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Qin F, Wang Y, Yang C, Ren Y, Wei Q, Tang Y, Xu J, Wang H, Luo F, Luo Q, Luo X, Liu X, Yang D, Zuo X, Yang Y, Cheng C, Xu J, Wang W, Liu T, Yi P. hnRNPL phase separation activates PIK3CB transcription and promotes glycolysis in ovarian cancer. Nat Commun 2025; 16:4828. [PMID: 40413189 PMCID: PMC12103590 DOI: 10.1038/s41467-025-60115-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 05/13/2025] [Indexed: 05/27/2025] Open
Abstract
Ovarian cancer has the highest mortality rate among gynecologic tumors worldwide, with unclear underlying mechanisms of pathogenesis. RNA-binding proteins (RBPs) primarily direct post-transcriptional regulation through modulating RNA metabolism. Recent evidence demonstrates that RBPs are also implicated in transcriptional control. However, the role and mechanism of RBP-mediated transcriptional regulation in tumorigenesis remain largely unexplored. Here, we show that the RBP heterogeneous ribonucleoprotein L (hnRNPL) interacts with chromatin and regulates gene transcription by forming phase-separated condensates in ovarian cancer. hnRNPL phase separation activates PIK3CB transcription and glycolysis, thus promoting ovarian cancer progression. Notably, we observe that the PIK3CB promoter is transcribed to produce a non-coding RNA which interacts with hnRNPL and promotes hnRNPL condensation. Furthermore, hnRNPL is significantly amplified in ovarian cancer, and its high expression predicts poor prognosis for ovarian cancer patients. By using cell-derived xenograft and patient-derived organoid models, we show that hnRNPL knockdown suppresses ovarian tumorigenesis. Together, our study reveals that phase separation of the chromatin-associated RBP hnRNPL promotes PIK3CB transcription and glycolysis to facilitate tumorigenesis in ovarian cancer. The formed hnRNPL-PIK3CB-AKT axis depending on phase separation can serve as a potential therapeutic target for ovarian cancer.
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Affiliation(s)
- Fengjiang Qin
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuya Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chenyue Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yifei Ren
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinglv Wei
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Tang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haocheng Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fatao Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qingya Luo
- Department of Pathology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xin Luo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyi Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinzhao Zuo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunming Cheng
- Department of Radiation Oncology James Comprehensive Cancer Center and College of Medicine, The Ohio State University, Columbus Ohio, USA
| | - Jing Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Cheng M, Zhu Y, Yu H, Shao L, Zhang Y, Li L, Tu H, Xie L, Chao H, Zhang P, Xin S, Feng C, Ivanisenko V, Orlov Y, Chen D, Wong A, Yang YE, Chen M. Non-coding RNA notations, regulations and interactive resources. Funct Integr Genomics 2024; 24:217. [PMID: 39557706 DOI: 10.1007/s10142-024-01494-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 10/28/2024] [Accepted: 11/01/2024] [Indexed: 11/20/2024]
Abstract
An increasing number of non-coding RNAs (ncRNAs) are found to have roles in gene expression and cellular regulations. However, there are still a large number of ncRNAs whose functions remain to be studied. Despite decades of research, the field continues to evolve, with each newly identified ncRNA undergoing processes such as biogenesis, identification, and functional annotation. Bioinformatics methodologies, alongside traditional biochemical experimental methods, have played an important role in advancing ncRNA research across various stages. Presently, over 50 types of ncRNAs have been characterized, each exhibiting diverse functions. However, there remains a need for standardization and integration of these ncRNAs within a unified framework. In response to this gap, this review traces the historical trajectory of ncRNA research and proposes a unified notation system. Additionally, we comprehensively elucidate the ncRNA interactome, detailing its associations with DNAs, RNAs, proteins, complexes, and chromatin. A web portal named ncRNA Hub ( https://bis.zju.edu.cn/nchub/ ) is also constructed to provide detailed notations of ncRNAs and share a collection of bioinformatics resources. This review aims to provide a broader perspective and standardized paradigm for advancing ncRNA research.
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Affiliation(s)
- Mengwei Cheng
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Yinhuan Zhu
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
- Wenzhou Institute, The University of Chinese Academy of Science, Wenzhou, 325001, China
| | - Han Yu
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Linlin Shao
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Yiming Zhang
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
- Wenzhou Institute, The University of Chinese Academy of Science, Wenzhou, 325001, China
| | - Lanxing Li
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Haohong Tu
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Luyao Xie
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Peijing Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Saige Xin
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Cong Feng
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Vladimir Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630060, Novosibirsk, Russia
| | - Yuriy Orlov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630060, Novosibirsk, Russia
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991, Moscow, Russia
| | - Dijun Chen
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Aloysius Wong
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Yixin Eric Yang
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China
| | - Ming Chen
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, 325060, China.
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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3
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Gu J, Chen J, Yin Q, Dong M, Zhang Y, Chen M, Chen X, Min J, He X, Tan Y, Zheng L, Jiang H, Wang B, Li X, Chen H. lncRNA JPX-Enriched Chromatin Microenvironment Mediates Vascular Smooth Muscle Cell Senescence and Promotes Atherosclerosis. Arterioscler Thromb Vasc Biol 2024; 44:156-176. [PMID: 37942612 DOI: 10.1161/atvbaha.122.319250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Senescence is a series of degenerative changes in the structure and physiological function of an organism. Whether JPX (just proximal to XIST)-a newly identified age-related noncoding RNA by us-is associated with atherosclerosis is still unknown. Our study was to investigate the role of JPX and provide insights into potential therapies targeting atherosclerosis. METHODS We analyzed clinical data from multiple tissues including meniscus tissue, leukemia cells, and peripheral blood monocytes to identify age-related noncoding RNAs in senescent vascular smooth muscle cells (VSMCs). The molecular mechanism of JPX was investigated by capture hybridization analysis of RNA targets and chromatin immunoprecipitation. IGVTools and real-time quantitative polymerase chain reaction were used to evaluate the JPX expression during phenotype regulation in age-related disease models. The therapeutic potential of JPX was evaluated after establishing an atherosclerosis model in smooth muscle-specific Jpx knockout mice. RESULTS JPX expression was upregulated in activated ras allele (H-rasV12)-induced senescent VSMCs and atherosclerotic arteries. JPX knockdown substantially reduced the elevation of senescence-associated secretory phenotype (SASP) genes in senescent VSMCs. Cytoplasmic DNA leaked from mitochondria via mitochondrial permeability transition pore formed by VDAC1 (voltage-dependent anion channel 1) oligomer activates the STING (stimulator of interferon gene) pathway. JPX could act as an enhancer for the SASP genes and functions as a scaffold molecule through interacting with phosphorylated p65/RelA and BRD4 (bromodomain-containing protein 4) in chromatin remodeling complex, promoting the transcription of SASP genes via epigenetic regulation. Smooth muscle knockout of Jpx in ApoeKO mice resulted in a decrease in plaque area, a reduction in SASP gene expression, and a decrease in senescence compared with controls. CONCLUSIONS As an enhancer RNA, JPX can integrate p65 and BRD4 to form a chromatin remodeling complex, activating SASP gene transcription and promoting cellular senescence. These findings suggest that JPX is a potential therapeutic target for the treatment of age-related atherosclerosis.
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Affiliation(s)
- Jiaming Gu
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Jiajing Chen
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China (J.C.)
| | - Quanwen Yin
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Mengdie Dong
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Yunjia Zhang
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Minghong Chen
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Xiang Chen
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Jiao Min
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Xian He
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Yongkang Tan
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Longbin Zheng
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Hong Jiang
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Bingjian Wang
- Department of Cardiology, Huai'an First People's Hospital Affiliated With Nanjing Medical University, China (B.W., H.C.)
| | - Xuesong Li
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
| | - Hongshan Chen
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy (J.G., Q.Y., M.D., Y.Z., M.C., X.C., J.M., X.H., Y.T., L.Z., H.J., X.L., H.C.), Nanjing Medical University, China
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine (H.C.), Nanjing Medical University, China
- Department of Cardiology, Huai'an First People's Hospital Affiliated With Nanjing Medical University, China (B.W., H.C.)
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanjing Medical University, China (H.C.)
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A novel promoter-associated non-coding small RNA paGLI1 recruits FUS/P65 to transactivate GLI1 gene expression and promotes infiltrating glioma progression. Cancer Lett 2022; 530:68-84. [DOI: 10.1016/j.canlet.2022.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/29/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022]
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5
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Emerging Functions for snoRNAs and snoRNA-Derived Fragments. Int J Mol Sci 2021; 22:ijms221910193. [PMID: 34638533 PMCID: PMC8508363 DOI: 10.3390/ijms221910193] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
The widespread implementation of mass sequencing has revealed a diverse landscape of small RNAs derived from larger precursors. Whilst many of these are likely to be byproducts of degradation, there are nevertheless metabolically stable fragments derived from tRNAs, rRNAs, snoRNAs, and other non-coding RNA, with a number of examples of the production of such fragments being conserved across species. Coupled with specific interactions to RNA-binding proteins and a growing number of experimentally reported examples suggesting function, a case is emerging whereby the biological significance of small non-coding RNAs extends far beyond miRNAs and piRNAs. Related to this, a similarly complex picture is emerging of non-canonical roles for the non-coding precursors, such as for snoRNAs that are also implicated in such areas as the silencing of gene expression and the regulation of alternative splicing. This is in addition to a body of literature describing snoRNAs as an additional source of miRNA-like regulators. This review seeks to highlight emerging roles for such non-coding RNA, focusing specifically on “new” roles for snoRNAs and the small fragments derived from them.
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Hon KW, Abu N, Ab Mutalib NS, Jamal R. miRNAs and lncRNAs as Predictive Biomarkers of Response to FOLFOX Therapy in Colorectal Cancer. Front Pharmacol 2018; 9:846. [PMID: 30127741 PMCID: PMC6088237 DOI: 10.3389/fphar.2018.00846] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/13/2018] [Indexed: 12/22/2022] Open
Abstract
Chemotherapy is one of the options for cancer treatment. FOLFOX is one of the widely used chemotherapeutic regimens used to treat primarily colorectal cancer and other cancers as well. However, the emergence of chemo-resistance clones during cancer treatment has become a critical challenge in the clinical setting. It is crucial to identify the potential biomarkers and therapeutics targets which could lead to an improvement in the success rate of the proposed therapies. Since non-coding RNAs have been known to be important players in the cellular system, the interest in their functional roles has intensified. Non-coding RNAs (ncRNAs) as regulators at the post-transcriptional level could be very promising to provide insights in overcoming chemo-resistance to FOLFOX. Hence, this mini review attempts to summarize the potential of ncRNAs correlating with chemo-sensitivity/resistance to FOLFOX.
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Affiliation(s)
- Kha Wai Hon
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Yu D, Ma X, Zuo Z, Wang H, Meng Y. Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants. Front Genet 2018; 9:168. [PMID: 29868116 PMCID: PMC5960741 DOI: 10.3389/fgene.2018.00168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
There is increasing evidence suggesting the contribution of non-coding RNAs (ncRNAs) to the phenotypic and physiological complexity of organisms. A novel ncRNA species has been identified near the transcription boundaries of protein-coding genes in eukaryotes, bacteria, and archaea. This review provides a detailed description of these transcription boundary-associated RNAs (TBARs), including their classification. Based on their genomic distribution, TBARs are divided into two major groups: promoter-associated RNAs (PARs) and terminus-associated RNAs (TARs). Depending on the sequence length, each group is further classified into long RNA species (>200 nt) and small RNA species (<200 nt). According to these rules of TBAR classification, divergent ncRNAs with confusing nomenclatures, such as promoter upstream transcripts (PROMPTs), upstream antisense RNAs (uaRNAs), stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), upstream non-coding transcripts (UNTs), transcription start site-associated RNAs (TSSaRNAs), transcription initiation RNAs (tiRNAs), and transcription termination site-associated RNAs (TTSaRNAs), were assigned to specific classes. Although the biogenesis pathways of PARs and TARs have not yet been clearly elucidated, previous studies indicate that some of the PARs have originated either through divergent transcription or via RNA polymerase pausing. Intriguing findings regarding the functional implications of the TBARs such as the long-range “gene looping” model, which explains their role in the transcriptional regulation of protein-coding genes, are also discussed. Altogether, this review provides a comprehensive overview of the current research status of TBARs, which will promote further investigations in this research area.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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8
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Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA. Transcriptional interference by small transcripts in proximal promoter regions. Nucleic Acids Res 2018; 46:1069-1088. [PMID: 29309647 PMCID: PMC5815073 DOI: 10.1093/nar/gkx1242] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 01/15/2023] Open
Abstract
Proximal promoter regions (PPR) are heavily transcribed yielding different types of small RNAs. The act of transcription within PPRs might regulate downstream gene expression via transcriptional interference (TI). For analysis, we investigated capped and polyadenylated small RNA transcripts within PPRs of human RefSeq genes in eight different cell lines. Transcripts of our datasets overlapped with experimentally determined transcription factor binding sites (TFBS). For TFBSs intersected by these small RNA transcripts, we established negative correlation of sRNA expression levels and transcription factor (TF) DNA binding affinities; suggesting that the transcripts acted via TI. Accordingly, datasets were designated as TFbiTrs (TF-binding interfering transcripts). Expression of most TFbiTrs was restricted to certain cell lines. This facilitated the analysis of effects related to TFbiTr expression for the same RefSeq genes across cell lines. We consistently uncovered higher relative TF/DNA binding affinities and concomitantly higher expression levels for RefSeq genes in the absence of TFbiTrs. Analysis of corresponding chromatin landscapes supported these results. ChIA-PET revealed the participation of distal enhancers in TFbiTr transcription. Enhancers regulating TFbiTrs, in effect, act as repressors for corresponding downstream RefSeq genes. We demonstrate the significant impact of TI on gene expression using selected small RNA datasets.
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Affiliation(s)
- Amit Pande
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, D-48149 Muenster, Germany
- Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
- Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
- Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany
| | - Izabela Makalowska
- Laboratory of Functional Genomics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Wojciech Makalowski
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, D-48149 Muenster, Germany
| | - Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
- Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany
- Institute of Medical Biochemistry (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
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9
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Poulain S, Kato S, Arnaud O, Morlighem JÉ, Suzuki M, Plessy C, Harbers M. NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes. Methods Mol Biol 2018; 1543:57-109. [PMID: 28349422 DOI: 10.1007/978-1-4939-6716-2_4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Transcripts in all eukaryotes are characterized by the 5'-end specific cap structure in mRNAs. Cap Analysis Gene Expression or CAGE makes use of these caps to specifically obtain cDNA fragments from the 5'-end of RNA and sequences those at high throughput for transcript identification and genome-wide mapping of transcription start sites for coding and noncoding genes. Here, we provide an improved version of our nanoCAGE protocol that has been developed for preparing CAGE libraries from as little as 50 ng of total RNA within three standard working days. Key steps in library preparation have been improved over our previously published protocol to obtain libraries having a good 5'-end selection and a more equal size distribution for higher sequencing efficiency on Illumina MiSeq and HiSeq sequencers. We recommend nanoCAGE as the method of choice for transcriptome profiling projects even from limited amounts of RNA, and as the best approach for genome-wide mapping of transcription start sites within promoter regions.
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Affiliation(s)
- Stéphane Poulain
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Sachi Kato
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ophélie Arnaud
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jean-Étienne Morlighem
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Av. da Abolição, 3207-Meireles, Fortaleza, CE, 60165-081, Brazil
| | - Makoto Suzuki
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- DNAFORM, Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan
| | - Charles Plessy
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Matthias Harbers
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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10
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Sun T, Pei G, Wang J, Chen L, Zhang W. A novel small RNA CoaR regulates coenzyme A biosynthesis and tolerance of Synechocystis sp. PCC6803 to 1-butanol possibly via promoter-directed transcriptional silencing. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:42. [PMID: 28239414 PMCID: PMC5319066 DOI: 10.1186/s13068-017-0727-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/09/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Microbial small RNAs (sRNAs) have been proposed as valuable regulatory elements for optimizing cellular metabolism for industrial purposes. However, little information is currently available on functional relevance of sRNAs to biofuels tolerance in cyanobacteria. RESULTS Here, we described the identification and functional characterization of a novel 124 nt sRNA Ncl1460 involved in tolerance to biofuel 1-butanol in Synechocystis sp. PCC 6803. The expression of Ncl1460 was verified by blotting assay and its length was determined through 3' RACE. Further analysis showed that Ncl1460 was a negative regulator of slr0847 (coaD) and slr0848 operon responsible for coenzyme A (CoA) synthesis possibly via promoter-directed transcriptional silencing mechanisms which has been widely discovered in eukaryote; thus Ncl1460 was designated as CoaR (CoA Biosynthesis Regulatory sRNA). The possible interaction between CoaR and target genes was suggested by CoA quantification and green fluorescent protein assays. Finally, a quantitative proteomics analysis showed that CoaR regulated tolerance to 1-butanol possibly by down-regulating CoA biosynthesis, resulting in a decrease of fatty acid metabolism and energy metabolism. CONCLUSIONS As the first reported sRNA involved CoA synthesis and 1-butanol tolerance in cyanobacteria, this study provides not only novel insights in regulating mechanisms of essential pathways in cyanobacteria, but also valuable target for biofuels tolerance and productivity modifications.
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Affiliation(s)
- Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Guangsheng Pei
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Jiangxin Wang
- Shenzhen Engineering Lab for Marine Algal Biotechnology, College of Life Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People’s Republic of China
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11
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Ma X, Han N, Shao C, Meng Y. Transcriptome-Wide Discovery of PASRs (Promoter-Associated Small RNAs) and TASRs (Terminus-Associated Small RNAs) in Arabidopsis thaliana. PLoS One 2017; 12:e0169212. [PMID: 28046132 PMCID: PMC5207706 DOI: 10.1371/journal.pone.0169212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/13/2016] [Indexed: 01/21/2023] Open
Abstract
Hints from animals point to the existence of two novel small RNA (sRNA) species surrounding the transcription start sites (TSSs) and the termini of the genes, respectively. In this study, we performed a comprehensive search for the two sRNA species named promoter-associated sRNAs (PASRs) and terminus-associated sRNAs (TASRs) in Arabidopsis. By using sRNA sequencing data from wild type plants and several mutants related to the sRNA biogenesis, Argonaute (AGO) 1- and AGO4-associated sRNA sequencing data, double-stranded RNA sequencing (dsRNA-seq) data, and DNA methylation profiling data, the biogenesis and action pathways of the PASRs and the TASRs were investigated. PASR and TASR peaks were identified on hundreds of the protein-coding genes. Deep analysis uncovered that some of the sRNA peaks were covered by dsRNA-seq reads, and these peaks were significantly repressed in specific mutants. Besides, certain PASRs and TASRs were preferentially recruited by AGO4, and site-specific DNA methylation signals encompassing the genomic loci of these sRNAs were also detected. Accordingly, we proposed a model that certain PASRs and TASRs were generated through a specific Pol IV-, RDR-, DCL-dependent pathway, and they were associated with AGO4 to perform site-specific DNA methylation on their host genes. The above results indicate the existence of PASRs and TASRs in plants. The proposed biogenesis pathway and action mode of the PASRs and TASRs could facilitate us to perform in-depth functional studies on these novel sRNA species.
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Affiliation(s)
- Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou, PR China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
- * E-mail:
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12
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Stutika C, Mietzsch M, Gogol-Döring A, Weger S, Sohn M, Chen W, Heilbronn R. Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation. PLoS One 2016; 11:e0161454. [PMID: 27611072 PMCID: PMC5017669 DOI: 10.1371/journal.pone.0161454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/05/2016] [Indexed: 01/10/2023] Open
Abstract
Most DNA viruses express small regulatory RNAs, which interfere with viral or cellular gene expression. For adeno-associated virus (AAV), a small ssDNA virus with a complex biphasic life cycle miRNAs or other small regulatory RNAs have not yet been described. This is the first comprehensive Illumina-based RNA-Seq analysis of small RNAs expressed by AAV alone or upon co-infection with helper adenovirus or HSV. Several hotspots of AAV-specific small RNAs were detected mostly close to or within the AAV-ITR and apparently transcribed from the newly identified anti-p5 promoter. An additional small RNA hotspot was located downstream of the p40 promoter, from where transcription of non-coding RNAs associated with the inhibition of adenovirus replication were recently described. Parallel detection of known Ad and HSV miRNAs indirectly validated the newly identified small AAV RNA species. The predominant small RNAs were analyzed on Northern blots and by human argonaute protein-mediated co-immunoprecipitation. None of the small AAV RNAs showed characteristics of bona fide miRNAs, but characteristics of alternative RNA processing indicative of differentially regulated AAV promoter-associated small RNAs. Furthermore, the AAV-induced regulation of cellular miRNA levels was analyzed at different time points post infection. In contrast to other virus groups AAV infection had virtually no effect on the expression of cellular miRNA, which underscores the long-established concept that wild-type AAV infection is apathogenic.
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Affiliation(s)
- Catrin Stutika
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
| | - Mario Mietzsch
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
| | | | - Stefan Weger
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
| | - Madlen Sohn
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin Institute for Medical Systems Biology, Laboratory for Functional Genomics and Systems Biology, Berlin, Germany
| | - Wei Chen
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin Institute for Medical Systems Biology, Laboratory for Functional Genomics and Systems Biology, Berlin, Germany
| | - Regine Heilbronn
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
- * E-mail:
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13
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Promoter-Associated RNAs Regulate HSPC152 Gene Expression in Malignant Melanoma. Noncoding RNA 2016; 2:ncrna2030007. [PMID: 29657265 PMCID: PMC5831909 DOI: 10.3390/ncrna2030007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 06/13/2016] [Accepted: 06/19/2016] [Indexed: 01/02/2023] Open
Abstract
The threshold of 200 nucleotides (nt) conventionally divides non-coding RNAs (ncRNA) into long ncRNA (lincRNA, that have more than 200 nt in length) and the remaining ones which are grouped as "small" RNAs (microRNAs, small nucleolar RNAs and piwiRNAs). Promoter-associated RNAs (paRNAs) are generally 200-500 nt long and are transcribed from sequences positioned in the promoter regions of genes. Growing evidence suggests that paRNAs play a crucial role in controlling gene transcription. Here, we used deep sequencing to identify paRNA sequences that show altered expression in a melanoma cell line compared to normal melanocytes. Thousands of reads were mapped to transcription start site (TSS) regions. We limited our search to paRNAs adjacent to genes with an expression that differed between melanoma and normal melanocytes and a length of 200-500 nt that did not overlap the gene mRNA by more than 300 nt, ultimately leaving us with 11 such transcripts. Using quantitative real-time PCR (qRT-PCR), we found a significant correlation between the expression of the mRNA and its corresponding paRNA for two studied genes: TYR and HSPC152. Ectopic overexpression of the paRNA of HSPC152 (designated paHSPC) enhanced the expression of the HSPC152 mRNA, and an siRNA targeting the paHSPC152 decreased the expression of the HSPC152 mRNA. Overexpression of paHSPC also affected the epigenetic structure of its putative promoter region along with effects on several biologic features of melanoma cells. The ectopic expression of the paRNA to TYR did not have any effect. Overall, our work indicates that paRNAs may serve as an additional layer in the regulation of gene expression in melanoma, thus meriting further investigation.
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14
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Villegas VE, Zaphiropoulos PG. Neighboring gene regulation by antisense long non-coding RNAs. Int J Mol Sci 2015; 16:3251-66. [PMID: 25654223 PMCID: PMC4346893 DOI: 10.3390/ijms16023251] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/22/2015] [Indexed: 02/06/2023] Open
Abstract
Antisense transcription, considered until recently as transcriptional noise, is a very common phenomenon in human and eukaryotic transcriptomes, operating in two ways based on whether the antisense RNA acts in cis or in trans. This process can generate long non-coding RNAs (lncRNAs), one of the most diverse classes of cellular transcripts, which have demonstrated multifunctional roles in fundamental biological processes, including embryonic pluripotency, differentiation and development. Antisense lncRNAs have been shown to control nearly every level of gene regulation—pretranscriptional, transcriptional and posttranscriptional—through DNA–RNA, RNA–RNA or protein–RNA interactions. This review is centered on functional studies of antisense lncRNA-mediated regulation of neighboring gene expression. Specifically, it addresses how these transcripts interact with other biological molecules, nucleic acids and proteins, to regulate gene expression through chromatin remodeling at the pretranscriptional level and modulation of transcriptional and post-transcriptional processes by altering the sense mRNA structure or the cellular compartmental distribution, either in the nucleus or the cytoplasm.
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Affiliation(s)
- Victoria E Villegas
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden.
- Faculty of Natural Sciences and Mathematics & Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá 11001000, Colombia.
| | - Peter G Zaphiropoulos
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden.
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15
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Vemuganti R, Silva VR, Mehta SL, Hazell AS. Acute liver failure-induced hepatic encephalopathy s associated with changes in microRNA expression rofiles in cerebral cortex of the mouse [corrected]. Metab Brain Dis 2014; 29:891-9. [PMID: 24861182 PMCID: PMC8487459 DOI: 10.1007/s11011-014-9545-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/07/2014] [Indexed: 12/11/2022]
Abstract
The mechanisms that promote brain dysfunction after acute liver failure (ALF) are not clearly understood. The small noncoding RNAs known as microRNAs (miRNAs) significantly control mRNA translation and thus normal and pathological functions in the mammalian body. To understand their significance in ALF, we currently profiled the expression of miRNAs in the cerebral cortex of mice sacrificed at coma stage following treatment with azoxymethane. Of the 470 miRNAs profiled using microarrays, 37 were significantly altered (20 up-and 17 down-regulated) in their expression in the ALF group compared to sham group. In silico analysis showed that the ALF-responsive miRNAs target on average 231 mRNAs/miRNA (range: 3 to 840 targets). Pathways analysis showed that many miRNAs altered after ALF target multiple mRNAs that are part of various biological and molecular pathways. Glutamatergic synapse, Wnt signaling, MAP-kinase signaling, axon guidance, PI3-kinase-AKT signaling, T-cell receptor signaling and ubiquitin-mediated proteolysis are the top pathways targeted by the ALF-sensitive miRNAs. At least 28 ALF-responsive miRNAs target each of the above pathways. We hypothesize that alterations in miRNAs and their down-stream mRNAs of signaling pathways might play a role in the induction and progression of neurological dysfunction observed during ALF.
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Affiliation(s)
- Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Vinícius R. Silva
- Departamento de Neurologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Suresh L. Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Alan S. Hazell
- Department of Medicine, University of Montreal, Montreal, QC, Canada
- Departamento de Neurologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
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16
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Wang Y, Wang X, Deng W, Fan X, Liu TT, He G, Chen R, Terzaghi W, Zhu D, Deng XW. Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis. MOLECULAR PLANT 2014; 7:514-27. [PMID: 24398630 DOI: 10.1093/mp/sst177] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300 nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half (58%) are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5'-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.
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Affiliation(s)
- Yuqiu Wang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
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17
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Yan BX, Ma JX, Zhang J, Guo Y, Mueller MD, Remick SC, Yu JJ. Prostasin may contribute to chemoresistance, repress cancer cells in ovarian cancer, and is involved in the signaling pathways of CASP/PAK2-p34/actin. Cell Death Dis 2014; 5:e995. [PMID: 24434518 PMCID: PMC4043260 DOI: 10.1038/cddis.2013.523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the deadliest of gynecologic cancers, largely due to the development of drug resistance in chemotherapy. Prostasin may have an essential role in the oncogenesis. In this study, we show that prostasin is decreased in an ovarian cancer drug-resistant cell line and in ovarian cancer patients with high levels of excision repair cross-complementing 1, a marker for chemoresistance. Our cell cultural model investigation demonstrates prostasin has important roles in the development of drug resistance and cancer cell survival. Forced overexpression of prostasin in ovarian cancer cells greatly induces cell death (resulting in 99% cell death in a drug-resistant cell line and 100% cell death in other tested cell lines). In addition, the surviving cells grow at a much lower rate compared with non-overexpressed cells. In vivo studies indicate that forced overexpression of prostasin in drug-resistant cells greatly inhibits the growth of tumors and may partially reverse drug resistance. Our investigation of the molecular mechanisms suggests that prostasin may repress cancer cells and/or contribute to chemoresistance by modulating the CASP/P21-activated protein kinase (PAK2)-p34 pathway, and thereafter PAK2-p34/JNK/c-jun and PAK2-p34/mlck/actin signaling pathways. Thus, we introduce prostain as a potential target for treating/repressing some ovarian tumors and have begun to identify their relevant molecular targets in specific signaling pathways.
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Affiliation(s)
- B-x Yan
- 1] Department of Biochemistry, School of Medicine, Department of Basic Pharmaceutical Sciences, School of Pharmacy, and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA [2] IcesnowYanyan Bioscience Association, Beijing 00094, China
| | - J-x Ma
- 1] Department of Biochemistry, School of Medicine, Department of Basic Pharmaceutical Sciences, School of Pharmacy, and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA [2] Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - J Zhang
- 1] IcesnowYanyan Bioscience Association, Beijing 00094, China [2] Beijing Animal Science Institute, Beijing 00097, China
| | - Y Guo
- Department of Biochemistry, School of Medicine, Department of Basic Pharmaceutical Sciences, School of Pharmacy, and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
| | - M D Mueller
- Department of Biochemistry, School of Medicine, Department of Basic Pharmaceutical Sciences, School of Pharmacy, and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
| | - S C Remick
- Department of Biochemistry, School of Medicine, Department of Basic Pharmaceutical Sciences, School of Pharmacy, and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
| | - J J Yu
- Department of Biochemistry, School of Medicine, Department of Basic Pharmaceutical Sciences, School of Pharmacy, and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
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18
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Dharap A, Pokrzywa C, Murali S, Pandi G, Vemuganti R. MicroRNA miR-324-3p induces promoter-mediated expression of RelA gene. PLoS One 2013; 8:e79467. [PMID: 24265774 PMCID: PMC3827167 DOI: 10.1371/journal.pone.0079467] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 09/28/2013] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are known to repress translation by binding to the 3’UTRs of mRNAs. Using bioinformatics, we recently reported that several miRNAs also have target sites in DNA particularly in the promoters of the protein-coding genes. To understand the functional significance of this phenomenon, we tested the effects of miR-324-3p binding to RelA promoter. In PC12 cells, co-transfection with premiR-324-3p induced a RelA promoter plasmid in a dose-dependent manner and this effect was lost when the miR-324-3p binding site in the promoter was mutated. PremiR-324-3p transfection also significantly induced the endogenous RelA mRNA and protein expression in PC12 cells. Furthermore, transfection with premiR-324-3p increased the levels of cleaved caspase-3 which is a marker of apoptosis. Importantly, the miR-324-3p effects were Ago2 mediated as Ago2 knockdown prevented RelA expression and cleavage of caspase-3. Thus, our studies show that miRNA-mediated transcriptional activation can be seen in PC12 cells which are neural in origin.
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Affiliation(s)
- Ashutosh Dharap
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Courtney Pokrzywa
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Shruthi Murali
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Gopal Pandi
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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19
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Comprehensive analysis of the transcriptional landscape of the human FMR1 gene reveals two new long noncoding RNAs differentially expressed in Fragile X syndrome and Fragile X-associated tremor/ataxia syndrome. Hum Genet 2013; 133:59-67. [PMID: 24005575 PMCID: PMC3898532 DOI: 10.1007/s00439-013-1356-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/25/2013] [Indexed: 01/23/2023]
Abstract
The majority of the human genome is transcribed but not translated, giving rise to noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs, >200 nt) that perform a wide range of functions in gene regulation. The Fragile X mental retardation 1 (FMR1) gene is a microsatellite locus that in the general population contains <55 CGG repeats in its 5′-untranslated region. Expansion of this repeat region to a size of 55-200 CGG repeats, known as premutation, is associated with Fragile X tremor and ataxia syndrome (FXTAS). Further expansion beyond 200 CGG repeats, or full mutation, leads to FMR1 gene silencing and results in Fragile X syndrome (FXS). Using a novel technology called “Deep-RACE”, which combines rapid amplification of cDNA ends (RACE) with next generation sequencing, we systematically interrogated the FMR1 gene locus for the occurrence of novel lncRNAs. We discovered two transcripts, FMR5 and FMR6. FMR5 is a sense lncRNA transcribed upstream of the FMR1 promoter, whereas FMR6 is an antisense transcript overlapping the 3′ region of FMR1. FMR5 was expressed in several human brain regions from unaffected individuals and from full and premutation patients. FMR6 was silenced in full mutation and, unexpectedly, in premutation carriers suggesting abnormal transcription and/or chromatin remodeling prior to transition to the full mutation. These lncRNAs may thus be useful as biomarkers, allowing for early detection and therapeutic intervention in FXS and FXTAS. Finally we show that FMR5 and FMR6 are expressed in peripheral blood leukocytes and propose future studies that correlate lncRNA expression with clinical outcomes.
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20
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Gomes AQ, Nolasco S, Soares H. Non-coding RNAs: multi-tasking molecules in the cell. Int J Mol Sci 2013; 14:16010-39. [PMID: 23912238 PMCID: PMC3759897 DOI: 10.3390/ijms140816010] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/15/2013] [Accepted: 07/19/2013] [Indexed: 12/15/2022] Open
Abstract
In the last years it has become increasingly clear that the mammalian transcriptome is highly complex and includes a large number of small non-coding RNAs (sncRNAs) and long noncoding RNAs (lncRNAs). Here we review the biogenesis pathways of the three classes of sncRNAs, namely short interfering RNAs (siRNAs), microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). These ncRNAs have been extensively studied and are involved in pathways leading to specific gene silencing and the protection of genomes against virus and transposons, for example. Also, lncRNAs have emerged as pivotal molecules for the transcriptional and post-transcriptional regulation of gene expression which is supported by their tissue-specific expression patterns, subcellular distribution, and developmental regulation. Therefore, we also focus our attention on their role in differentiation and development. SncRNAs and lncRNAs play critical roles in defining DNA methylation patterns, as well as chromatin remodeling thus having a substantial effect in epigenetics. The identification of some overlaps in their biogenesis pathways and functional roles raises the hypothesis that these molecules play concerted functions in vivo, creating complex regulatory networks where cooperation with regulatory proteins is necessary. We also highlighted the implications of biogenesis and gene expression deregulation of sncRNAs and lncRNAs in human diseases like cancer.
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Affiliation(s)
- Anita Quintal Gomes
- Health Technology College of Lisbon—Polytechnic Institute of Lisbon, 1990-096 Lisbon, Portugal; E-Mails: (A.Q.G.); (S.N.)
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
| | - Sofia Nolasco
- Health Technology College of Lisbon—Polytechnic Institute of Lisbon, 1990-096 Lisbon, Portugal; E-Mails: (A.Q.G.); (S.N.)
- Gulbenkian Science Institute, 2780-256 Oeiras, Portugal
- Interdisciplinary Centre of Research in Animal Health (CIISA), Faculty of Veterinary Medicine, 1300-666 Lisbon, Portugal
| | - Helena Soares
- Health Technology College of Lisbon—Polytechnic Institute of Lisbon, 1990-096 Lisbon, Portugal; E-Mails: (A.Q.G.); (S.N.)
- Gulbenkian Science Institute, 2780-256 Oeiras, Portugal
- Center for Chemistry and Biochemistry, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +351-217-500-853; Fax: +351-217-500-088
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Falaleeva M, Stamm S. Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs. Bioessays 2012. [PMID: 23180440 DOI: 10.1002/bies.201200117] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent experimental evidence suggests that most of the genome is transcribed into non-coding RNAs. The initial transcripts undergo further processing generating shorter, metabolically stable RNAs with diverse functions. Small nucleolar RNAs (snoRNAs) are non-coding RNAs that modify rRNAs, tRNAs, and snRNAs that were considered stable. We review evidence that snoRNAs undergo further processing. High-throughput sequencing and RNase protection experiments showed widespread expression of snoRNA fragments, known as snoRNA-derived RNAs (sdRNAs). Some sdRNAs resemble miRNAs, these can associate with argonaute proteins and influence translation. Other sdRNAs are longer, form complexes with hnRNPs and influence gene expression. C/D box snoRNA fragmentation patterns are conserved across multiple cell types, suggesting a processing event, rather than degradation. The loss of expression from genetic loci that generate canonical snoRNAs and processed snoRNAs results in diseases, such as Prader-Willi Syndrome, indicating possible physiological roles for processed snoRNAs. We propose that processed snoRNAs acquire new roles in gene expression and represent a new class of regulatory RNAs distinct from canonical snoRNAs.
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Affiliation(s)
- Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, KY, USA
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