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Wang X, Hua J, Li J, Zhang J, Dzakah EE, Cao G, Lin W. Mechanisms of non-coding RNA-modulated alternative splicing in cancer. RNA Biol 2022; 19:541-547. [PMID: 35427215 PMCID: PMC9037454 DOI: 10.1080/15476286.2022.2062846] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative splicing (AS) is a common and pivotal process for eukaryotic gene expression regulation, which enables a precursor RNA to produce multiple transcript variants with diverse cellular functions. Aberrant AS represents a hallmark of cancer, engaged in all stages of tumorigenesis from initiation to metastasis. Accumulating pieces of evidence have revealed the involvement of non-coding RNAs (ncRNAs) in regulating AS in human cancers. In this review, we overview the underlying mechanisms of non-coding RNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) modulated AS at diverse levels in human cancers, and summarize their regulatory functions in tumorigenesis.
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Affiliation(s)
- Xiaolin Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science (Hips), Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- University of Science and Technology of China, Hefei, Anhui, P. R. China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, HIPS, Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- High Magnetic Field Laboratory of Anhui Province, Hefei, Anhui, P. R. China
| | - Jinghan Hua
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science (Hips), Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Jingxin Li
- University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Jiahui Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science (Hips), Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Emmanuel Enoch Dzakah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Guozhen Cao
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science (Hips), Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Wenchu Lin
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science (Hips), Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, HIPS, Chinese Academy of Sciences, Hefei, Anhui, P. R. China
- High Magnetic Field Laboratory of Anhui Province, Hefei, Anhui, P. R. China
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Zeng C, Takeda A, Sekine K, Osato N, Fukunaga T, Hamada M. Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs. Methods Mol Biol 2022; 2509:315-340. [PMID: 35796972 DOI: 10.1007/978-1-0716-2380-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
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Affiliation(s)
- Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.
| | - Atsushi Takeda
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Kotaro Sekine
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Naoki Osato
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.
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Zhang J, Chang Y, Xia H, Xu L, Wei X. HIST1H2BN induced cell proliferation and EMT phenotype in prostate cancer via NF-κB signal pathway. Genes Genomics 2021; 43:1361-1369. [PMID: 34537918 DOI: 10.1007/s13258-021-01164-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The potential role of HIST1H2BN in prostate cancer remains unclear. OBJECTIVE To evaluate the carcinogenic role of HIST1H2BN in prostate cancer. METHODS The expression of HIST1H2BN in prostate cancer was analyzed using TCGA database and clinical samples. The roles and mechanisms of HIST1H2BN were investigated in DU145 and PC3 cells. RESULTS HIST1H2BN was significantly upregulated in prostate cancer. HIST1H2BN knockdown inhibited cell proliferation, migration and EMT phenotype in prostate cancer cells. Downregulating HIST1H2BN diminished the expression and binding activity of NF-κB p65, then influenced the expression of MMP2 and MMP9. CONCLUSION : This is the first study to elaborate a HIST1H2BN-NF-κB-EMT regulatory axis in oncogenesis, indicating that HIST1H2BN might be potential therapeutic target for prostate cancer.
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Affiliation(s)
- Juan Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Yuhan Chang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Haiyan Xia
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
| | - Luwei Xu
- Department of Urinary surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
| | - Xiaowei Wei
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
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Wang Y, Mao Y, Zhao Y, Yi X, Ding G, Yu C, Sheng J, Liu X, Meng Y, Huang H. Early-life undernutrition induces enhancer RNA remodeling in mice liver. Epigenetics Chromatin 2021; 14:18. [PMID: 33789751 PMCID: PMC8011416 DOI: 10.1186/s13072-021-00392-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/19/2021] [Indexed: 01/10/2023] Open
Abstract
Background Maternal protein restriction diet (PRD) increases the risk of metabolic dysfunction in adulthood, the mechanisms during the early life of offspring are still poorly understood. Apart from genetic factors, epigenetic mechanisms are crucial to offer phenotypic plasticity in response to environmental situations and transmission. Enhancer-associated noncoding RNAs (eRNAs) transcription serves as a robust indicator of enhancer activation, and have potential roles in mediating enhancer functions and gene transcription. Results Using global run-on sequencing (GRO-seq) of nascent RNA including eRNA and total RNA sequencing data, we show that early-life undernutrition causes remodeling of enhancer activity in mouse liver. Differentially expressed nascent active genes were enriched in metabolic pathways. Besides, our work detected a large number of high confidence enhancers based on eRNA transcription at the ages of 4 weeks and 7 weeks, respectively. Importantly, except for ~ 1000 remodeling enhancers, the early-life undernutrition induced instability of enhancer activity which decreased in 4 weeks and increased in adulthood. eRNA transcription mainly contributes to the regulation of some important metabolic enzymes, suggesting a link between metabolic dysfunction and enhancer transcriptional control. We discovered a novel eRNA that is positively correlated to the expression of circadian gene Cry1 with increased binding of epigenetic cofactor p300. Conclusions Our study reveals novel insights into mechanisms of metabolic dysfunction. Enhancer activity in early life acts on metabolism-associated genes, leading to the increased susceptibility of metabolic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00392-w.
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Affiliation(s)
- Yinyu Wang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiting Mao
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiran Zhao
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xianfu Yi
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Guolian Ding
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanjin Yu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China
| | - Jianzhong Sheng
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinmei Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China
| | - Yicong Meng
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China. .,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China.
| | - Hefeng Huang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China. .,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China.
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