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Pamula MC, Lehmann R. How germ granules promote germ cell fate. Nat Rev Genet 2024:10.1038/s41576-024-00744-8. [PMID: 38890558 DOI: 10.1038/s41576-024-00744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation.
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Affiliation(s)
| | - Ruth Lehmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Sun M, Fan X, Long Q, Zang H, Zhang Y, Liu X, Feng P, Song Y, Li K, Wu Y, Jiang H, Chen D, Guo R. First Characterization and Regulatory Function of piRNAs in the Apis mellifera Larval Response to Ascosphaera apis Invasion. Int J Mol Sci 2023; 24:16358. [PMID: 38003547 PMCID: PMC10671575 DOI: 10.3390/ijms242216358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
piRNAs are a class of small non-coding RNAs that play essential roles in modulating gene expression and abundant biological processes. To decode the piRNA-regulated larval response of western honeybees (Apis mellifera) to Ascosphaera apis infection, the expression pattern of piRNAs in Apis mellifera ligustica larval guts after A. apis inoculation was analyzed based on previously obtained high-quality small RNA-seq datasets, followed by structural characterization, target prediction, regulatory network investigation, and functional dissection. Here, 504, 657, and 587 piRNAs were respectively identified in the 4-, 5-, and 6-day-old larval guts after inoculation with A. apis, with 411 ones shared. These piRNAs shared a similar length distribution and first base bias with mammal piRNAs. Additionally, 96, 103, and 143 DEpiRNAs were detected in the 4-, 5-, and 6-day-old comparison groups. Targets of the DEpiRNAs were engaged in diverse pathways such as the phosphatidylinositol signaling system, inositol phosphate metabolism, and Wnt signaling pathway. These targets were involved in three energy metabolism-related pathways, eight development-associated signaling pathways, and seven immune-relevant pathways such as the Jak-STAT signaling pathway. The expression trends of five randomly selected DEpiRNAs were verified using a combination of RT-PCR and RT-qPCR. The effective overexpression and knockdown of piR-ame-945760 in A. apis-infected larval guts were achieved by feeding a specific mimic and inhibitor. Furthermore, piR-ame-945760 negatively regulated the expression of two target immune mRNAs, SOCS5 and ARF1, in the larval gut during the A. apis infection. These findings indicated that the overall expression level of piRNAs was increased and the expression pattern of piRNAs in larval guts was altered due to the A. apis infection, DEpiRNAs were putative regulators in the A. apis-response of A. m. ligustica worker larvae. Our data provide not only a platform for the functional investigation of piRNAs in honeybees, especially in bee larvae, but also a foundation for illuminating the piRNA-involved mechanisms underlying the host response to the A. apis infection.
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Affiliation(s)
- Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Peilin Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Yuxuan Song
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Kunze Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (Y.W.); (H.J.)
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (Y.W.); (H.J.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, Nakagawa S. Nondomain biopolymers: Flexible molecular strategies to acquire biological functions. Genes Cells 2023; 28:539-552. [PMID: 37249032 DOI: 10.1111/gtc.13050] [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: 04/30/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
A long-standing assumption in molecular biology posits that the conservation of protein and nucleic acid sequences emphasizes the functional significance of biomolecules. These conserved sequences fold into distinct secondary and tertiary structures, enable highly specific molecular interactions, and regulate complex yet organized molecular processes within living cells. However, recent evidence suggests that biomolecules can also function through primary sequence regions that lack conservation across species or gene families. These regions typically do not form rigid structures, and their inherent flexibility is critical for their functional roles. This review examines the emerging roles and molecular mechanisms of "nondomain biomolecules," whose functions are not easily predicted due to the absence of conserved functional domains. We propose the hypothesis that both domain- and nondomain-type molecules work together to enable flexible and efficient molecular processes within the highly crowded intracellular environment.
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Grants
- 21H05273 Ministry of Education, Culture, Sports, Science and Technology
- 21H05274 Ministry of Education, Culture, Sports, Science and Technology
- 21H05275 Ministry of Education, Culture, Sports, Science and Technology
- 21H05276 Ministry of Education, Culture, Sports, Science and Technology
- 21H05277 Ministry of Education, Culture, Sports, Science and Technology
- 21H05278 Ministry of Education, Culture, Sports, Science and Technology
- 21H05279 Ministry of Education, Culture, Sports, Science and Technology
- 21H05280 Ministry of Education, Culture, Sports, Science and Technology
- 21H05281 Ministry of Education, Culture, Sports, Science and Technology
- 21H05282 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Toshie Kai
- Germline Biology Laboratory, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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Qu J, Betting V, van Iterson R, Kwaschik FM, van Rij RP. Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA biogenesis in mosquitoes. Cell Rep 2023; 42:112257. [PMID: 36930642 DOI: 10.1016/j.celrep.2023.112257] [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: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
The piRNA pathway in mosquitoes differs substantially from other model organisms, with an expanded PIWI gene family and functions in antiviral defense. Here, we define core piRNA clusters as genomic loci that show ubiquitous piRNA expression in both somatic and germline tissues. These core piRNA clusters are enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation and depend on key biogenesis factors, Veneno, Tejas, Yb, and Shutdown. Combined transcriptome and chromatin state analyses identify transcriptional readthrough as a conserved mechanism for cluster-derived piRNA biogenesis in the vector mosquitoes Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Comparative analyses between the two Aedes species suggest that piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Our systematic transcriptome and chromatin state analyses lay the foundation for studies of gene regulation, genome evolution, and piRNA function in these important vector species.
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Affiliation(s)
- Jieqiong Qu
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Valerie Betting
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ruben van Iterson
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Florence M Kwaschik
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands.
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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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Quarato P, Singh M, Bourdon L, Cecere G. Inheritance and maintenance of small RNA-mediated epigenetic effects. Bioessays 2022; 44:e2100284. [PMID: 35338497 DOI: 10.1002/bies.202100284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 11/08/2022]
Abstract
Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA-dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
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Affiliation(s)
- Piergiuseppe Quarato
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Meetali Singh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Loan Bourdon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Germano Cecere
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
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Cai A, Hu Y, Zhou Z, Qi Q, Wu Y, Dong P, Chen L, Wang F. PIWI-Interacting RNAs (piRNAs): Promising Applications as Emerging Biomarkers for Digestive System Cancer. Front Mol Biosci 2022; 9:848105. [PMID: 35155584 PMCID: PMC8829394 DOI: 10.3389/fmolb.2022.848105] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a novel type of small non-coding RNAs (sncRNAs), which are 26–31 nucleotides in length and bind to PIWI proteins. Although piRNAs were originally discovered in germline cells and are thought to be essential regulators for germline preservation, they can also influence gene expression in somatic cells. An increasing amount of data has shown that the dysregulation of piRNAs can both promote and repress the emergence and progression of human cancers through DNA methylation, transcriptional silencing, mRNA turnover, and translational control. Digestive cancers are currently a major cause of cancer deaths worldwide. piRNAs control the expression of essential genes and pathways associated with digestive cancer progression and have been reported as possible biomarkers for the diagnosis and treatment of digestive cancer. Here, we highlight recent advances in understanding the involvement of piRNAs, as well as potential diagnostic and therapeutic applications of piRNAs in various digestive cancers.
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Affiliation(s)
- Aiting Cai
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuhao Hu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhou Zhou
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qianyi Qi
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yixuan Wu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Peixin Dong
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
| | - Lin Chen
- Department of Gastroenterology and Laboratory Medicine, Nantong Third Hospital Affiliated to Nantong University, Nantong, China
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
| | - Feng Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
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Abbaszadegan MR, Taghehchian N, Aarabi A, Akbari F, Saburi E, Moghbeli M. MAEL as a diagnostic marker for the early detection of esophageal squamous cell carcinoma. Diagn Pathol 2021; 16:36. [PMID: 33902648 PMCID: PMC8077922 DOI: 10.1186/s13000-021-01098-z] [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: 02/15/2020] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background Esophageal cancer is one of the most common malignancies among Iranians and is categorized as adenocarcinoma and squamous cell carcinoma. Various environmental and genetic factors are involved in this malignancy. Despite the recent advances in therapeutic modalities there is still a noticeable mortality rate among such patients which can be related to the late diagnosis. Regarding high ratio of esophageal squamous cell carcinoma (ESCC) in Iran, therefore it is required to assess molecular biology of ESCC to introduce novel diagnostic markers. In present study we assessed the role of Maelstrom (MAEL) cancer testis gene in biology of ESCC among Iranian patients. Methods Forty-five freshly normal and tumor tissues were enrolled to evaluate the levels of MAEL mRNA expression using Real time polymerase chain reaction. Results MAEL under and over expressions were observed in 12 (26.7%) and 9 (20%) of patients, respectively. MAEL fold changes were ranged between -4.33 to -1.87 (mean SD: -2.90± 0.24) and 1.92 to 7.72 (mean SD: 3.97± 0.69) in under and over expressed cases, respectively. There was a significant association between stage and MAEL expression in which majority of MAEL over expressed tumors (8/9, 88.9%) were in stage I/II (p<0.001). There was also a significant correlation between MAEL expression and depth of invasion in which tumor with T1/2 had higher levels of MAEL expression compared with T3/4 tumors (p=0.017). Moreover, there were significant correlations between MAEL expression, tumor size (p=0.028), and grade (p=0.003) among male patients. Conclusions Our data showed that the MAEL was mainly involved in primary stages of tumor progression and it has a declining expression levels toward the advanced stages and higher depth of tumor invasions. Therefore, MAEL can be efficiently introduced as an early detection marker among Iranian ESCC patients.
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Affiliation(s)
| | - Negin Taghehchian
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Azadeh Aarabi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faride Akbari
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Soleimani S, Valizadeh Arshad Z, Moradi S, Ahmadi A, Davarpanah SJ, Azimzadeh Jamalkandi S. Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions. Brief Funct Genomics 2020; 19:309-323. [PMID: 32219422 DOI: 10.1093/bfgp/elaa005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 02/06/2023] Open
Abstract
RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster (D. melanogaster). Functionally, these small ncRNAs play critical roles in virtually all biological systems and developmental pathways. Identification and processing of dsRNAs and activation of RNAi machinery are the three major academic interests that surround RNAi research. Mechanistically, some of the important biological functions of RNAi are achieved through: (i) supporting genomic stability via degradation of foreign viral genomes; (ii) suppressing the movement of transposable elements and, most importantly, (iii) post-transcriptional regulation of gene expression by miRNAs that contribute to regulation of epigenetic modifications such as heterochromatin formation and genome imprinting. Here, we review various routes of small ncRNA biogenesis, as well as different RNAi-mediated pathways in D. melanogaster with a particular focus on signaling pathways. In addition, a critical discussion of the most relevant and latest findings that concern the significant contribution of small ncRNAs to the regulation of D. melanogaster physiology and pathophysiology is presented.
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Żelazowska M, Halajian A. Asymmetry in the cytoplasm of oocytes of largescale yellowfish Labeobarbus marequensis Smith 1841 (Teleostei: Cypriniformes: Cyprinidae). J Morphol 2020; 281:997-1009. [PMID: 32562511 DOI: 10.1002/jmor.21228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/13/2020] [Accepted: 06/05/2020] [Indexed: 11/08/2022]
Abstract
The ovaries of the largescale yellowfish, Labeobarbus marequensis (Teleostei: Cypriniformes: Cyprinidae), are made up of the germinal epithelium, nests of late chromatin nucleolus stage oocytes, and ovarian follicles. Each follicle is composed of a single oocyte, which is surrounded by somatic follicular cells and a basal lamina covered by thecal cells. We describe polarization and ultrastructure of oocytes during the primary growth stage. The oocyte nucleus contains lampbrush chromosomes, nuclear bodies and fibrillar material in which multiple nucleoli arise. Nuage aggregations composed of material of a nuclear origin are present in the perinuclear cytoplasm. The Balbiani body (Bb) contains aggregations of nuage, rough endoplasmic reticulum, individual mitochondria and complexes of mitochondria with nuage (cement). Some mitochondria in the Bb come into close contact with endoplasmic reticulum cisternae and vesicles that contain granular material. At the start of primary growth, the Bb is present in the cytoplasm close to the nucleus. Next, it expands towards the oocyte plasma membrane. In these oocytes, a spherical structure, the so-called yolk nucleus, arises in the Bb. It consists of granular nuage in which mitochondria and vesicles containing granular material are immersed. Later, the Bb becomes fragmented and a fully grown yolk nucleus is present in the vegetal region. It contains numerous threads composed of granular nuage, mitochondria, lysosome-like organelles and autophagosomes. We discuss the formation of autophagosomes in the cytoplasm of primary growth oocytes. During the final step of primary growth, the cortical alveoli arise in the cytoplasm and are distributed evenly. The eggshell is deposited on the external surface of the oocyte plasma membrane and is made up of two egg envelopes that are pierced by numerous pore canals. The external egg envelope is covered in protuberances. During primary growth no lipid droplets are synthesized or stored in the oocytes.
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Affiliation(s)
- Monika Żelazowska
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - Ali Halajian
- DST-NRF SARChI Research Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo, Sovenga, 0727, South Africa
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Zhang X, Liang Z, Zhang Y, Zhu M, Zhu Y, Li S, Zhao W, Hu X, Wang J. Specific PIWI-interacting small noncoding RNA expression patterns in pulmonary tuberculosis patients. Epigenomics 2019; 11:1779-1794. [PMID: 31755303 DOI: 10.2217/epi-2018-0142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: PIWI-interacting RNAs (piRNAs) play crucial roles in germline development and carcinogenesis. The expression patterns of piRNAs in pulmonary tuberculosis (PTB) are still unclear. Materials & methods: Small RNA sequencing was applied to investigate peripheral blood piRNA expression patterns in PTB patients and healthy individuals. Results: A total of 428 upregulated and 349 downregulated piRNAs were identified from PTB patients. Target genes of dysregulated piRNAs were mainly involved in transcription and protein binding. Dysregulated piRNAs were enriched in many pathways related with immunity. Many target genes were regulated by the same piRNAs. Nucleotide bias of these piRNAs showed that piRNAs in peripheral blood may be formed from the primary biogenesis pathway. Conclusion: Findings demonstrated that the PIWI-piRNA pathway is active in human peripheral blood, where it may represent a new player in the PTB pathogenesis.
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Affiliation(s)
- Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Zi Liang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Yunshan Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Yueping Zhu
- Department of Infectious Disease, First Affiliated Hospital of Soochow University, Suzhou 215006, PR China
| | - Sumei Li
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, PR China
| | - Weifeng Zhao
- Department of Tuberculosis, The Fifth People's Hospital of Suzhou, Suzhou 215000, PR China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Ji Wang
- Department of Infectious Disease, The Fifth People's Hospital of Suzhou, Suzhou 215000, PR China
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Żelazowska M, Halajian A. Previtellogenic oocytes of South African largemouth bass Micropterus salmoides
Lacépède 1802 (Actinopterygii, Perciformes) - the Balbiani body, cortical alveoli and developing eggshell. J Morphol 2019; 280:360-369. [DOI: 10.1002/jmor.20948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/14/2018] [Accepted: 12/23/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Monika Żelazowska
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research; Jagiellonian University; Kraków Poland
| | - Ali Halajian
- Department of Biodiversity; University of Limpopo; Sovenga South Africa
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13
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Xie YF, Shang F, Ding BY, Wu YB, Niu JZ, Wei D, Dou W, Christiaens O, Smagghe G, Wang JJ. Tudor knockdown disrupts ovary development in Bactrocera dorsalis. INSECT MOLECULAR BIOLOGY 2019; 28:136-144. [PMID: 30182401 DOI: 10.1111/imb.12533] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
One of the main functions of the piwi-interacting RNA pathway is the post-transcriptional silencing of transposable elements in the germline of many species. In insects, proteins belonging to the Tudor superfamily proteins belonging to the Tudor superfamily play an important role in to play an important role in this mechanism. In this study, we identified the tudor gene in the oriental fruit fly, Bactrocera dorsalis, investigated the spatiotemporal expressional profile of the gene, and performed a functional analysis using RNA interference. We identified one transcript for a tudor homologue in the B. dorsalis transcriptome, which encodes a protein containing the typical 10 Tudor domains and an Adenosine triphosphate (ATP) synthase delta subunit signature. Phylogenetic analysis confirmed the identity of this transcript as a tudor homologue in this species. The expression profile indicated a much higher expression in the adult and pupal stages compared to the larval stages (up to a 60-fold increase), and that the gene was mostly expressed in the ovaries, Malpighian tubules and fat body. Finally, gene knockdown of tudor in B. dorsalis led to clearly underdeveloped ovaries in the female adult and reductions in copulation rate and amount of oviposition, indicating its important role in reproduction. The results of this study shed more light on the role of tudor in ovary development and reproduction.
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Affiliation(s)
- Y-F Xie
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Hunan Academy of Forestry, Changsha, China
| | - F Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - B-Y Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Y-B Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - J-Z Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - D Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - W Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - O Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - G Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - J-J Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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14
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Seydoux G. The P Granules of C. elegans: A Genetic Model for the Study of RNA-Protein Condensates. J Mol Biol 2018; 430:4702-4710. [PMID: 30096346 DOI: 10.1016/j.jmb.2018.08.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 01/25/2023]
Abstract
P granules are RNA/protein condensates in the germline of Caenorhabditis elegans. Genetic analyses have begun to identify the proteins that regulate P granule assembly in the cytoplasm of zygotes. Among them, the RGG-domain protein PGL-3, the intrinsically disordered protein MEG-3, and the RNA helicase LAF-1 all bind and phase separate with RNA in vitro. We discuss how RNA-induced phase separation, competition with other RNA-binding proteins, and reversible phosphorylation contribute to the asymmetric localization of P granules in the cytoplasm of newly fertilized embryos. P granules contain RNA silencing complexes that monitor the germline transcriptome and may provide an RNA memory of germline gene expression across generations.
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Affiliation(s)
- Geraldine Seydoux
- Department of Molecular Biology and Genetics, HHMI, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.
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15
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Ghartey-Kwansah G, Li Z, Feng R, Wang L, Zhou X, Chen FZ, Xu MM, Jones O, Mu Y, Chen S, Bryant J, Isaacs WB, Ma J, Xu X. Comparative analysis of FKBP family protein: evaluation, structure, and function in mammals and Drosophila melanogaster. BMC DEVELOPMENTAL BIOLOGY 2018; 18:7. [PMID: 29587629 PMCID: PMC5870485 DOI: 10.1186/s12861-018-0167-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/12/2018] [Indexed: 12/19/2022]
Abstract
Background FK506-binding proteins (FKBPs) have become the subject of considerable interest in several fields, leading to the identification of several cellular and molecular pathways in which FKBPs impact prenatal development and pathogenesis of many human diseases. Main body This analysis revealed differences between how mammalian and Drosophila FKBPs mechanisms function in relation to the immunosuppressant drugs, FK506 and rapamycin. Differences that could be used to design insect-specific pesticides. (1) Molecular phylogenetic analysis of FKBP family proteins revealed that the eight known Drosophila FKBPs share homology with the human FKBP12. This indicates a close evolutionary relationship, and possible origination from a common ancestor. (2) The known FKBPs contain FK domains, that is, a prolyl cis/trans isomerase (PPIase) domain that mediates immune suppression through inhibition of calcineurin. The dFKBP59, CG4735/Shutdown, CG1847, and CG5482 have a Tetratricopeptide receptor domain at the C-terminus, which regulates transcription and protein transportation. (3) FKBP51 and FKBP52 (dFKBP59), along with Cyclophilin 40 and protein phosphatase 5, function as Hsp90 immunophilin co-chaperones within steroid receptor-Hsp90 heterocomplexes. These immunophilins are potential drug targets in pathways associated with normal physiology and may be used to treat a variety of steroid-based diseases by targeting exocytic/endocytic cycling and vesicular trafficking. (4) By associating with presinilin, a critical component of the Notch signaling pathway, FKBP14 is a downstream effector of Notch activation at the membrane. Meanwhile, Shutdown associates with transposons in the PIWI-interacting RNA pathway, playing a crucial role in both germ cells and ovarian somas. Mutations in or silencing of dFKBPs lead to early embryonic lethality in Drosophila. Therefore, further understanding the mechanisms of FK506 and rapamycin binding to immunophilin FKBPs in endocrine, cardiovascular, and neurological function in both mammals and Drosophila would provide prospects in generating unique, insect specific therapeutics targeting the above cellular signaling pathways. Conclusion This review will evaluate the functional roles of FKBP family proteins, and systematically summarize the similarities and differences between FKBP proteins in Drosophila and Mammals. Specific therapeutics targeting cellular signaling pathways will also be discussed.
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Affiliation(s)
- George Ghartey-Kwansah
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Zhongguang Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Rui Feng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Liyang Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Xin Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China.,Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Meng Meng Xu
- Department of Pharmacology, Duke University Medical Center, Durham, NC, USA
| | - Odell Jones
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yulian Mu
- State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Joseph Bryant
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Jianjie Ma
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Xuehong Xu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China. .,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China.
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16
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Wong JT, Akhbar F, Ng AYE, Tay MLI, Loi GJE, Pek JW. DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1. Nat Commun 2017; 8:759. [PMID: 28970471 PMCID: PMC5624886 DOI: 10.1038/s41467-017-00684-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/19/2017] [Indexed: 01/09/2023] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are by-products of splicing and regulate gene expression. How sisRNAs are regulated is unclear. Here we report that a double-stranded RNA binding protein, Disco-interacting protein 1 (DIP1) regulates sisRNAs in Drosophila. DIP1 negatively regulates the abundance of sisR-1 and INE-1 sisRNAs. Fine-tuning of sisR-1 by DIP1 is important to maintain female germline stem cell homeostasis by modulating germline stem cell differentiation and niche adhesion. Drosophila DIP1 localizes to a nuclear body (satellite body) and associates with the fourth chromosome, which contains a very high density of INE-1 transposable element sequences that are processed into sisRNAs. DIP1 presumably acts outside the satellite bodies to regulate sisR-1, which is not on the fourth chromosome. Thus, our study identifies DIP1 as a sisRNA regulatory protein that controls germline stem cell self-renewal in Drosophila. Stable intronic sequence RNAs (sisRNAs) are by-products of splicing from introns with roles in embryonic development in Drosophila. Here, the authors show that the RNA binding protein DIP1 regulates sisRNAs in Drosophila, which is necessary for germline stem cell homeostasis.
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Affiliation(s)
- Jing Ting Wong
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore
| | - Farzanah Akhbar
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore, 529757, Singapore
| | - Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Gladys Jing En Loi
- National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore.
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17
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Huang X, Fejes Tóth K, Aravin AA. piRNA Biogenesis in Drosophila melanogaster. Trends Genet 2017; 33:882-894. [PMID: 28964526 DOI: 10.1016/j.tig.2017.09.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense system that protects the genome integrity of the animal germline from deleterious transposable elements. Targets of silencing are recognized by small noncoding piRNAs that are processed from long precursor molecules. Although piRNAs and other classes of small noncoding RNAs, such as miRNAs and small interfering (si)RNAs, interact with members of the same family of Argonaute (Ago) proteins and their function in target repression is similar, the biogenesis of piRNAs differs from those of the other two small RNAs. Recently, many aspects of piRNA biogenesis have been revealed in Drosophila melanogaster. In this review, we elaborate on piRNA biogenesis in Drosophila somatic and germline cells. We focus on the mechanisms by which piRNA precursor transcription is regulated and highlight recent work that has advanced our understanding of piRNA precursor processing to mature piRNAs. We finish by discussing current models to the still unresolved question of how piRNA precursors are selected and channeled into the processing machinery.
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Affiliation(s)
- Xiawei Huang
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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18
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Pritykin Y, Brito T, Schupbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA (NEW YORK, N.Y.) 2017; 23:1097-1109. [PMID: 28420675 PMCID: PMC5473144 DOI: 10.1261/rna.058594.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 04/03/2017] [Indexed: 06/01/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock, and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila ovaries and analyzing these data together with other publicly available data sets. In agreement with previous studies, we confirm that Cutoff is involved in the transcriptional regulation of piRNA clusters and in the repression of transposable elements in germ cells. Surprisingly, however, we find that Cutoff is enriched at and affects the expression of other noncoding RNAs, including spliceosomal RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). At least in some instances, Cutoff appears to act at a transcriptional level in concert with Rhino and perhaps Deadlock. Finally, we show that mutations in Cutoff result in the deregulation of hundreds of protein-coding genes in germ cells. Our study uncovers a broader function for the RDC complex in the Drosophila germline development.
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Affiliation(s)
- Yuri Pritykin
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tarcisio Brito
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-902, Brazil
| | - Trudi Schupbach
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Mona Singh
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, USA
| | - Attilio Pane
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-902, Brazil
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19
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Dehghani M, Lasko P. C-terminal residues specific to Vasa among DEAD-box helicases are required for its functions in piRNA biogenesis and embryonic patterning. Dev Genes Evol 2016; 226:401-412. [DOI: 10.1007/s00427-016-0560-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
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20
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Abstract
Germ granules are the hallmark of all germ cells. These membrane-less, electron-dense structures were first observed over 100 years ago. Today, their role in regulating and processing transcripts critical for the establishment, maintenance, and protection of germ cells is well established, and pathways outlining the biochemical mechanisms and physical properties associated with their biogenesis are emerging.
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Affiliation(s)
- Ruth Lehmann
- Howard Hughes Medical Institute (HHMI), Department of Cell Biology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, USA.
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21
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Abstract
Primordial germ cells are the progenitor cells that give rise to the gametes. In some animals, the germline is induced by zygotic transcription factors, whereas in others, primordial germ cell specification occurs via inheritance of maternally provided gene products known as germ plasm. Once specified, the primordial germ cells of some animals must acquire motility and migrate to the gonad in order to survive. In all animals examined, perinuclear structures called germ granules form within germ cells. This review focuses on some of the recent studies, conducted by several groups using diverse systems, from invertebrates to vertebrates, which have provided mechanistic insight into the molecular regulation of germ cell specification and migration.
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Affiliation(s)
- Florence Marlow
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, 10461, USA; Department of Neuroscience, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, 10461, USA
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22
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Luo LF, Hou CC, Yang WX. Small non-coding RNAs and their associated proteins in spermatogenesis. Gene 2015; 578:141-57. [PMID: 26692146 DOI: 10.1016/j.gene.2015.12.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022]
Abstract
The importance of the gene regulation roles of small non-coding RNAs and their protein partners is of increasing focus. In this paper, we reviewed three main small RNA species which appear to affect spermatogenesis. MicroRNAs (miRNAs) are single stand RNAs derived from transcripts containing stem-loops and hairpins which target corresponding mRNAs and affect their stability or translation. Many miRNA species have been found to be related to normal male germ cell development. The biogenesis of piRNAs is still largely unknown but several models have been proposed. Some piRNAs and PIWIs target transposable elements and it is these that may be active in regulating translation or stem cell maintenance. endo-siRNAs may also participate in sperm development. Some possible interactions between different kinds of small RNAs have even been suggested. We also show that male germ granules are seen to have a close relationship with a considerable number of mRNAs and small RNAs. Those special structures may also participate in sperm development.
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Affiliation(s)
- Ling-Feng Luo
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Cong-Cong Hou
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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23
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Sellars MJ, Trewin C, McWilliam SM, Glaves RSE, Hertzler PL. Transcriptome profiles of Penaeus (Marsupenaeus) japonicus animal and vegetal half-embryos: identification of sex determination, germ line, mesoderm, and other developmental genes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:252-265. [PMID: 25634056 DOI: 10.1007/s10126-015-9613-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
There is virtually no knowledge of the molecular events controlling early embryogenesis in Penaeid shrimp. A combination of controlled spawning environment, shrimp embryo micro-dissection techniques, and next-generation sequencing was used to produce transcriptome EST datasets of Penaeus japonicus animal and vegetal half-embryos. Embryos were collected immediately after spawning, and then blastomeres were separated at the two-cell stage and allowed to develop to late gastrulation, then pooled for RNA isolation and cDNA synthesis. Ion Torrent sequencing of cDNA from approximately 500 pooled animal and vegetal half-embryos from multiple spawnings resulted in 560,516 and 493,703 reads, respectively. Reads from each library were assembled and Gene Ontogeny analysis produced 3479 annotated animal contigs and 4173 annotated vegetal contigs, with 159/139 hits for developmental processes in the animal/vegetal contigs, respectively. Contigs were subject to BLAST for selected developmental toolbox genes. Some of the genes found included the sex determination genes sex-lethal and transformer; the germ line genes argonaute 1, boule, germ cell-less, gustavus, maelstrom, mex-3, par-1, pumilio, SmB, staufen, and tudor; the mesoderm genes brachyury, mef2, snail, and twist; the axis determination/segmentation genes β-catenin, deformed, distal-less, engrailed, giant, hairy, hunchback, kruppel, orthodenticle, patched, tailless, and wingless/wnt-8c; and a number of cell-cycle regulators. Animal and vegetal contigs were computationally subtracted from each other to produce sets unique to either half-embryo library. Genes expressed only in the animal half included bmp1, kruppel, maelstrom, and orthodenticle. Genes expressed only in the vegetal half included boule, brachyury, deformed, dorsal, engrailed, hunchback, spalt, twist, and wingless/wnt-8c.
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Affiliation(s)
- Melony J Sellars
- CSIRO Agriculture Flagship, Integrated Sustainable Aquaculture, Dutton Park, Qld, 4102, Australia,
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24
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Bozzetti MP, Specchia V, Cattenoz PB, Laneve P, Geusa A, Sahin HB, Di Tommaso S, Friscini A, Massari S, Diebold C, Giangrande A. The Drosophila fragile X mental retardation protein participates in the piRNA pathway. J Cell Sci 2015; 128:2070-84. [PMID: 25908854 DOI: 10.1242/jcs.161810] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/10/2015] [Indexed: 12/19/2022] Open
Abstract
RNA metabolism controls multiple biological processes, and a specific class of small RNAs, called piRNAs, act as genome guardians by silencing the expression of transposons and repetitive sequences in the gonads. Defects in the piRNA pathway affect genome integrity and fertility. The possible implications in physiopathological mechanisms of human diseases have made the piRNA pathway the object of intense investigation, and recent work suggests that there is a role for this pathway in somatic processes including synaptic plasticity. The RNA-binding fragile X mental retardation protein (FMRP, also known as FMR1) controls translation and its loss triggers the most frequent syndromic form of mental retardation as well as gonadal defects in humans. Here, we demonstrate for the first time that germline, as well as somatic expression, of Drosophila Fmr1 (denoted dFmr1), the Drosophila ortholog of FMRP, are necessary in a pathway mediated by piRNAs. Moreover, dFmr1 interacts genetically and biochemically with Aubergine, an Argonaute protein and a key player in this pathway. Our data provide novel perspectives for understanding the phenotypes observed in Fragile X patients and support the view that piRNAs might be at work in the nervous system.
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Affiliation(s)
- Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Pierre B Cattenoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Pietro Laneve
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Annamaria Geusa
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - H Bahar Sahin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Silvia Di Tommaso
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Antonella Friscini
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Serafina Massari
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Celine Diebold
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
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25
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Abstract
The maternally expressed Drosophila melanogaster DEAD-box helicase Vasa (Vas) is necessary for many cellular and developmental processes, including specification of primordial germ cells (pole cells), posterior patterning of the embryo, piRNA-mediated repression of transposon-encoded mRNAs, translational activation of gurken (grk) mRNA, and completion of oogenesis itself. Vas protein accumulates in the perinuclear nuage in nurse cells soon after their specification, and then at stage 10 Vas translocates to the posterior pole plasm of the oocyte. We produced a series of transgenic constructs encoding eGFP-Vas proteins carrying mutations affecting different regions of the protein, and analyzed in vivo which Vas functions each could support. We identified novel domains in the N- and C-terminal regions of the protein that are essential for localization, transposon repression, posterior patterning, and pole cell specification. One such functional region, the most C-terminal seven amino acids, is specific to Vas orthologues and is thus critical to distinguishing Vas from other closely related DEAD-box helicases. Surprisingly, we also found that many eGFP-Vas proteins carrying mutations that would be expected to abrogate DEAD-box helicase function localized to the nuage and posterior pole, and retained the capacity to support oogenesis, although they did not function in embryonic patterning, pole cell specification, grk activation, or transposon repression. We conclude from these experiments that Vas, a multifunctional protein, uses different domains and different molecular associations to carry out its various cellular and developmental roles.
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Affiliation(s)
- Mehrnoush Dehghani
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada
| | - Paul Lasko
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada
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26
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Abstract
Piwi proteins and Piwi-interacting RNAs (piRNAs) are essential for gametogenesis, embryogenesis, and stem cell maintenance in animals. Piwi proteins act on transposon RNAs by cleaving the RNAs and by interacting with factors involved in RNA regulation. Additionally, piRNAs generated from transposons and psuedogenes can be used by Piwi proteins to regulate mRNAs at the posttranscriptional level. Here we discuss piRNA biogenesis, recent findings on posttranscriptional regulation of mRNAs by the piRNA pathway, and the potential importance of this posttranscriptional regulation for a variety of biological processes such as gametogenesis, developmental transitions, and sex determination.
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Affiliation(s)
- Toshiaki Watanabe
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06519, USA.
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06519, USA.
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27
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Patil VS, Anand A, Chakrabarti A, Kai T. The Tudor domain protein Tapas, a homolog of the vertebrate Tdrd7, functions in the piRNA pathway to regulate retrotransposons in germline of Drosophila melanogaster. BMC Biol 2014; 12:61. [PMID: 25287931 PMCID: PMC4210518 DOI: 10.1186/s12915-014-0061-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 07/25/2014] [Indexed: 01/21/2023] Open
Abstract
Background Piwi-interacting RNAs (piRNAs) are a special class of small RNAs that provide defense against transposable elements in animal germline cells. In Drosophila, germline piRNAs are thought to be processed at a unique perinuclear structure, the nuage, that houses piRNA pathway proteins including the Piwi clade of Argonaute family proteins, along with several Tudor domain proteins, RNA helicases and nucleases. We previously demonstrated that Tudor domain protein Tejas (Tej), an ortholog of vertebrate Tdrd5, is an important component of the piRNA pathway. Results In the current study, we identified the paralog of the Drosophila tej gene, tapas (tap), which is an ortholog of vertebrate Tdrd7. Like Tej, Tap is localized at the nuage. Alone, tap loss leads to a mild increase in transposon expression and decrease in piRNAs targeting transposons expressed in the germline. The tap gene genetically interacts with other piRNA pathway genes and we also show that Tap physically interacts with piRNA pathway components, such as Piwi family proteins Aubergine and Argonaute3 and the RNA helicases Spindle-E and Vasa. Together with tej, tap is required for survival of germline cells during early stages and for polarity formation. We further observed that loss of tej and tap together results in more severe defects in the piRNA pathway in germline cells compared to single mutants: the double-mutant ovaries exhibit mis-localization of piRNA pathway components and significantly greater reduction of piRNAs against transposons predominantly expressed in germline compared to single mutants. The single or double mutants did not have any reduction in piRNAs mapping to transposons predominantly expressed in gonadal somatic cells or those derived from unidirectional clusters such as flamenco. Consistently, the loss of both tej and tap function resulted in mis-localization of Piwi in germline cells, whereas Piwi remained localized to the nucleus in somatic cells. Conclusions Our observations suggest that tej and tap work together for germline maintenance. tej and tap also function in a synergistic manner to maintain examined piRNA components at the perinuclear nuage and for piRNA production in Drosophila germline cells. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0061-9) contains supplementary material, which is available to authorized users.
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28
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Fu Q, Wang PJ. Mammalian piRNAs: Biogenesis, function, and mysteries. SPERMATOGENESIS 2014; 4:e27889. [PMID: 25077039 DOI: 10.4161/spmg.27889] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/23/2013] [Accepted: 01/16/2014] [Indexed: 12/20/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs specifically expressed in the germline of many species. They are most notably required for transposon silencing. Loss of piRNAs results in defects in germ cell development, and thus, infertility. Most studies of piRNAs have been done in Drosophila, but much progress has also been made on piRNAs in the germline of mammals and other species in the past few years. This review provides a summary of our current knowledge of the biogenesis and functions of piRNAs during mouse spermatogenesis and discusses challenges in the mammalian piRNA field.
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Affiliation(s)
- Qi Fu
- Department of Animal Biology; University of Pennsylvania School of Veterinary Medicine; Philadelphia, PA USA
| | - P Jeremy Wang
- Department of Animal Biology; University of Pennsylvania School of Veterinary Medicine; Philadelphia, PA USA
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29
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YUAN LIQIN, XIAO YUZHONG, ZHOU QIUZHI, YUAN DONGMEI, WU BAIPING, CHEN GANNONG, ZHOU JIANLIN. Proteomic analysis reveals that MAEL, a component of nuage, interacts with stress granule proteins in cancer cells. Oncol Rep 2013; 31:342-50. [DOI: 10.3892/or.2013.2836] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 10/21/2013] [Indexed: 11/06/2022] Open
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30
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Abstract
The past two decades have seen an explosion in research on non-coding RNAs and their physiological and pathological functions. Several classes of small (20-30 nucleotides) and long (>200 nucleotides) non-coding RNAs have been firmly established as key regulators of gene expression in myriad processes ranging from embryonic development to innate immunity. In this review, we focus on our current understanding of the molecular mechanisms underlying the biogenesis and function of small interfering RNAs (siRNAs), microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs). In addition, we briefly review the relevance of small and long non-coding RNAs to human physiology and pathology and their potential to be exploited as therapeutic agents.
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Affiliation(s)
- Veena S Patil
- Program for RNA Biology, Sanford-Burnham Medical Research Institute , La Jolla, CA , USA
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31
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Pek JW, Ng BF, Kai T. Polo-mediated phosphorylation of Maelstrom regulates oocyte determination during oogenesis in Drosophila. Development 2012; 139:4505-13. [DOI: 10.1242/dev.082867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Drosophila, Maelstrom is a conserved component of the perinuclear nuage, a germline-unique structure that appears to serve as a site for Piwi-interacting RNA (piRNA) production to repress deleterious transposons. Maelstrom also functions in the nucleus as a transcriptional regulator to repress the expression of microRNA-7, a process that is essential for the proper differentiation of germline stem cells. In this paper, we report another function of Maelstrom in regulating oocyte determination independently of its transposon silencing and germline stem cell differentiation activities. In Drosophila, the conserved serine 138 residue in Maelstrom is required for its phosphorylation, an event that promotes oocyte determination. Phosphorylation of Maelstrom is required for the repression of the pachytene checkpoint protein Sir2, but not for transposon silencing or for germline stem cell differentiation. We identify Polo as a kinase that mediates the phosphorylation of Maelstrom. Our results suggest that the Polo-mediated phosphorylation of Maelstrom may be a mechanism that controls oocyte determination by inactivating the pachytene checkpoint via the repression of Sir2 in Drosophila ovaries.
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Affiliation(s)
- Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604
| | - Bing Fu Ng
- Department of Biological Sciences, National University of Singapore, Singapore 117604
| | - Toshie Kai
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604
- Department of Biological Sciences, National University of Singapore, Singapore 117604
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32
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Abstract
Tudor domain proteins function as molecular adaptors, binding methylated arginine or lysine residues on their substrates to promote physical interactions and the assembly of macromolecular complexes. Here, we discuss the emerging roles of Tudor domain proteins during development, most notably in the Piwi-interacting RNA pathway, but also in other aspects of RNA metabolism, the DNA damage response and chromatin modification.
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Affiliation(s)
- Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | - Amit Anand
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | - Toshie Kai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117604
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