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Vestergaard AL, Andersen MK, Olesen RV, Bor P, Larsen A. High-Dose Vitamin D Supplementation Significantly Affects the Placental Transcriptome. Nutrients 2023; 15:5032. [PMID: 38140291 PMCID: PMC10745524 DOI: 10.3390/nu15245032] [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: 11/04/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Vitamin D deficiency is a highly prevalent obstetrical concern associated with an increased risk of complications like pre-eclampsia, gestational diabetes, and growth retardation. Vitamin D status in pregnancy is also linked to long-term offspring health, e.g., the risk of obesity, metabolic disease, and neurodevelopmental problems. Despite the suspected role of vitamin D in placental diseases and fetal development, there is limited knowledge on the effect of vitamin D on placental function. Thus, we performed next-generation RNA sequencing, comparing the placental transcriptome from uncomplicated term pregnancies receiving the often-recommended dose of 10 µg vitamin D/day (n = 36) with pregnancies receiving 90 µg/day (n = 34) from late first trimester to delivery. Maternal vitamin D status in the first trimester was also considered. We found that signaling pathways related to cell adhesion, immune function, and neurodevelopment were affected, supporting that increased vitamin D supplementation benefits placental function in established pregnancies without severe vitamin D deficiency, also underlining the importance of vitamin D in brain development. Specific effects of the first trimester vitamin D status and offspring sex were also identified. Further studies are warranted, addressing the optimal vitamin status during pregnancy with a focus on organ-specific vitamin D needs in individual pregnancies.
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Affiliation(s)
- Anna Louise Vestergaard
- Department of Obstetrics and Gynecology, Randers Regional Hospital, 8930 Randers, Denmark (P.B.)
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
| | - Matilde K. Andersen
- Department of Obstetrics and Gynecology, Randers Regional Hospital, 8930 Randers, Denmark (P.B.)
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark (A.L.)
| | - Rasmus V. Olesen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark (A.L.)
| | - Pinar Bor
- Department of Obstetrics and Gynecology, Randers Regional Hospital, 8930 Randers, Denmark (P.B.)
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
- Department of Obstetrics and Gynecology, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Agnete Larsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark (A.L.)
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2
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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3
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Zhang X, Xie Q, Xiang L, Lei Z, Huang Q, Zhang J, Cai M, Chen T. AtSIEK, an EXD1-like protein with KH domain, involves in salt stress response by interacting with FRY2/CPL1. Int J Biol Macromol 2023; 233:123369. [PMID: 36693612 DOI: 10.1016/j.ijbiomac.2023.123369] [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: 11/27/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Abiotic stress has great impacts on plant germination, growth and development and crop yield. Therefore, it is important to understand the molecular mechanism of plants response to abiotic stress. In this study, we identified a plant specific protein AtSIEK (stress-induced protein with EXD1-like domain and KH domain) response to salt stress. AtSIEK encodes a hnRNP K homology (KH) protein localized in nucleus. Amino acid sequences analysis found that SIEK protein is specific in plants, containing two domains with EXD1-like domain and KH domain, while SIEK homolog in animals only had EXD1-like domain without KH domain. Physiology experiments revealed that AtSIEK was significantly induced under salt stress and the siek mutant shows sensitive to salt stress, indicating that AtSIEK was a positive regulator in stress response. Further, molecular, biochemical, and genetic assays suggested that AtSIEK interacts with FRY2/CPL1, a known regulator in response to abiotic stress, and they function synergistically in response to salt stress. Taken together, these results shed new light on the regulation of plant adaption to abiotic stress, which deepen our understanding of the molecular mechanisms of abiotic stress regulation in plants.
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Affiliation(s)
- Xiangxiang Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Qinyu Xie
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Lijun Xiang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Zhonghua Lei
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Qixiu Huang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Juncheng Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Maohong Cai
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China.
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China.
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4
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Olotu O, Dowling M, Homolka D, Wojtas MN, Tran P, Lehtiniemi T, Da Ros M, Pillai RS, Kotaja N. Intermitochondrial cement (IMC) harbors piRNA biogenesis machinery and exonuclease domain-containing proteins EXD1 and EXD2 in mouse spermatocytes. Andrology 2023; 11:710-723. [PMID: 36624638 DOI: 10.1111/andr.13361] [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: 09/16/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Germ granules are large cytoplasmic ribonucleoprotein complexes that emerge in the germline to participate in RNA regulation. The two most prominent germ granules are the intermitochondrial cement (IMC) in meiotic spermatocytes and the chromatoid body (CB) in haploid round spermatids, both functionally linked to the PIWI-interacting RNA (piRNA) pathway. AIMS In this study, we clarified the IMC function by identifying proteins that form complexes with a well-known IMC protein PIWIL2/MILI in the mouse testis. RESULTS The PIWIL2 interactome included several proteins with known functions in piRNA biogenesis. We further characterized the expression and localization of two of the identified proteins, Exonuclease 3'-5' domain-containing proteins EXD1 and EXD2, and confirmed their localization to the IMC. We showed that EXD2 interacts with PIWIL2, and that the mutation of Exd2 exonuclease domain in mice induces misregulation of piRNA levels originating from specific pachytene piRNA clusters, but does not disrupt male fertility. CONCLUSION Altogether, this study highlights the central role of the IMC as a platform for piRNA biogenesis, and suggests that EXD1 and EXD2 function in the IMC-mediated RNA regulation in postnatal male germ cells.
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Affiliation(s)
- Opeyemi Olotu
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Mark Dowling
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland
| | - Magdalena N Wojtas
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | - Panyi Tran
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Tiina Lehtiniemi
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Matteo Da Ros
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland
| | - Noora Kotaja
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
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5
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Chattopadhyay T, Gupta P, Nayak R, Mallick B. Genome-wide profiling of dysregulated piRNAs and their target genes implicated in oncogenicity of Tongue Squamous Cell Carcinoma. Gene 2022; 849:146919. [PMID: 36179965 DOI: 10.1016/j.gene.2022.146919] [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: 06/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are single-stranded, 23-36 nucleotide long RNAs that regulate gene expression in the germline but are also detected in some cancers. However, there are no reports yet on piRNA expression in tongue squamous cell carcinoma (TSCC), the most common oral cancer (80-90% percent of all oral cancers). We performed small RNA and whole transcriptome sequencing in H357 tongue cancer and HOK cells (GEO database accession numbers: GSE196674 and GSE196688). We also examined nine published sets of gene expression array data of TSCC tissues from the GEO database to decode piRNAs and their putative targets that may be involved in tumorigenesis. We identified a pool of 16058 and 25677 piRNAs in H357 and HOK, respectively, among which 406 are differentially expressed. We also found that 2094 protein-coding genes are differentially expressed in either TSCC tissues or cell lines. We performed target predictions for these piRNA, pathway and disease function (DF) analyses, as well as qRT-PCR validation of piRNA-target pairs. These experiments revealed one up-regulated (FDFT1) and four down-regulated (OGA, BDH1, TAT, HYAL4) target genes that are enriched in 11 canonical pathways (CPs), with postulated roles in the initiation and progression of TSCC. Downregulation of piR-33422 is predicted to upregulate the FDFT1 gene, which encodes a mevalonate/cholesterol-pathway related farnesyl-diphosphate farnesyltransferase. The FDFT1 appears to be involved in the largest number of oncogenesis-related processes and is interacting with statins, which is a classical cancer drug. This study provides the first evidence of the piRNome of TSCC, which could be investigated further to decode piRNA-mediated gene regulations in malignancy and potential drug targets, such as FDFT1.
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Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Pooja Gupta
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Rojalin Nayak
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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6
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The birth of piRNAs: how mammalian piRNAs are produced, originated, and evolved. Mamm Genome 2021; 33:293-311. [PMID: 34724117 PMCID: PMC9114089 DOI: 10.1007/s00335-021-09927-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs), small noncoding RNAs 24–35 nucleotides long, are essential for animal fertility. They play critical roles in a range of functions, including transposable element suppression, gene expression regulation, imprinting, and viral defense. In mammals, piRNAs are the most abundant small RNAs in adult testes and the only small RNAs that direct epigenetic modification of chromatin in the nucleus. The production of piRNAs is a complex process from transcription to post-transcription, requiring unique machinery often distinct from the biogenesis of other RNAs. In mice, piRNA biogenesis occurs in specialized subcellular locations, involves dynamic developmental regulation, and displays sexual dimorphism. Furthermore, the genomic loci and sequences of piRNAs evolve much more rapidly than most of the genomic regions. Understanding piRNA biogenesis should reveal novel RNA regulations recognizing and processing piRNA precursors and the forces driving the gain and loss of piRNAs during animal evolution. Such findings may provide the basis for the development of engineered piRNAs capable of modulating epigenetic regulation, thereby offering possible single-dose RNA therapy without changing the genomic DNA. In this review, we focus on the biogenesis of piRNAs in mammalian adult testes that are derived from long non-coding RNAs. Although piRNA biogenesis is believed to be evolutionarily conserved from fruit flies to humans, recent studies argue for the existence of diverse, mammalian-specific RNA-processing pathways that convert precursor RNAs into piRNAs, perhaps associated with the unique features of mammalian piRNAs or germ cell development. We end with the discussion of major questions in the field, including substrate recognition and the birth of new piRNAs.
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7
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Kojima-Kita K, Kuramochi-Miyagawa S, Nakayama M, Miyata H, Jacobsen SE, Ikawa M, Koseki H, Nakano T. MORC3, a novel MIWI2 association partner, as an epigenetic regulator of piRNA dependent transposon silencing in male germ cells. Sci Rep 2021; 11:20472. [PMID: 34650118 PMCID: PMC8516955 DOI: 10.1038/s41598-021-98940-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/13/2021] [Indexed: 11/28/2022] Open
Abstract
The PIWI (P-element-induced wimpy testis)-interacting-RNA (piRNA) pathway plays a crucial role in the repression of TE (transposable element) expression via de novo DNA methylation in mouse embryonic male germ cells. Various proteins, including MIWI2 are involved in the process. TE silencing is ensured by piRNA-guided MIWI2 that recruits some effector proteins of the DNA methylation machinery to TE regions. However, the molecular mechanism underlying the methylation is complex and has not been fully elucidated. Here, we identified MORC3 as a novel associating partner of MIWI2 and also a nuclear effector of retrotransposon silencing via piRNA-dependent de novo DNA methylation in embryonic testis. Moreover, we show that MORC3 is important for transcription of piRNA precursors and subsequently affects piRNA production. Thus, we provide the first mechanistic insights into the role of this effector protein in the first stage of piRNA biogenesis in embryonic TE silencing mechanism.
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Affiliation(s)
- Kanako Kojima-Kita
- Department of Pathology, Medical School, Osaka University, Yamada-oka 2-2 Suita, Osaka, 565-0871, Japan.
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Medical School, Osaka University, Yamada-oka 2-2 Suita, Osaka, 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 2-2 Suita, Osaka, 565-0871, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Haruhiko Miyata
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1 Suita, Osaka, 565-0871, Japan
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
- Department of Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1 Suita, Osaka, 565-0871, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Toru Nakano
- Department of Pathology, Medical School, Osaka University, Yamada-oka 2-2 Suita, Osaka, 565-0871, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 2-2 Suita, Osaka, 565-0871, Japan.
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8
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Factors Regulating the Activity of LINE1 Retrotransposons. Genes (Basel) 2021; 12:genes12101562. [PMID: 34680956 PMCID: PMC8535693 DOI: 10.3390/genes12101562] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) is a class of autonomous mobile genetic elements that form somatic mosaicisms in various tissues of the organism. The activity of L1 retrotransposons is strictly controlled by many factors in somatic and germ cells at all stages of ontogenesis. Alteration of L1 activity was noted in a number of diseases: in neuropsychiatric and autoimmune diseases, as well as in various forms of cancer. Altered activity of L1 retrotransposons for some pathologies is associated with epigenetic changes and defects in the genes involved in their repression. This review discusses the molecular genetic mechanisms of the retrotransposition and regulation of the activity of L1 elements. The contribution of various factors controlling the expression and distribution of L1 elements in the genome occurs at all stages of the retrotransposition. The regulation of L1 elements at the transcriptional, post-transcriptional and integration into the genome stages is described in detail. Finally, this review also focuses on the evolutionary aspects of L1 accumulation and their interplay with the host regulation system.
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9
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Lite C, Sridhar VV, Sriram S, Juliet M, Arshad A, Arockiaraj J. Functional role of piRNAs in animal models and its prospects in aquaculture. REVIEWS IN AQUACULTURE 2021; 13:2038-2052. [DOI: 10.1111/raq.12557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/01/2021] [Indexed: 10/16/2023]
Abstract
AbstractThe recent advances in the field of aquaculture over the last decade has helped the cultured‐fish industry production sector to identify problems and choose the best approaches to achieve high‐volume production. Understanding the emerging roles of non‐coding RNA (ncRNA) in the regulation of fish physiology and health will assist in gaining knowledge on the possible applications of ncRNAs for the advancement of aquaculture. There is information available on the practical considerations of epigenetic mechanisms like DNA methylation, histone modification and ncRNAs, such as microRNA in aquaculture, for both fish and shellfish. Among the non‐coding RNAs, PIWI‐interacting RNA (piRNA) is 24–31 bp long transcripts, which is primarily involved in silencing the germline transposons. Besides, the burgeoning reports and studies establish piRNAs' role in various aspects of biology. Till date, there are no reviews that summarize the recent findings available on piRNAs in animal models, especially on piRNAs biogenesis and biological action. To gain a better understanding and get an overview on the process of piRNA genesis among the different animals, this work reviews the literature available on the processes of piRNA biogenesis in animal models with special reference to aquatic animal model zebrafish. This review also presents a short discussion and prospects of piRNA’s application in relevance to the aquaculture industry.
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Affiliation(s)
- Christy Lite
- Endocrine and Exposome (E2) Laboratory Department of Zoology Madras Christian College Chennai India
| | - Vasisht Varsh Sridhar
- Department of Biotechnology School of Bioengineering SRM Institute of Science and Technology Chennai India
| | - Swati Sriram
- Department of Biotechnology School of Bioengineering SRM Institute of Science and Technology Chennai India
| | - Melita Juliet
- Department of Oral and Maxillofacial Surgery SRM Dental College and Hospital, SRM Institute of Science and Technology Chennai India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
- Department of Aquaculture Faculty of Agriculture Universiti Putra Malaysia Serdang Malaysia
| | - Jesu Arockiaraj
- SRM Research Institute SRM Institute of Science and Technology Chennai India
- Department of Biotechnology, Faculty of Science and Humanities SRM Institute of Science and Technology Chennai India
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10
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Guay C, Jacovetti C, Bayazit MB, Brozzi F, Rodriguez-Trejo A, Wu K, Regazzi R. Roles of Noncoding RNAs in Islet Biology. Compr Physiol 2020; 10:893-932. [PMID: 32941685 DOI: 10.1002/cphy.c190032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The discovery that most mammalian genome sequences are transcribed to ribonucleic acids (RNA) has revolutionized our understanding of the mechanisms governing key cellular processes and of the causes of human diseases, including diabetes mellitus. Pancreatic islet cells were found to contain thousands of noncoding RNAs (ncRNAs), including micro-RNAs (miRNAs), PIWI-associated RNAs, small nucleolar RNAs, tRNA-derived fragments, long non-coding RNAs, and circular RNAs. While the involvement of miRNAs in islet function and in the etiology of diabetes is now well documented, there is emerging evidence indicating that other classes of ncRNAs are also participating in different aspects of islet physiology. The aim of this article will be to provide a comprehensive and updated view of the studies carried out in human samples and rodent models over the past 15 years on the role of ncRNAs in the control of α- and β-cell development and function and to highlight the recent discoveries in the field. We not only describe the role of ncRNAs in the control of insulin and glucagon secretion but also address the contribution of these regulatory molecules in the proliferation and survival of islet cells under physiological and pathological conditions. It is now well established that most cells release part of their ncRNAs inside small extracellular vesicles, allowing the delivery of genetic material to neighboring or distantly located target cells. The role of these secreted RNAs in cell-to-cell communication between β-cells and other metabolic tissues as well as their potential use as diabetes biomarkers will be discussed. © 2020 American Physiological Society. Compr Physiol 10:893-932, 2020.
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Affiliation(s)
- Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Flora Brozzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Adriana Rodriguez-Trejo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Kejing Wu
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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11
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Mentis AFA, Dardiotis E, Romas NA, Papavassiliou AG. PIWI family proteins as prognostic markers in cancer: a systematic review and meta-analysis. Cell Mol Life Sci 2020; 77:2289-2314. [PMID: 31814070 PMCID: PMC11104808 DOI: 10.1007/s00018-019-03403-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND P-element-induced-wimpy-testis-(PIWI)-like proteins are implicated in germ cells' regulation and detected in numerous cancer types. In this meta-analysis, we aimed to associate, for the first time, the prognosis in cancer patients with intratumoral expression of PIWI family proteins. METHODS PubMed, Embase, and Web of Knowledge databases were searched, and studies investigating the association between intratumoral mRNA or protein expression of different PIWI family proteins and survival, metastasis, or recurrence of various cancer types were reviewed. Study qualities were assessed using the REMARK criteria. Studies' heterogeneity was evaluated using I2 index and Cochran Q test. Publication bias was assessed by funnel plots and Egger's regression. Pooled hazard ratios (HR) with 95% confidence intervals (95% CIs) were calculated for different PIWI family proteins separately. Specifically, log of calculated HR was pooled using random-effects model. RESULTS Twenty-six studies (4299 participants) were included. The pooled HR of mortality in high versus low expression of PIWIL1, PIWIL2, and PIWIL4 was 1.87 (95% CI: 1.31-2.66, p < 0.05), 1.09 (95% CI: 0.58-2.07, p = 0.79), and 0.44 (95% CI: 0.25-0.76, p < 0.05), respectively. The pooled HR of recurrence in high versus low expression of PIWIL1 and PIWIL2 was 1.72 (95% CI: 1.20-2.49, p < 0.05) and 1.98 (95% CI: 0.65-5.98, p = 0.23), respectively. CONCLUSIONS Highly variable results were observed for different cancer types. Higher PIWIL1 and lower piwil4 and PIWIL4 expression levels could potentially indicate worse prognosis in cancer. These proteins' expressions could be used for personalized prognosis and treatment in the future.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Public Health Laboratories, Hellenic Pasteur Institute, Athens, Greece
- Department of Microbiology, University Hospital of Thessaly, Larissa, Greece
| | | | - Nicholas A Romas
- Department of Urology, Columbia University Medical Center, Vagelos College of Physicians and Surgeons, New York, USA
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street - Bldg. 16, 11527, Athens, Greece.
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Zhang GW, Wang L, Chen H, Guan J, Wu Y, Zhao J, Luo Z, Huang W, Zuo F. Promoter hypermethylation of PIWI/piRNA pathway genes associated with diminished pachytene piRNA production in bovine hybrid male sterility. Epigenetics 2020; 15:914-931. [PMID: 32141383 DOI: 10.1080/15592294.2020.1738026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Hybrid male sterility (HMS) is a postzygotic reproductive isolation mechanism that enforces speciation. A bovine example of HMS is the yattle (also called dzo), an interspecies hybrid of taurine cattle (Bos taurus) and yak (Bos grunniens). The molecular mechanisms underlying HMS of yattle are not well understood. Epigenetic modifications of DNA methylation and P-element induced wimpy testis (PIWI)-interacting RNA (piRNAs) are important regulators in spermatogenesis. In this study, we investigated DNA methylation patterns and piRNA expression in adult testes in hybrid infertile yattle bulls and fertile cattle and yak bulls using whole genome bisulphite-seq and small RNA-seq. Promoter hypermethylation in yattle were associated with DNA methylation involved in gamete generation, piRNA metabolic processes, spermatogenesis, and spermatid development (P < 2.6 × 10-5). Male infertility in yattle was associated with the promoter hypermethylation-associated silencing of PIWI/piRNA pathway genes including PIWIL1, DDX4, PLD6, MAEL, FKBP6, TDRD1 and TDRD5. The downstream effects of silencing these genes were diminished production of 29- to 31- nucleotide pachytene piRNAs in yattle testes. Hypermethylation events at transposable element loci (LINEs, SINEs, and LTRs) were found in yattle. LINE-derived prepachytene piRNAs increased and SINE-derived prepachytene piRNAs were reduced in yattle testes. Our data suggests that DNA methylation affects the PIWI/piRNA pathway and is involved in gene expression and pachytene piRNA production during spermatogenesis in bovine HMS. DNA hypermethylation and disruption of piRNA production contributed to unsuccessful germ cell development that may drive bovine HMS.
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Affiliation(s)
- Gong-Wei Zhang
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Ling Wang
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Huiyou Chen
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Jiuqiang Guan
- Yak Research Institution, Sichuan Academy of Grassland Science , Chengdu, Sichuan, China
| | - Yuhui Wu
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Jianjun Zhao
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Zonggang Luo
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Wenming Huang
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Fuyuan Zuo
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
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Gan B, Chen S, Liu H, Min J, Liu K. Structure and function of eTudor domain containing TDRD proteins. Crit Rev Biochem Mol Biol 2019; 54:119-132. [DOI: 10.1080/10409238.2019.1603199] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Bing Gan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Huan Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
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14
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Todd CD, Deniz Ö, Taylor D, Branco MR. Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells. eLife 2019; 8:e44344. [PMID: 31012843 PMCID: PMC6544436 DOI: 10.7554/elife.44344] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/20/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that they play significant roles in gene regulation. Here we tested a set of long terminal repeat TE families for roles as enhancers in mouse embryonic and trophoblast stem cells. Epigenomic and transcriptomic data suggested that a large number of TEs helped to establish tissue-specific gene expression programmes. Genetic editing of individual TEs confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a subset of TEs are important for gene regulation in early mouse development, and highlight the importance of functional experiments when evaluating gene regulatory roles of TEs.
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Affiliation(s)
- Christopher D Todd
- Blizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUnited Kingdom
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUnited Kingdom
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Darren Taylor
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Miguel R Branco
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
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15
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Paul C, Delpech H, Haouzi D, Hamamah S, Sardet C, Fabbrizio E. Coprs inactivation leads to a derepression of LINE1 transposons in spermatocytes. FEBS Open Bio 2019; 9:159-168. [PMID: 30652083 PMCID: PMC6325579 DOI: 10.1002/2211-5463.12562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/08/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Repression of retrotransposons is essential for genome integrity during germ cell development and is tightly controlled through epigenetic mechanisms. In primordial germ cells, protein arginine N‐methyltransferase (Prmt5) is involved in retrotransposon repression by methylating Piwi proteins, which is part of the piRNA pathway. Here, we show that in mice, genetic inactivation of coprs (which is highly expressed in testis and encodes a histone‐binding protein required for the targeting of Prmt5 activity) affects the maturation of spermatogonia to spermatids. Mass spectrometry analysis revealed the presence of Miwi in testis protein lysates immunoprecipitated with an anti‐Coprs antibody. The observed deregulation of Miwi and pachytene pre‐piRNAs levels and the derepression of LINE1 repetitive sequences observed in coprs‐/‐ mice suggest that Coprs is implicated in genome surveillance mechanisms.
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Affiliation(s)
- Conception Paul
- Institut de Génétique Moléculaire de Montpellier UMR5535, CNRS, Montpellier University, France
| | - Hélène Delpech
- Institut de Recherche en Cancérologie de Montpellier U1194, Inserm, ICM, CNRS, Montpellier University, Montpellier Cedex 5, France
| | - Delphine Haouzi
- ART-PGD Department, Institute of Regenerative Medicine and Biotherapy, CHU Montpellier, Inserm U1203, UFR of Medicine, Saint-Eloi Hospital, Montpellier University, France
| | - Samir Hamamah
- ART-PGD Department, Institute of Regenerative Medicine and Biotherapy, CHU Montpellier, Inserm U1203, UFR of Medicine, Saint-Eloi Hospital, Montpellier University, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier U1194, Inserm, ICM, CNRS, Montpellier University, Montpellier Cedex 5, France
| | - Eric Fabbrizio
- Institut de Recherche en Cancérologie de Montpellier U1194, Inserm, ICM, CNRS, Montpellier University, Montpellier Cedex 5, France
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