjuries, including physiological and functional changes. However, the molecular mechanisms of sperm cryoinjury and cryoresistance are still unknown. Cryoresistance or the freeze tolerance of sperm varies across species, and boar sperm is more susceptible to cold stress. Contrary to boar sperm, giant panda sperm appears to be strongly freeze-tolerant and is capable of surviving repeated cycles of freeze-thawing. In this study, differentially expressed (DE) PIWI-interacting RNAs (piRNAs) of fresh and frozen-thawed sperm with different freeze tolerance capacity from giant panda and boar were evaluated. The results showed that 1,160 (22 downregulated and 1,138 upregulated) and 384 (110 upregulated and 274 downregulated) DE piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE messenger RNAs (mRNAs) of DE piRNAs were mainly enriched in biological regulation, cellular, and metabolic processes in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed in DNA replication and the cyclic adenosine monophosphate (cAMP) signaling pathway in giant panda, but the cAMP, cyclic guanosine monophosphate (cGMP), and mitogen-activated protein kinase (MAPK) signaling pathways in boar sperm were considered as part of the olfactory transduction pathway. In conclusion, we speculated that the difference in the piRNA profiles and the DE piRNAs involved in the cAMP signaling pathway in boar and giant panda may have contributed to the different freeze tolerance capacities between giant panda and boar sperm, which helps to elucidate the molecular mechanism behind sperm cryoinjury and cryoresistance.
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Affiliation(s)
- Yihan Wang
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yingmin Zhou
- China Conservation and Research Center for the Giant Panda, Chengdu, China
| | - Malik Ahsan Ali
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Department of Theriogenology, Riphah College of Veterinary Sciences, Lahore, Pakistan
| | - Jiaman Zhang
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Wencan Wang
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Chengdu, China
| | - Bo Luo
- China Conservation and Research Center for the Giant Panda, Chengdu, China
| | - Heming Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu, China
| | - Ziyue Qin
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Zhang
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ming Zhang
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guangbin Zhou
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Changjun Zeng
- College of Animal Sciences and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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36
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Computational Methods and Online Resources for Identification of piRNA-Related Molecules. Interdiscip Sci 2021; 13:176-191. [PMID: 33886096 DOI: 10.1007/s12539-021-00428-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
piRNAs are a class of small non-coding RNA molecules, which interact with the PIWI family and have many important and diverse biological functions. The present review is aimed to provide guidelines and contribute to piRNA research. We focused on the four types of identification models on piRNA-related molecules, including piRNA, piRNA cluster, piRNA target, and disease-related piRNA. We evaluated the types of tools for the identification of piRNAs based on five aspects: datasets, features, classifiers, performance, and usability. We found the precision of 2lpiRNApred was the highest in datasets of model organisms, piRNN had a better performance of datasets of non-model organisms, and 2L-piRNA had the fastest recognition speed of all tools. In addition, we presented an overview of piRNA databases. The databases were divided into six categories: basic annotation, comprehensive annotation, isoform, cluster, target, and disease. We found that piRNA data of non-model organisms, piRNA target data, and piRNA-disease-associated data should be strengthened. Our review might assist researchers in selecting appropriate tools or datasets for their studies, reveal potential problems and shed light on future bioinformatics studies.
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37
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38
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Ipsaro JJ, O'Brien PA, Bhattacharya S, Palmer AG, Joshua-Tor L. Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Rep 2021; 34:108914. [PMID: 33789107 DOI: 10.1016/j.celrep.2021.108914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/15/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway safeguards genomic integrity by silencing transposable elements (transposons) in the germline. While Piwi is the central piRNA factor, others including Asterix/Gtsf1 have also been demonstrated to be critical for effective silencing. Here, using enhanced crosslinking and immunoprecipitation (eCLIP) with a custom informatic pipeline, we show that Asterix/Gtsf1 specifically binds tRNAs in cellular contexts. We determined the structure of mouse Gtsf1 by NMR spectroscopy and identified the RNA-binding interface on the protein's first zinc finger, which was corroborated by biochemical analysis as well as cryo-EM structures of Gtsf1 in complex with co-purifying tRNA. Consistent with the known dependence of long terminal repeat (LTR) retrotransposons on tRNA primers, we demonstrate that LTR retrotransposons are, in fact, preferentially de-repressed in Asterix mutants. Together, these findings link Asterix/Gtsf1, tRNAs, and LTR retrotransposon silencing and suggest that Asterix exploits tRNA dependence to identify transposon transcripts and promote piRNA silencing.
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Affiliation(s)
- Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Paul A O'Brien
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | | | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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39
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Ramat A, Simonelig M. Functions of PIWI Proteins in Gene Regulation: New Arrows Added to the piRNA Quiver. Trends Genet 2021; 37:188-200. [DOI: 10.1016/j.tig.2020.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022]
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40
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Geles K, Palumbo D, Sellitto A, Giurato G, Cianflone E, Marino F, Torella D, Mirici Cappa V, Nassa G, Tarallo R, Weisz A, Rizzo F. WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data. F1000Res 2021; 10:1. [PMID: 34316353 PMCID: PMC8276195 DOI: 10.12688/f1000research.27868.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on germline-derived piRNAs and piRNA-clusters. Frequently, they suffer from outdated piRNA databases, questionable quantification methods, and lack of reproducibility. Often, pipelines specific to miRNA analysis are used for the piRNA research
in silico. Furthermore, the absence of a well-established database for piRNA annotation, as for miRNA, leads to uniformity issues between studies and generates confusion for data analysts and biologists. For these reasons, we have developed WIND (
Workflow for p
IRNAs a
Nd beyon
D), a bioinformatics workflow that addresses the crucial issue of piRNA annotation, thereby allowing a reliable analysis of small RNA sequencing data for the identification of piRNAs and other small non-coding RNAs (sncRNAs) that in the past have been incorrectly classified as piRNAs. WIND allows the creation of a comprehensive annotation track of sncRNAs combining information available in RNAcentral, with piRNA sequences from piRNABank, the first database dedicated to piRNA annotation. WIND was built with Docker containers for reproducibility and integrates widely used bioinformatics tools for sequence alignment and quantification. In addition, it includes Bioconductor packages for exploratory data and differential expression analysis. Moreover, WIND implements a "dual" approach for the evaluation of sncRNAs expression level quantifying the aligned reads to the annotated genome and carrying out an alignment-free transcript quantification using reads mapped to the transcriptome. Therefore, a broader range of piRNAs can be annotated, improving their quantification and easing the subsequent downstream analysis. WIND performance has been tested with several small RNA-seq datasets, demonstrating how our approach can be a useful and comprehensive resource to analyse piRNAs and other classes of sncRNAs.
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Affiliation(s)
- Konstantinos Geles
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,Genomix4Life, via S. Allende 43/L, Baronissi, Salerno (SA), 84081, Italy
| | - Domenico Palumbo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,Clinical Research and Innovation, Clinica Montevergine S.p.A., Mercogliano, Mercogliano, 83013, Italy
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,Genomix4Life, via S. Allende 43/L, Baronissi, Salerno (SA), 84081, Italy.,CRGS (Genome Research Center for Health), University of Salerno Campus of Medicine, Baronissi, Salerno (SA), 84081, Italy
| | - Eleonora Cianflone
- Department of Medical and Surgical Sciences, Magna Graecia University, Viale Europa, Catanzaro, 88100, Italy
| | - Fabiola Marino
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, Catanzaro, 88100, Italy
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, Catanzaro, 88100, Italy
| | - Valeria Mirici Cappa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,Genomix4Life, via S. Allende 43/L, Baronissi, Salerno (SA), 84081, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,Genomix4Life, via S. Allende 43/L, Baronissi, Salerno (SA), 84081, Italy.,CRGS (Genome Research Center for Health), University of Salerno Campus of Medicine, Baronissi, Salerno (SA), 84081, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,CRGS (Genome Research Center for Health), University of Salerno Campus of Medicine, Baronissi, Salerno (SA), 84081, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,CRGS (Genome Research Center for Health), University of Salerno Campus of Medicine, Baronissi, Salerno (SA), 84081, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno (SA), 84081, Italy.,Genomix4Life, via S. Allende 43/L, Baronissi, Salerno (SA), 84081, Italy.,CRGS (Genome Research Center for Health), University of Salerno Campus of Medicine, Baronissi, Salerno (SA), 84081, Italy
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41
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Abstract
Liver cancer is one of the most common and deadly cancers in the world. In recent years, non-coding RNA has been a hot topic in liver cancer research. piRNAs (PIWI-interacting RNAs) are a new type of small non-coding RNA, which are formed by the PIWI proteins interacting with RNA. The latest research shows that piRNA and PIWI proteins are abnormally expressed in various cancers, including pancreatic, colorectal, breast, etc. piRNA plays an important regulatory role in liver cancer. In this review, we discuss the biological function of piRNAs and new progress in the development of liver cancer, and new targets and ideas for piRNA and PIWI proteins in the diagnosis and treatment of liver cancer.
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Affiliation(s)
- Jiamin Xu
- Graduate School of Nursing, Huzhou University, Huzhou, China
| | - Xi Yang
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| | - Qing Zhou
- Department of Critical Care Medicine, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| | - Jing Zhuang
- Graduate School of Nursing, Huzhou University, Huzhou, China
| | - Shuwen Han
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
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42
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Ord J, Heath PR, Fazeli A, Watt PJ. Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs. Mol Ecol 2020; 29:2722-2735. [PMID: 32525590 DOI: 10.1111/mec.15505] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]
Abstract
While the importance of maternal effects has long been appreciated, a growing body of evidence now points to the paternal environment having an important influence on offspring phenotype. Indeed, research on rodent models suggests that paternal stress leaves an imprint on the behaviour and physiology of offspring via nongenetic information carried in the spermatozoa; however, fish have been understudied with regard to these sperm-mediated effects. Here, we investigated whether the zebrafish was subjected to heritable influences of paternal stress by exposing males to stressors (conspecific-derived alarm cue, chasing and bright light) before mating and assessing the behavioural and endocrine responses of their offspring, including their behavioural response to conspecific-derived alarm cue. We found that after males are exposed to stress, their larval offspring show weakened responses to stressors. Small RNA sequencing subsequently revealed that the levels of several small noncoding RNAs, including microRNAs, PIWI-interacting RNAs and tRNA-derived small RNAs, were altered in the spermatozoa of stressed fathers, suggesting that stress-induced alterations to the spermatozoal RNA landscape may contribute to shaping offspring phenotype. The work demonstrates that paternal stress should not be overlooked as a source of phenotypic variation and that spermatozoal small RNAs may be important intergenerational messengers in fish.
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Affiliation(s)
- James Ord
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Academic Unit of Reproductive and Developmental Medicine, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Paul R Heath
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Alireza Fazeli
- Academic Unit of Reproductive and Developmental Medicine, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Penelope J Watt
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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43
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Tan M, van Tol HT, Rosenkranz D, Roovers EF, Damen MJ, Stout TA, Wu W, Roelen BA. PIWIL3 Forms a Complex with TDRKH in Mammalian Oocytes. Cells 2020; 9:cells9061356. [PMID: 32486081 PMCID: PMC7349845 DOI: 10.3390/cells9061356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/15/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
P-element induced wimpy testis (PIWIs) are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 gene is absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression, distribution, and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrial-recruited three-membered complex with Tudor and KH domain-containing protein (TDRKH) and poly(A)-specific ribonuclease-like domain containing 1 (PNLDC1), and demonstrated by mutagenesis that PIWIL3 N-terminal arginines are required for complex assembly. Finally, we sequenced the piRNAs bound to PIWIL3-TDRKH-PNLDC1 and report here that about 50% of these piRNAs map to transposable elements, recapitulating the important role of PIWIL3 in maintaining genome integrity in mammalian oocytes.
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Affiliation(s)
- Minjie Tan
- Farm Animal Health, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM Utrecht, The Netherlands; (M.T.); (H.T.A.v.T.)
| | - Helena T.A. van Tol
- Farm Animal Health, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM Utrecht, The Netherlands; (M.T.); (H.T.A.v.T.)
| | - David Rosenkranz
- Johannes Gutenberg-University Mainz, Institute of Organismic and Molecular Evolution, Anselm-Franz-von-Bentzel-Weg 7, 55128 Mainz, Germany;
| | - Elke F. Roovers
- Biology of Non-coding RNA Group, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany;
| | - Mirjam J. Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tom A.E. Stout
- Equine Sciences, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112, 3584 CM Utrecht, The Netherlands;
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Correspondence: (W.W.); (B.A.J.R.)
| | - Bernard A.J. Roelen
- Embryology, Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence: (W.W.); (B.A.J.R.)
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44
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Wang J, Zhang P, Lu Y, Li Y, Zheng Y, Kan Y, Chen R, He S. piRBase: a comprehensive database of piRNA sequences. Nucleic Acids Res 2020; 47:D175-D180. [PMID: 30371818 PMCID: PMC6323959 DOI: 10.1093/nar/gky1043] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/22/2018] [Indexed: 12/25/2022] Open
Abstract
PIWI-interacting RNAs are a class of small RNAs that is most abundantly expressed in animal germline. Substantial research is going on to reveal the functions of piRNAs in the epigenetic and post-transcriptional regulation of transposons and genes. To collect and annotate these data, we developed piRBase, a database assisting piRNA functional study. Since its launch in 2014, piRBase has integrated 264 data sets from 21 organisms, and the number of collected piRNAs has reached 173 million. The latest piRBase release (v2.0, 2018) was more focused on the comprehensive annotation of piRNA sequences, as well as the increasing number of piRNAs. In addition, piRBase release v2.0 also contained the potential information of piRNA targets and disease related piRNA. All datasets in piRBase is free to access, and available for browse, search and bulk downloads at http://www.regulatoryrna.org/database/piRNA/.
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Affiliation(s)
- Jiajia Wang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001,China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Science, Beijing 100049, China
| | - Yu Zheng
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Science, Beijing 100049, China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, Nanyang, Henan 473061,China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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45
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Wei H, Xu Y, Liu B. iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning. Brief Bioinform 2020; 22:5829704. [PMID: 32393982 DOI: 10.1093/bib/bbaa058] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/15/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Accumulated researches have revealed that Piwi-interacting RNAs (piRNAs) are regulating the development of germ and stem cells, and they are closely associated with the progression of many diseases. As the number of the detected piRNAs is increasing rapidly, it is important to computationally identify new piRNA-disease associations with low cost and provide candidate piRNA targets for disease treatment. However, it is a challenging problem to learn effective association patterns from the positive piRNA-disease associations and the large amount of unknown piRNA-disease pairs. In this study, we proposed a computational predictor called iPiDi-PUL to identify the piRNA-disease associations. iPiDi-PUL extracted the features of piRNA-disease associations from three biological data sources, including piRNA sequence information, disease semantic terms and the available piRNA-disease association network. Principal component analysis (PCA) was then performed on these features to extract the key features. The training datasets were constructed based on known positive associations and the negative associations selected from the unknown pairs. Various random forest classifiers trained with these different training sets were merged to give the predictive results via an ensemble learning approach. Finally, the web server of iPiDi-PUL was established at http://bliulab.net/iPiDi-PUL to help the researchers to explore the associated diseases for newly discovered piRNAs.
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46
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Luo Z, Wang X, Jiang H, Wang R, Chen J, Chen Y, Xu Q, Cao J, Gong X, Wu J, Yang Y, Li W, Han C, Cheng CY, Rosenfeld MG, Sun F, Song X. Reorganized 3D Genome Structures Support Transcriptional Regulation in Mouse Spermatogenesis. iScience 2020; 23:101034. [PMID: 32315832 PMCID: PMC7170994 DOI: 10.1016/j.isci.2020.101034] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/30/2019] [Accepted: 03/30/2020] [Indexed: 01/22/2023] Open
Abstract
Three-dimensional chromatin structures undergo dynamic reorganization during mammalian spermatogenesis; however, their impacts on gene regulation remain unclear. Here, we focused on understanding the structure-function regulation of meiotic chromosomes by Hi-C and other omics techniques in mouse spermatogenesis across five stages. Beyond confirming recent reports regarding changes in compartmentalization and reorganization of topologically associating domains (TADs), we further demonstrated that chromatin loops are present prior to and after, but not at, the pachytene stage. By integrating Hi-C and RNA-seq data, we showed that the switching of A/B compartments between spermatogenic stages is tightly associated with meiosis-specific mRNAs and piRNAs expression. Moreover, our ATAC-seq data indicated that chromatin accessibility per se is not responsible for the TAD and loop diminishment at pachytene. Additionally, our ChIP-seq data demonstrated that CTCF and cohesin remain bound at TAD boundary regions throughout meiosis, suggesting that dynamic reorganization of TADs does not require CTCF and cohesin clearance.
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Affiliation(s)
- Zhengyu Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaorong Wang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, Jiangsu 226000, China
| | - Hong Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ruoyu Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusheng Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, CAS Center for Excellence in Molecular Cell Science, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qianlan Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jun Cao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaowen Gong
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Wu
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yungui Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, CAS Center for Excellence in Molecular Cell Science, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - C Yan Cheng
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, School and Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0651, USA
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, Jiangsu 226000, China.
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China.
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47
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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48
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Sellem E, Marthey S, Rau A, Jouneau L, Bonnet A, Perrier JP, Fritz S, Le Danvic C, Boussaha M, Kiefer H, Jammes H, Schibler L. A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds. Epigenetics Chromatin 2020; 13:19. [PMID: 32228651 PMCID: PMC7106649 DOI: 10.1186/s13072-020-00340-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Mature sperm carry thousands of RNAs, including mRNAs, lncRNAs, tRNAs, rRNAs and sncRNAs, though their functional significance is still a matter of debate. Growing evidence suggests that sperm RNAs, especially sncRNAs, are selectively retained during spermiogenesis or specifically transferred during epididymis maturation, and are thus delivered to the oocyte at fertilization, providing resources for embryo development. However , a deep characterization of the sncRNA content of bull sperm and its expression profile across breeds is currently lacking. To fill this gap, we optimized a guanidinium–Trizol total RNA extraction protocol to prepare high-quality RNA from frozen bull sperm collected from 40 representative bulls from six breeds. Deep sequencing was performed (40 M single 50-bp reads per sample) to establish a comprehensive repertoire of cattle sperm sncRNA. Results Our study showed that it comprises mostly piRNAs (26%), rRNA fragments (25%), miRNAs (20%) and tRNA fragments (tsRNA, 14%). We identified 5p-halves as the predominant tsRNA subgroup in bull sperm, originating mostly from Gly and Glu isoacceptors. Our study also increased by ~ 50% the sperm repertoire of known miRNAs and identified 2022 predicted miRNAs. About 20% of sperm miRNAs were located within genomic clusters, expanding the list of known polycistronic pri-miRNA clusters and defining several networks of co-expressed miRNAs. Strikingly, our study highlighted the great diversity of isomiRs, resulting mainly from deletions and non-templated additions (A and U) at the 3p end. Substitutions within miRNA sequence accounted for 40% of isomiRs, with G>A, U>C and C>U substitutions being the most frequent variations. In addition, many sncRNAs were found to be differentially expressed across breeds. Conclusions Our study provides a comprehensive overview of cattle sperm sncRNA, and these findings will pave the way for future work on the role of sncRNAs in embryo development and their relevance as biomarkers of semen fertility.
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Affiliation(s)
- Eli Sellem
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.
| | - Sylvain Marthey
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Andrea Rau
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris Saclay, UVSQ, INRAE, BREED, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Aurelie Bonnet
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France
| | - Jean-Philippe Perrier
- Université Paris Saclay, UVSQ, INRAE, BREED, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Sébastien Fritz
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | | | - Mekki Boussaha
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Hélène Kiefer
- Université Paris Saclay, UVSQ, INRAE, BREED, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Hélène Jammes
- Université Paris Saclay, UVSQ, INRAE, BREED, 78350, Jouy en Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
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49
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Li J, Kho AT, Chase RP, Pantano L, Farnam L, Amr SS, Tantisira KG. COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis. Sci Rep 2020; 10:4552. [PMID: 32165660 PMCID: PMC7067867 DOI: 10.1038/s41598-020-61495-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
Small RNA-Seq is a common means to interrogate the small RNA’ome or the full spectrum of small RNAs (<200 nucleotide length) of a biological system. A pivotal problem in NGS based small RNA analysis is identifying and quantifying the small RNA’ome constituent components. For example, small RNAs in the circulatory system (circulating RNAs) are potential disease biomarkers and their function is being actively investigated. Most existing NGS data analysis tools focus on the microRNA component and a few other small RNA types like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate the full small RNA’ome, a prerequisite for down-stream data analysis. We present COMPSRA, a comprehensive modular stand-alone platform for identifying and quantifying small RNAs from small RNA sequencing data. COMPSRA contains prebuilt customizable standard RNA databases and sequence processing tools to enable turnkey basic small RNA analysis. We evaluated COMPSRA against comparable existing tools on small RNA sequencing data set from serum samples of 12 healthy human controls, and COMPSRA identified a greater diversity and abundance of small RNA molecules. COMPSRA is modular, stand-alone and integrates multiple customizable RNA databases and sequence processing tool and is distributed under the GNU General Public License free to non-commercial registered users at https://github.com/cougarlj/COMPSRA.
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Affiliation(s)
- Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | | | - Robert P Chase
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorena Pantano
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Leanna Farnam
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sami S Amr
- Partners Personalized Medicine, Boston, MA, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
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50
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Russell SJ, Menezes K, Balakier H, Librach C. Comprehensive profiling of Small RNAs in human embryo-conditioned culture media by improved sequencing and quantitative PCR methods. Syst Biol Reprod Med 2020; 66:129-139. [PMID: 32053759 DOI: 10.1080/19396368.2020.1716108] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Embryo implantation depends on two primary factors: the quality of the embryo and endometrial receptivity. Small RNAs have been shown to be potent epigenetic regulators influencing cell proliferation, differentiation, and communication even in the context of early embryonic development. However, previous reports are limited to miRNAs and lack sensitivity. Here, we describe a platform for non-invasive small RNA biomarker discovery and validation from embryo-conditioned culture media (ECCM). We hypothesize that small non-coding RNAs (sncRNAs) are secreted by the embryo into the ECCM and test the limit of detection for profiling sncRNA by deep sequencing and quantitative PCR. In the first set of experiments, we evaluated sequencing sensitivity by comparing sncRNA profiles from pools of 10, 5, 3, and single ECCM drops. Next, we performed a similar test for TaqMan qPCR sensitivity by measuring select sncRNAs in 5, 3 and single drop ECCM pools. Finally, we compared the expression of an sncRNA panel by qPCR in single ECCM vs no-embryo control media . We report the first comprehensive sequencing of sncRNAs in ECCM with a sequencing sensitivity of 3 single embryo drops, capturing ~150 miRNAs and an abundance of tRNA-derived small RNAs (tsRNAs). We then profiled 15 sncRNAs by qPCR and determined that the assay maintains sensitivity in single ECCM drops. Finally, we found significant differences in these sncRNA expression between control and ECCM drops. Improving embryo selection is crucial for reducing time to pregnancy. Here we describe a sensitive technique for biomarker discovery by sequencing and qPCR validation in ECCM, demonstrating that the majority of sncRNAs are embryo derived. We also report an abundance of tsRNAs which suggests these sncRNAs may have functions in endometrial-maternal communication beyond the microRNAs which have been described previously.Abbreviations: PGT-A: Preimplantation genetic testing for aneuploidies; ECCM: Embryo-conditioned culture media; sncRNAs: Small non-coding RNAs; miRNAs: microRNAs; EVs: Extracellular vesicles; PCA: Principal component analysis.
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Affiliation(s)
| | | | | | - Clifford Librach
- Create Fertility Centre, Toronto, Ontario, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada.,Department of Obstetrics and Gynecology, Women's College Hospital, Toronto, Ontario, Canada
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