Article
Multidisciplinary Sciences
Taichiro Iki, Shinichi Kawaguchi, Toshie Kai
Summary: PIWI-interacting RNA (piRNA) pathways are important in animal gamete formation, but the mechanisms of piRNA biogenesis are not fully understood. In this study, we discovered that protein coding sequences (CDSs) in Drosophila melanogaster testes can serve as origins for noncoding piRNA biogenesis. These CDS-piRNAs form silencing complexes with Aubergine (Aub) in germ cells. Our findings also reveal that CDS-piRNAs and cluster/TE-piRNAs are different species and their loading onto Aub depends on chaperone Cyclophilin 40. Furthermore, the activities of Argonaute 2 (Ago2) and Dicer-2 are critical for CDS-piRNA production.
Article
Multidisciplinary Sciences
Hiroya Yamazaki, Yurika Namba, Shogo Kuriyama, Kazumichi M. Nishida, Asako Kajiya, Mikiko C. Siomi
Summary: Bombyx Vasa assembles Vasa bodies in germ cells, which are responsible for transposon silencing and Ago3-piRISC biogenesis. It is found that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa play important roles in self-association and RNA binding, respectively, for Vasa body assembly and droplet formation via phase separation. BmVasa preferentially binds transposon mRNAs, enabling their sequestration and enrichment in Vasa bodies, leading to effective Siwi-dependent transposon repression and Ago3-piRISC biogenesis.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yixing Pi, Zitian Liang, Qianzhou Jiang, Ding Chen, Zhikang Su, Yuanting Ouyang, Zhiyi Zhang, Jiaohong Liu, Siyi Wen, Li Yang, Tao Luo, Lvhua Guo
Summary: Angiogenesis is a process in which resting endothelial cells start forming new blood vessels, and it plays a crucial role in bone tissue repair. Naringin, a main active component in traditional Chinese medicine, has various biological activities. The mechanism of naringin in angiogenesis is still unclear. This study aims to investigate the potential angiogenic and bone regeneration properties of naringin and explore its mechanism of action by regulating piRNAs and related target genes.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Review
Endocrinology & Metabolism
Jingcheng Zhang, Wentao Zhang, Yuchao Liu, Man Pi, Yufeng Jiang, Ailiyaer Ainiwaer, Shiyu Mao, Haotian Chen, Yuefei Ran, Shuwen Sun, Wei Li, Xudong Yao, Zhengyan Chang, Yang Yan
Summary: The piRNA is a small molecule, non-coding RNA with a length of 24-32nt. It was originally found in germ cells and is considered a regulator of germ cell function. It can interact with PIWI protein and play a role in gene transcription regulation and transposable factors silencing. Abnormal expression of piRNAs has been found in various cancer tissues and patient fluids, making them potential diagnostic tools, therapeutic targets, staging markers, and prognostic evaluation tools for cancer. This article reviews recent research on piRNA, focusing on its structural characteristics, production mechanism, applications, and role in urological tumors, providing valuable insights for the regulation of urological tumors by piRNA.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Oncology
Michael Bartos, Frantisek Siegl, Alena Kopkova, Lenka Radova, Jan Oppelt, Marek Vecera, Tomas Kazda, Radim Jancalek, Michal Hendrych, Marketa Hermanova, Petra Kasparova, Zuzana Pleskacova, Vaclav Vybihal, Pavel Fadrus, Martin Smrcka, Radek Lakomy, Radim Lipina, Tomas Cesak, Ondrej Slaby, Jiri Sana
Summary: Small RNA sequencing analysis identified 58 significantly deregulated piRNA molecules in glioblastoma samples compared to non-tumor brain tissues, and some of these piRNAs were found to be associated with tumor cell proliferation and patient survival rates.
FRONTIERS IN ONCOLOGY
(2021)
Review
Oncology
Chao Yuan, Hao Qin, Murugavel Ponnusamy, Yong Chen, Zhijuan Lin
Summary: PIWI-interacting RNA is a type of non-coding small RNA found primarily in mammalian germ cells, which cooperates with PIWI protein family to participate in germ cell development and maintain genomic stability. Abnormal expression of piRNAs is associated with various human cancers, potentially serving as oncogenes or tumor suppressors and providing new opportunities for cancer diagnosis, treatment, or prognosis monitoring.
Article
Biochemistry & Molecular Biology
Tiziana Corsello, Andrzej S. Kudlicki, Tianshuang Liu, Antonella Casola
Summary: piRNAs, small non-coding RNAs, play crucial roles in maintaining genome integrity and regulating gene expression in response to viral infections. This study identified time-dependent changes in piRNA expression in RSV-infected SAE cells, with potential target genes related to cytoskeletal organization and nucleic acid binding. Cluster analysis revealed distinct patterns of regulation of potential piRNA targets in infected cells, highlighting the importance of understanding piRNA roles in viral lung-mediated diseases.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biology
Amna Asif-Laidin, Karine Casier, Zoheir Ziriat, Antoine Boivin, Elise Viode, Valerie Delmarre, Stephane Ronsseray, Clement Carre, Laure Teysset
Summary: In gonads, the activity of transposable elements (TEs) is repressed by PIWI-interacting RNAs (piRNAs) synthesized by piRNA clusters. Horizontal transfer (HT) of TEs can threaten genome integrity, but naive genomes can eventually produce new piRNAs to target the invaders. The emergence of these new piRNAs is linked to piRNA cluster transcription and depends on genetic and epigenetic properties.
Article
Biochemical Research Methods
Kai Zheng, Xin-Lu Zhang, Lei Wang, Zhu-Hong You, Zhao-Hui Zhan, Hao-Yuan Li
Summary: PIWI proteins and piRNAs are commonly found in human cancers and are associated with poorer clinical outcomes. A new graph neural network framework called line graph attention networks (LGAT) is developed for predicting the association between PiRNAs and diseases. Experimental results show that LGAT performs excellently in identifying potential associations.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Songqian Huang, Kazutoshi Yoshitake, Shuichi Asakawa
Summary: PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that play important biological functions in metazoans, defending against transposable elements in germ lines. Recent studies have discovered ubiquitously expressed piRNAs in both soma and germ lines in humans and animals, offering new insights into their diverse functions. Although the exact role of piRNAs remains unclear, ongoing sRNA-seq studies are revealing different activities of piRNAs in the genome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Neurosciences
Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Summary: MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were found to be dysregulated in Parkinson's disease (PD) tissues. When comparing miRNA and piRNA dysregulation in transgenic C. elegans nematodes overexpressing human alpha-synuclein wild-type (WT) or mutant A53T, genetic crosses with tdp-1 null mutants improved behavioral deficits and altered the number of dysregulated miRNAs and piRNAs. Prediction of target genes by specific miRNAs shed light on the molecular landscape of small non-coding RNA dysregulation in PD-associated neurodegenerative disorders.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Biochemical Research Methods
Kai Zheng, Xin-Lu Zhang, Lei Wang, Zhu-Hong You, Bo-Ya Ji, Xiao Liang, Zheng-Wei Li
Summary: This study proposes a novel computational model called SPRDA based on the structural perturbation method to predict potential disease-associated piRNAs. SPRDA shows high performance on the benchmark dataset and demonstrates the robustness of the method for predicting 10 diseases. This approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Christopher Noyes, Shunsuke Kitajima, Fengkai Li, Yusuke Suita, Saradha Miriyala, Shakson Isaac, Nagib Ahsan, Erik Knelson, Amir Vajdi, Tetsuo Tani, Tran C. Thai, Derek Xu, Junko Murai, Nikos Tapinos, Chiaki Takahashi, David A. Barbie, Mamiko Yajima
Summary: DDX4, a conserved germline factor and RNA helicase, promotes small cell lung cancer cell survival by regulating DNA damage and immune response pathways, and contributes to cisplatin-mediated drug resistance. Proteomic analysis suggests that DDX4 expression upregulates proteins related to DNA repair and immune/inflammatory response. The relatively higher DDX4 expression in SCLC patients correlates with decreased survival and increased expression of immune/inflammatory response markers. Thus, DDX4 may be an important therapeutic target in SCLC.
COMMUNICATIONS BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Aiting Cai, Yuhao Hu, Zhou Zhou, Qianyi Qi, Yixuan Wu, Peixin Dong, Lin Chen, Feng Wang
Summary: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that play a role in the development and progression of digestive cancers. They can regulate gene expression through various mechanisms and have potential applications in cancer diagnosis and treatment.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Cell Biology
Yuxuan Lin, Ritsuko Suyama, Shinichi Kawaguchi, Taichiro Iki, Toshie Kai
Summary: This study provides a detailed analysis of the molecular mechanism of the Tdrd protein Tej in piRNA biogenesis. The results demonstrate that Tej plays a core role in recruiting Vas and Spn-E into nuage, and modulating the mobility of nuage components to engage in further processing of piRNA precursors.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Emilie Quenerch'du, Amit Anand, Toshie Kai
Article
Multidisciplinary Sciences
Jing Ting Wong, Farzanah Akhbar, Amanda Yunn Ee Ng, Mandy Li-Ian Tay, Gladys Jing En Loi, Jun Wei Pek
NATURE COMMUNICATIONS
(2017)
Article
Genetics & Heredity
Ryan J. Gleason, Amit Anand, Toshie Kai, Xin Chen
Editorial Material
Genetics & Heredity
Jun Wei Pek
TRENDS IN GENETICS
(2018)
Article
Multidisciplinary Sciences
Ryan Yee Wei Teo, Amit Anand, Vishweshwaren Sridhar, Katsutomo Okamura, Toshie Kai
NATURE COMMUNICATIONS
(2018)
Article
Genetics & Heredity
Ryan J. Gleason, Amit Anand, Toshie Kai, Xin Chen
Article
Cell & Tissue Engineering
Amanda Yunn Ee Ng, Kimberly Rae Guzman Peralta, Jun Wei Pek
Article
Cell & Tissue Engineering
Ismail Osman, Jun Wei Pek
Review
Biochemistry & Molecular Biology
Seow Neng Chan, Jun Wei Pek
TRENDS IN BIOCHEMICAL SCIENCES
(2019)
Article
Genetics & Heredity
Mandy Li-Ian Tay, Jun Wei Pek
Article
Multidisciplinary Sciences
Shinichi Kawaguchi, Mizuki Ueki, Toshie Kai
Editorial Material
Biology
Ryusuke Niwa, Toshie Kai
CURRENT OPINION IN INSECT SCIENCE
(2020)
Article
Biochemistry & Molecular Biology
Lin-Xenia Lim, Wakana Isshiki, Taichiro Iki, Shinichi Kawaguchi, Toshie Kai
Summary: A study shows that the Kots protein in fruit flies plays an important role in maintaining genome stability and fertility. Kots localizes to nuage in the reproductive cells and regulates the piRNA pathway by forming cytoplasmic condensates, thereby ensuring the silencing of transposable elements.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Cell Biology
Yuxuan Lin, Ritsuko Suyama, Shinichi Kawaguchi, Taichiro Iki, Toshie Kai
Summary: This study provides a detailed analysis of the molecular mechanism of the Tdrd protein Tej in piRNA biogenesis. The results demonstrate that Tej plays a core role in recruiting Vas and Spn-E into nuage, and modulating the mobility of nuage components to engage in further processing of piRNA precursors.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Taichiro Iki, Shinichi Kawaguchi, Toshie Kai
Summary: PIWI-interacting RNA (piRNA) pathways are important in animal gamete formation, but the mechanisms of piRNA biogenesis are not fully understood. In this study, we discovered that protein coding sequences (CDSs) in Drosophila melanogaster testes can serve as origins for noncoding piRNA biogenesis. These CDS-piRNAs form silencing complexes with Aubergine (Aub) in germ cells. Our findings also reveal that CDS-piRNAs and cluster/TE-piRNAs are different species and their loading onto Aub depends on chaperone Cyclophilin 40. Furthermore, the activities of Argonaute 2 (Ago2) and Dicer-2 are critical for CDS-piRNA production.