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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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Herridge RP, Dolata J, Migliori V, de Santis Alves C, Borges F, Schorn AJ, van Ex F, Lin A, Bajczyk M, Parent JS, Leonardi T, Hendrick A, Kouzarides T, Martienssen RA. Pseudouridine guides germline small RNA transport and epigenetic inheritance. Nat Struct Mol Biol 2024:10.1038/s41594-024-01392-6. [PMID: 39242979 DOI: 10.1038/s41594-024-01392-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/15/2024] [Indexed: 09/09/2024]
Abstract
Developmental epigenetic modifications in plants and animals are mostly reset during gamete formation but some are inherited from the germline. Small RNAs guide these epigenetic modifications but how inherited small RNAs are distinguished in plants and animals is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs. Germline small RNAs, namely epigenetically activated small interfering RNAs (easiRNAs) in Arabidopsis pollen and Piwi-interacting RNAs in mouse testes, are enriched for Ψ. In pollen, pseudouridylated easiRNAs are transported to sperm cells from the vegetative nucleus, and PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ and is required for this transport. We further show that Exportin-t is required for the triploid block: small RNA dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, Ψ has a conserved role in marking inherited small RNAs in the germline.
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Affiliation(s)
- Rowan P Herridge
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Jakub Dolata
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Valentina Migliori
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- CNRS, INRA Versailles, Versailles, France
| | - Andrea J Schorn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Frédéric van Ex
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Inari LLC, Ghent, Belgium
| | - Ann Lin
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Stanford University, Stanford, CA, USA
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Jean-Sebastien Parent
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Agriculture Canada, Ottawa, Ontario, Canada
| | - Tommaso Leonardi
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Center for Genomic Science of IIT@SEMM, Instituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Alan Hendrick
- Storm Therapeutics, Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge, UK
| | | | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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3
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Du L, Chen W, Zhang D, Cui Y, He Z. The functions and mechanisms of piRNAs in mediating mammalian spermatogenesis and their applications in reproductive medicine. Cell Mol Life Sci 2024; 81:379. [PMID: 39222270 PMCID: PMC11369131 DOI: 10.1007/s00018-024-05399-6] [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: 01/09/2024] [Revised: 07/10/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
As the most abundant small RNAs, piwi-interacting RNAs (piRNAs) have been identified as a new class of non-coding RNAs with 24-32 nucleotides in length, and they are expressed at high levels in male germ cells. PiRNAs have been implicated in the regulation of several biological processes, including cell differentiation, development, and male reproduction. In this review, we focused on the functions and molecular mechanisms of piRNAs in controlling spermatogenesis, including genome stability, regulation of gene expression, and male germ cell development. The piRNA pathways include two major pathways, namely the pre-pachytene piRNA pathway and the pachytene piRNA pathway. In the pre-pachytene stage, piRNAs are involved in chromosome remodeling and gene expression regulation to maintain genome stability by inhibiting transposon activity. In the pachytene stage, piRNAs mediate the development of male germ cells via regulating gene expression by binding to mRNA and RNA cleavage. We further discussed the correlations between the abnormalities of piRNAs and male infertility and the prospective of piRNAs' applications in reproductive medicine and future studies. This review provides novel insights into mechanisms underlying mammalian spermatogenesis and offers new targets for diagnosing and treating male infertility.
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Affiliation(s)
- Li Du
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University School of Medicine, The Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, 410013, China
| | - Wei Chen
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University School of Medicine, The Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, 410013, China
| | - Dong Zhang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University School of Medicine, The Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, 410013, China
| | - Yinghong Cui
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University School of Medicine, The Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, 410013, China
| | - Zuping He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University School of Medicine, The Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, 410013, China.
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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McJunkin K, Gottesman S. What goes up must come down: off switches for regulatory RNAs. Genes Dev 2024; 38:597-613. [PMID: 39111824 PMCID: PMC11368247 DOI: 10.1101/gad.351934.124] [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] [Indexed: 08/22/2024]
Abstract
Small RNAs base pair with and regulate mRNA translation and stability. For both bacterial small regulatory RNAs and eukaryotic microRNAs, association with partner proteins is critical for the stability and function of the regulatory RNAs. We review the mechanisms for degradation of these RNAs: displacement of the regulatory RNA from its protein partner (in bacteria) or destruction of the protein and its associated microRNAs (in eukaryotes). These mechanisms can allow specific destruction of a regulatory RNA via pairing with a decay trigger RNA or function as global off switches by disrupting the stability or function of the protein partner.
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Affiliation(s)
- Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, Maryland 20892, USA;
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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5
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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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6
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Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
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Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
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7
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Pavelka J, Poláková S, Pavelková V, Galeta P. An epigenetic change in a moth is generated by temperature and transmitted to many subsequent generations mediated by RNA. PLoS One 2024; 19:e0292179. [PMID: 38451888 PMCID: PMC10919628 DOI: 10.1371/journal.pone.0292179] [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: 10/28/2022] [Accepted: 09/14/2023] [Indexed: 03/09/2024] Open
Abstract
Epigenetic changes in sexually reproducing animals may be transmitted usually only through a few generations. Here we discovered a case where epigenetic change lasts 40 generations. This epigenetic phenomenon occurs in the short antennae (sa) mutation of the flour moth (Ephestia kuehniella). We demonstrate that is probably determined by a small RNA (e.g., piRNA, miRNA, tsRNA) and transmitted in this way to subsequent generations through the male and female gametes. The observed epigenetic change cancels sa mutation and creates a wild phenotype (a moth that appears to have no mutation). It persists for many generations (40 recorded). This epigenetic transgenerational effect (suppression homozygous mutation for short antennae) in the flour moth is induced by changes during ontogenetic development, such as increased temperature on pupae development, food, different salts in food, or injection of RNA from the sperm of already affected individuals into the eggs. The epigenetic effect may occasionally disappear in some individuals and/or progeny of a pair in the generation chain in which the effect transfers. We consider that the survival of RNA over many generations has adaptive consequences. It is mainly a response to environmental change that is transmitted to offspring via RNA. In this study, we test an interesting epigenetic effect with an unexpected length after 40 generations and test what is its cause. Such transfer of RNA to subsequent generations may have a greater evolutionary significance than previously thought. Based on some analogies, we also discuss of the connection with the SIR2 gene.
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Affiliation(s)
- Jaroslav Pavelka
- University of West Bohemia, Centre of Biology, Pilsen, Czech Republic
| | - Simona Poláková
- Ministry of the Environment of the Czech Republic, Praha, Czech Republic
| | - Věra Pavelková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Patrik Galeta
- Department of Anthropology, University of West Bohemia, Pilsen, Czech Republic
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8
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Li J, Hong X, Jiang M, Kho AT, Tiwari A, Wang AL, Chase RP, Celedón JC, Weiss ST, McGeachie MJ, Tantisira KG. A novel piwi-interacting RNA associates with type 2-high asthma phenotypes. J Allergy Clin Immunol 2024; 153:695-704. [PMID: 38056635 DOI: 10.1016/j.jaci.2023.10.032] [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: 02/23/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs), comprising the largest noncoding RNA group, regulate transcriptional processes. Whether piRNAs are associated with type 2 (T2)-high asthma is unknown. OBJECTIVE We sought to investigate the association between piRNAs and T2-high asthma in childhood asthma. METHODS We sequenced plasma samples from 462 subjects in the Childhood Asthma Management Program (CAMP) as the discovery cohort and 1165 subjects in the Genetics of Asthma in Costa Rica Study (GACRS) as a replication cohort. Sequencing reads were filtered first, and piRNA reads were annotated and normalized. Linear regression was used for the association analysis of piRNAs and peripheral blood eosinophil count, total serum IgE level, and long-term asthma exacerbation in children with asthma. Mediation analysis was performed to investigate the effect direction. We then ascertained if the circulating piRNAs were present in asthmatic airway epithelial cells in a Gene Expression Omnibus (GEO; www.ncbi.nlm.nih.gov/geo) public data set. RESULTS Fifteen piRNAs were significantly associated with eosinophil count in CAMP (P ≤ .05), and 3 were successfully replicated in GACRS. Eleven piRNAs were associated with total IgE in CAMP, and one of these was replicated in GACRS. All 22 significant piRNAs were identified in epithelial cells in vitro, and 6 of these were differentially expressed between subjects with asthma and healthy controls. Fourteen piRNAs were associated with long-term asthma exacerbation, and effect of piRNAs on long-term asthma exacerbation are mediated through eosinophil count and serum IgE level. CONCLUSION piRNAs are associated with peripheral blood eosinophils and total serum IgE in childhood asthma and may play important roles in T2-high asthma.
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Affiliation(s)
- Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Computational Health Informatics Program, Boston Children's Hospital, Boston, Mass
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pa
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Partners Personalized Medicine, Partners Healthcare, Boston, Mass
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego, La Jolla, Calif.
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9
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Wei C, Yan X, Mann JM, Geng R, Xie H, Demireva EY, Sun L, Ding D, Chen C. PNLDC1 catalysis and postnatal germline function are required for piRNA trimming, LINE1 silencing, and spermatogenesis in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573375. [PMID: 38234819 PMCID: PMC10793440 DOI: 10.1101/2023.12.26.573375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
PIWI-interacting RNAs (piRNAs) play critical and conserved roles in transposon silencing and gene regulation in the animal germline. Two distinct piRNA populations are present during mouse spermatogenesis: pre-pachytene piRNAs in fetal/neonatal testes and pachytene piRNAs in adult testes. PNLDC1 is required for both pre-pachytene piRNA and pachytene piRNA 3' end maturation in multiple species. However, whether PNLDC1 is the bona fide piRNA trimmer and the physiological role of 3' trimming of two distinct piRNA populations in spermatogenesis remain unclear. Here, by inactivating Pnldc1 exonuclease activity in vitro and in mice, we reveal that PNLDC1 trimmer activity is required for both pre-pachytene piRNA and pachytene piRNA 3' end trimming and male fertility. Furthermore, conditional inactivation of Pnldc1 in postnatal germ cells causes LINE1 transposon de-repression and spermatogenic arrest in mice. This indicates that pachytene piRNA trimming, but not pre-pachytene piRNA trimming, is essential for mouse germ cell development and transposon silencing. Our findings highlight the potential of inhibiting germline piRNA trimmer activity as a potential means for male contraception.
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Affiliation(s)
- Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824, USA
| | - Xiaoyuan Yan
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824, USA
| | - Jeffrey M. Mann
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824, USA
| | - Ruirong Geng
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Huirong Xie
- Transgenic and Genome Editing Facility, Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Elena Y. Demireva
- Transgenic and Genome Editing Facility, Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Deqiang Ding
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan 49503, USA
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10
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Säflund M, Özata DM. The MYBL1/TCFL5 transcription network: two collaborative factors with central role in male meiosis. Biochem Soc Trans 2023; 51:2163-2172. [PMID: 38015556 PMCID: PMC10754281 DOI: 10.1042/bst20231007] [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: 08/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
Male gametogenesis, spermatogenesis, is a stepwise developmental process to generate mature sperm. The most intricate process of spermatogenesis is meiosis during which two successive cell divisions ensue with dramatic cellular and molecular changes to produce haploid cells. After entry into meiosis, several forms of regulatory events control the orderly progression of meiosis and the timely entry into post-meiotic sperm differentiation. Among other mechanisms, changes to gene expression are controlled by key transcription factors. In this review, we will discuss the gene regulatory mechanisms underlying meiotic entry, meiotic progression, and post-meiotic differentiation with a particular emphasis on the MYBL1/TCFL5 regulatory architecture and how this architecture involves in various forms of transcription network motifs to regulate gene expression.
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Affiliation(s)
- Martin Säflund
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Deniz M. Özata
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
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11
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Herridge RP, Dolata J, Migliori V, de Santis Alves C, Borges F, Schorn AJ, Van Ex F, Parent JS, Lin A, Bajczyk M, Leonardi T, Hendrick A, Kouzarides T, Martienssen RA. Pseudouridine guides germline small RNA transport and epigenetic inheritance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542553. [PMID: 37398006 PMCID: PMC10312437 DOI: 10.1101/2023.05.27.542553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes1. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation2,3. In C. elegans, these inherited small RNAs have poly (UG) tails4, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop novel assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors. We also detect substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and piwi-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are localized to sperm cells, and we found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ and is required for transport of easiRNAs into sperm cells from the vegetative nucleus. We further show that Exportin-t is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, Ψ has a conserved role in marking inherited small RNAs in the germline.
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Affiliation(s)
- Rowan P Herridge
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Jakub Dolata
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Valentina Migliori
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Andrea J Schorn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Frédéric Van Ex
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Jean-Sebastien Parent
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Ann Lin
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Tommaso Leonardi
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Center for Genomic Science of IIT@SEMM, Instituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Alan Hendrick
- Storm Therapeutics, Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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12
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Zhang Z, Liu N. PIWI interacting RNA-13643 contributes to papillary thyroid cancer development through acting as a novel oncogene by facilitating PRMT1 mediated GLI1 methylation. Biochim Biophys Acta Gen Subj 2023; 1867:130453. [PMID: 37657666 DOI: 10.1016/j.bbagen.2023.130453] [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: 11/22/2022] [Revised: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Recently, aberrant expression of PIWI-interacting RNAs (piRNAs) has been discovered in a variety of cancer cells. However, the roles of PIWI proteins and piRNAs in papillary thyroid carcinoma (PTC) are still elusive. METHODS RT-qPCR and Northern blotting were used to evaluate piR-13643 levels in PTC and para-carcinoma tissues, as well as in PTC cell lines. piR-13643 mimic and piR-13643 inhibitor were transfected into K-1 and B-CPAP cells. CCK-8, Transwell, annexin V-FITC/PI, flow cytometry and Western blot assays were performed to measure cell proliferation, invasion, apoptosis, cell cycle and E-cadherin and Vimentin proteins, respectively. Total RNA from B-CPAP cells was pulled down with PIWIL1, PIWIL2, or PIWIL3 specific antibodies or IgG as a control, respectively, followed by detection of piR-13643 expression with RT-qPCR. Immunoblotting of PRMT1 was detected in piR-13643 / PIWIL1 complex immune-precipitates by Co-IP assay. Subsequently, PRMT1 protein expression was detected by stably transfection of Flag tagged GLI1 (Flag-GLI1) into B-CPAP cells. Methylation assay with PRMT1 and wild-type or R597 lysine (R597K)-mutant GLI1. Then rescue experiments were applied to explore effects of piR-13643 and GLI1 on the malignant behavior of PTC cells. B-CPAP cells transfected with piR-13643 inhibitor were subcutaneously injected into nude mice to evaluate the effect of piR-13643 knockdown on the xenograft tumor growth of PTC. RESULTS piR-13643 was elevated in PTC patient specimens and cell lines. piR-13643 overexpression facilitated cell proliferation, invasion and Vimentin level, and restrained apoptosis and E-cadherin expression, whereas piR-13643 knockdown showed the opposite results. Mechanically, piR-13643 could bind to PIWIL1 to form the PIWIL1/piR-13643 complex, and PRMT1 enhanced GLI1 transcription by methylating GLI1 at R597. Further, PIWIL1/piR-13643 promoted PRMT1-mediated GLI1 methylation. GLI1 knockdown countered the effects of piR-13643 mimic on cell malignant behaviors. piR-13643 knockdown preeminently prevented the xenograft tumor growth of PTC in vivo. CONCLUSIONS This study confirmed that piR-13643 facilitates PTC malignant behaviors in vitro and in vivo by promoting PRMT1-mediated GLI1 methylation via forming a complex with PIWIL1, which may provide a novel insight for PTC treatment.
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Affiliation(s)
- Zhongbo Zhang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Ning Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.
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13
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Venkei ZG, Gainetdinov I, Bagci A, Starostik MR, Choi CP, Fingerhut JM, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, Yamashita YM. A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila. Nat Cell Biol 2023; 25:1495-1505. [PMID: 37723298 PMCID: PMC10567549 DOI: 10.1038/s41556-023-01227-4] [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: 09/26/2022] [Accepted: 08/09/2023] [Indexed: 09/20/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) direct PIWI proteins to silence complementary targets such as transposons. In Drosophila and other species with a maternally specified germline, piRNAs deposited in the egg initiate piRNA biogenesis in the progeny. However, Y chromosome loci cannot participate in such a chain of intergenerational inheritance. How then can the biogenesis of Y-linked piRNAs be initiated? Here, using Suppressor of Stellate (Su(Ste)), a Y-linked Drosophila melanogaster piRNA locus as a model, we show that Su(Ste) piRNAs are made in the early male germline via 5'-to-3' phased piRNA biogenesis initiated by maternally deposited 1360/Hoppel transposon piRNAs. Notably, deposition of Su(Ste) piRNAs from XXY mothers obviates the need for phased piRNA biogenesis in sons. Together, our study uncovers a developmentally programmed, intergenerational mechanism that allows fly mothers to protect their sons using a Y-linked piRNA locus.
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Affiliation(s)
- Zsolt G Venkei
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ayca Bagci
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Charlotte P Choi
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peiwei Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chiraag Balsara
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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14
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Gou LT, Zhu Q, Liu MF. Small RNAs: An expanding world with therapeutic promises. FUNDAMENTAL RESEARCH 2023; 3:676-682. [PMID: 38933305 PMCID: PMC11197668 DOI: 10.1016/j.fmre.2023.03.003] [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: 12/09/2022] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 04/09/2023] Open
Abstract
Small non-coding RNAs (sncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNA (tRNA)-derived small RNAs (tsRNAs), play essential roles in regulating various cellular and developmental processes. Over the past three decades, researchers have identified novel sncRNA species from various organisms. These molecules demonstrate dynamic expression and diverse functions, and they are subject to intricate regulation through RNA modifications in both healthy and diseased states. Notably, certain sncRNAs in gametes, particularly sperm, respond to environmental stimuli and facilitate epigenetic inheritance. Collectively, the in-depth understanding of sncRNA functions and mechanisms has accelerated the development of small RNA-based therapeutics. In this review, we present the recent advances in the field, including new sncRNA species and the regulatory influences of RNA modifications. We also discuss the current limitations and challenges associated with using small RNAs as either biomarkers or therapeutic drugs.
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Affiliation(s)
- Lan-Tao Gou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qifan Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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15
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van Wolfswinkel JC. Insights in piRNA targeting rules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1811. [PMID: 37632327 PMCID: PMC10895071 DOI: 10.1002/wrna.1811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023]
Abstract
PIWI-interacting RNAs (piRNAs) play an important role in the defense against transposons in the germline and stem cells of animals. To what extent other transcripts are also regulated by piRNAs is an ongoing topic of debate. The amount of sequence complementarity between piRNA and target that is required for effective downregulation of the targeted transcript is guiding in this discussion. Over the years, various methods have been applied to infer targeting requirements from the collections of piRNAs and potential target transcripts, and recent structural studies of the PIWI proteins have provided an additional perspective. In this review, I summarize the findings from these studies and propose a set of requirements that can be used to predict targets to the best of our current abilities. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA-Based Catalysis > RNA-Mediated Cleavage.
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Affiliation(s)
- Josien C van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Center for Stem Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
- Center for RNA Biology and Medicine, Yale School of Medicine, New Haven, Connecticut, USA
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16
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Mann JM, Wei C, Chen C. How genetic defects in piRNA trimming contribute to male infertility. Andrology 2023; 11:911-917. [PMID: 36263612 PMCID: PMC10115909 DOI: 10.1111/andr.13324] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/25/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022]
Abstract
In germ cells, small non-coding PIWI-interacting RNAs (piRNAs) work to silence harmful transposons to maintain genomic stability and regulate gene expression to ensure fertility. However, these piRNAs must undergo a series of steps during biogenesis to be properly loaded onto PIWI proteins and reach the correct nucleotide length. This review is focused on what we are learning about a crucial step in this process, piRNA trimming, in which pre-piRNAs are shortened to final lengths of 21-35 nucleotides. Recently, the 3'-5' exonuclease trimmer has been identified in various models as PNLDC1/PARN-1. Mutations of the piRNA trimmers in vivo lead to increased transposon expression, elevated levels of untrimmed pre-piRNAs, decreased piRNA stability, and male infertility. Here, we will discuss the role of piRNA trimmers in piRNA biogenesis and function, describe consequences of piRNA trimmer mutations using mammalian models and human patients, and examine future avenues of piRNA trimming-related study for clinical advancements for male infertility.
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Affiliation(s)
- Jeffrey M. Mann
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA
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17
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Gainetdinov I, Vega-Badillo J, Cecchini K, Bagci A, Colpan C, De D, Bailey S, Arif A, Wu PH, MacRae IJ, Zamore PD. Relaxed targeting rules help PIWI proteins silence transposons. Nature 2023:10.1038/s41586-023-06257-4. [PMID: 37344600 PMCID: PMC10338343 DOI: 10.1038/s41586-023-06257-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023]
Abstract
In eukaryotes, small RNA guides, such as small interfering RNAs and microRNAs, direct AGO-clade Argonaute proteins to regulate gene expression and defend the genome against external threats. Only animals make a second clade of Argonaute proteins: PIWI proteins. PIWI proteins use PIWI-interacting RNAs (piRNAs) to repress complementary transposon transcripts1,2. In theory, transposons could evade silencing through target site mutations that reduce piRNA complementarity. Here we report that, unlike AGO proteins, PIWI proteins efficiently cleave transcripts that are only partially paired to their piRNA guides. Examination of target binding and cleavage by mouse and sponge PIWI proteins revealed that PIWI slicing tolerates mismatches to any target nucleotide, including those flanking the scissile phosphate. Even canonical seed pairing is dispensable for PIWI binding or cleavage, unlike plant and animal AGOs, which require uninterrupted target pairing from the seed to the nucleotides past the scissile bond3,4. PIWI proteins are therefore better equipped than AGO proteins to target newly acquired or rapidly diverging endogenous transposons without recourse to new small RNA guides. Conversely, the minimum requirements for PIWI slicing are sufficient to avoid inadvertent silencing of host RNAs. Our results demonstrate the biological advantage of PIWI over AGO proteins in defending the genome against transposons and suggest an explanation for why the piRNA pathway was retained in animal evolution.
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Affiliation(s)
- Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Joel Vega-Badillo
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Katharine Cecchini
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ayca Bagci
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cansu Colpan
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Voyager Therapeutics, Cambridge, MA, USA
| | - Dipayan De
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shannon Bailey
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amena Arif
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Beam Therapeutics, Cambridge, MA, USA
| | - Pei-Hsuan Wu
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- University of Geneva, Geneva, Switzerland
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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18
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Limanówka P, Ochman B, Świętochowska E. PiRNA Obtained through Liquid Biopsy as a Possible Cancer Biomarker. Diagnostics (Basel) 2023; 13:diagnostics13111895. [PMID: 37296747 DOI: 10.3390/diagnostics13111895] [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: 04/20/2023] [Revised: 05/21/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
In recent years PIWI-interacting RNAs (piRNAs) have gained the interest of scientists, mainly because of their possible implications in cancer. Many kinds of research showed how their expression can be linked to malignant diseases. However, most of them evaluated the expression of piRNAs in tumor tissues. It was shown how these non-coding RNAs can interfere with many signaling pathways involved in the regulation of proliferation or apoptosis. A comparison of piRNA expression in tumor tissue and adjacent healthy tissues has demonstrated they can be used as biomarkers. However, this way of obtaining samples has a significant drawback, which is the invasiveness of such a procedure. Liquid biopsy is an alternative for acquiring biological material with little to no harm to a patient. Several different piRNAs in various types of cancer were shown to be expressed in bodily fluids such as blood or urine. Furthermore, their expression significantly differed between cancer patients and healthy individuals. Hence, this review aimed to assess the possible use of liquid biopsy for cancer diagnosis with piRNAs as biomarkers.
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Affiliation(s)
- Piotr Limanówka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Błażej Ochman
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
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19
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Uddin N, Binzel DW, Shu D, Fu TM, Guo P. Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome. Acta Pharm Sin B 2023; 13:1383-1399. [PMID: 37139430 PMCID: PMC10149909 DOI: 10.1016/j.apsb.2022.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022] Open
Abstract
Exosome is an excellent vesicle for in vivo delivery of therapeutics, including RNAi and chemical drugs. The extremely high efficiency in cancer regression can partly be attributed to its fusion mechanism in delivering therapeutics to cytosol without endosome trapping. However, being composed of a lipid-bilayer membrane without specific recognition capacity for aimed-cells, the entry into nonspecific cells can lead to potential side-effects and toxicity. Applying engineering approaches for targeting-capacity to deliver therapeutics to specific cells is desirable. Techniques with chemical modification in vitro and genetic engineering in cells have been reported to decorate exosomes with targeting ligands. RNA nanoparticles have been used to harbor tumor-specific ligands displayed on exosome surface. The negative charge reduces nonspecific binding to vital cells with negatively charged lipid-membrane due to the electrostatic repulsion, thus lowering the side-effect and toxicity. In this review, we focus on the uniqueness of RNA nanoparticles for exosome surface display of chemical ligands, small peptides or RNA aptamers, for specific cancer targeting to deliver anticancer therapeutics, highlighting recent advances in targeted delivery of siRNA and miRNA that overcomes the previous RNAi delivery roadblocks. Proper understanding of exosome engineering with RNA nanotechnology promises efficient therapies for a wide range of cancer subtypes.
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Affiliation(s)
- Nasir Uddin
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Daniel W. Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Dan Shu
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry & Pharmacology, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
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20
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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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21
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The epigenetic regulatory mechanism of PIWI/piRNAs in human cancers. Mol Cancer 2023; 22:45. [PMID: 36882835 PMCID: PMC9990219 DOI: 10.1186/s12943-023-01749-3] [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: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
PIWI proteins have a strong correlation with PIWI-interacting RNAs (piRNAs), which are significant in development and reproduction of organisms. Recently, emerging evidences have indicated that apart from the reproductive function, PIWI/piRNAs with abnormal expression, also involve greatly in varieties of human cancers. Moreover, human PIWI proteins are usually expressed only in germ cells and hardly in somatic cells, so the abnormal expression of PIWI proteins in different types of cancer offer a promising opportunity for precision medicine. In this review, we discussed current researches about the biogenesis of piRNA, its epigenetic regulatory mechanisms in human cancers, such as N6-methyladenosine (m6A) methylation, histone modifications, DNA methylation and RNA interference, providing novel insights into the markers for clinical diagnosis, treatment and prognosis in human cancers.
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22
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Wang X, Ramat A, Simonelig M, Liu MF. Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nat Rev Mol Cell Biol 2023; 24:123-141. [PMID: 36104626 DOI: 10.1038/s41580-022-00528-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 02/02/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with proteins of the PIWI clade of the Argonaute family. First identified in animal germ line cells, piRNAs have essential roles in germ line development. The first function of PIWI-piRNA complexes to be described was the silencing of transposable elements, which is crucial for maintaining the integrity of the germ line genome. Later studies provided new insights into the functions of PIWI-piRNA complexes by demonstrating that they regulate protein-coding genes. Recent studies of piRNA biology, including in new model organisms such as golden hamsters, have deepened our understanding of both piRNA biogenesis and piRNA function. In this Review, we discuss the most recent advances in our understanding of piRNA biogenesis, the molecular mechanisms of piRNA function and the emerging roles of piRNAs in germ line development mainly in flies and mice, and in infertility, cancer and neurological diseases in humans.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Anne Ramat
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
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23
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Han J, Mendell JT. MicroRNA turnover: a tale of tailing, trimming, and targets. Trends Biochem Sci 2023; 48:26-39. [PMID: 35811249 PMCID: PMC9789169 DOI: 10.1016/j.tibs.2022.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) post-transcriptionally repress gene expression by guiding Argonaute (AGO) proteins to target mRNAs. While much is known about the regulation of miRNA biogenesis, miRNA degradation pathways are comparatively poorly understood. Although miRNAs generally exhibit slow turnover, they can be rapidly degraded through regulated mechanisms that act in a context- or sequence-specific manner. Recent work has revealed a particularly important role for specialized target interactions in controlling rates of miRNA degradation. Engagement of these targets is associated with the addition and removal of nucleotides from the 3' ends of miRNAs, a process known as tailing and trimming. Here we review these mechanisms of miRNA modification and turnover, highlighting the contexts in which they impact miRNA stability and discussing important questions that remain unanswered.
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Affiliation(s)
- Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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24
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Arif A, Bailey S, Izumi N, Anzelon TA, Ozata DM, Andersson C, Gainetdinov I, MacRae IJ, Tomari Y, Zamore PD. GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins. Nature 2022; 608:618-625. [PMID: 35772669 PMCID: PMC9385479 DOI: 10.1038/s41586-022-05009-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Argonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins have diverse biological functions and many retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, the PIWI proteins-a specialized class of Argonaute proteins-use 21-35 nucleotide PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalysed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2) and MIWI22-4 (PIWIL4). The piRNA-guided endoribonuclease activities of MIWI and MILI are essential for the production of functional sperm5,6. piRNA-directed silencing in mice and insects also requires GTSF1, a PIWI-associated protein of unknown function7-12. Here we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 is thus an example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.
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Affiliation(s)
- Amena Arif
- Department of Biochemistry and Molecular Biotechnology Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Beam Therapeutics, Cambridge, MA, USA
| | - Shannon Bailey
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Natsuko Izumi
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Todd A Anzelon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Deniz M Ozata
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Cecilia Andersson
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Phillip D Zamore
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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25
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Abstract
Small RNAs are ubiquitous regulators of gene expression that participate in nearly all aspects of physiology in a wide range of organisms. There are many different classes of eukaryotic small RNAs that play regulatory roles at every level of gene expression, including transcription, RNA stability, and translation. While eukaryotic small RNAs display diverse functions across and within classes, they are generally grouped functionally based on the machinery required for their biogenesis, the effector proteins they associate with, and their molecular characteristics. The development of techniques to clone and sequence small RNAs has been critical for their identification, yet the ligation-dependent addition of RNA adapters and the use of reverse transcriptase to generate cDNA in traditional library preparation protocols can be unsuitable to detect certain small RNA subtypes. In particular, 3' or 5' chemical modifications that are characteristic of specific types of small RNAs can impede the ligation-dependent addition of RNA adapters, while internal RNA modifications can interfere with accurate reverse transcription. The inability to clone certain small RNA subtypes with traditional protocols results in an inaccurate assessment of small RNA abundance and diversity, where some RNAs appear over-represented and others are not detected. This overview aims to guide users on how to design small RNA cloning workflows in eukaryotes to more accurately capture specific small RNAs of interest. Hence, we discuss the molecular biology underlying the identification and quantitation of small RNAs, explore the limitations of commonly used protocols, and detail the alternative approaches that can be used to enrich specific small RNA classes. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Olivia J Crocker
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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26
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Saritas G, Main AM, Winge SB, Mørup N, Almstrup K. PIWI-interacting RNAs and human testicular function. WIREs Mech Dis 2022; 14:e1572. [PMID: 35852002 PMCID: PMC9788060 DOI: 10.1002/wsbm.1572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022]
Abstract
Small noncoding RNAs (sncRNAs) are pieces of RNA with a length below 200 bp and represent a diverse group of RNAs having many different biological functions. The best described subtype is the microRNAs which primarily function in posttranscriptional gene regulation and appear essential for most physiological processes. Of particular interest for the germline is the PIWI-interacting RNAs (piRNAs) which are a class of sncRNA of 21-35 bp in length that are almost exclusively found in germ cells. Recently, it has become clear that piRNAs are essential for testicular function, and in this perspective, we outline the current knowledge of piRNAs in humans. Although piRNAs appear unique to germ cells, they have also been described in various somatic cancers and biofluids. Here, we discuss the potential function of piRNAs in somatic tissues and whether detection in biofluids may be used as a biomarker for testicular function. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Gülizar Saritas
- The Department of Growth and ReproductionCopenhagen University HospitalCopenhagenDenmark,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC)CopenhagenDenmark
| | - Ailsa Maria Main
- The Department of Growth and ReproductionCopenhagen University HospitalCopenhagenDenmark,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC)CopenhagenDenmark
| | - Sofia Boeg Winge
- The Department of Growth and ReproductionCopenhagen University HospitalCopenhagenDenmark,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC)CopenhagenDenmark
| | - Nina Mørup
- The Department of Growth and ReproductionCopenhagen University HospitalCopenhagenDenmark,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC)CopenhagenDenmark
| | - Kristian Almstrup
- The Department of Growth and ReproductionCopenhagen University HospitalCopenhagenDenmark,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC)CopenhagenDenmark,The Department of Cellular and Molecular MedicineFaculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
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27
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Li X, Peng J, Yi C. The epitranscriptome of small non-coding RNAs. Noncoding RNA Res 2021; 6:167-173. [PMID: 34820590 PMCID: PMC8581453 DOI: 10.1016/j.ncrna.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
Small non-coding RNAs are short RNA molecules and involved in many biological processes, including cell proliferation and differentiation, immune response, cell death, epigenetic regulation, metabolic control. A diversity of RNA modifications have been identified in these small non-coding RNAs, including transfer RNAs (tRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNA (snRNA), small nucleolar RNAs (snoRNAs), and tRNA-derived small RNAs (tsRNAs). These post-transcriptional modifications are involved in the biogenesis and function of these small non-coding RNAs. In this review, we will summarize the existence of RNA modifications in the small non-coding RNAs and the emerging roles of these epitranscriptomic marks.
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Affiliation(s)
- Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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