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Role of noncoding rnas in orthodontic tooth movement: new insights into periodontium remodeling

JOUrnaL OF TRANSLATIONAL MEDICINE 2023年第1期21卷 1-20页

作者： Chen, Yuming Zhang, Chao Southern Med Univ Stomatol Hosp Guangzhou 510280 Peoples R China

Orthodontic tooth movement (OTM) is biologically based on the spatiotemporal remodeling process in periodontium, the mechanisms of which remain obscure. noncoding rnas (ncrnas), especially micrornas and long noncoding rnas, play a pivotal role in maintaining periodontal homeostasis at the transcriptional, post-transcriptional, and epigenetic levels. Under force stimuli, mechanosensitive ncrnas with altered expression levels transduce mechanical load to modulate intracellular genes. These ncrnas regulate the biomechanical responses of periodontium in the catabolic, anabolic, and coupling phases throughout OTM. To achieve this, down or upregulated ncrnas actively participate in cell proliferation, differentiation, autophagy, inflammatory, immune, and neurovascular responses. This review highlights the regulatory mechanism of fine-tuning ncrnas in periodontium remodeling during OTM, laying the foundation for safe, precise, and personalized orthodontic treatment.

关键词： Orthodontic tooth movement noncoding rna Periodontium remodeling Orthodontic treatment

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A screen for conserved sequences with biased base composition identifies noncoding rnas in the A-T rich genome of Plasmodium falciparum

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MOLECULAR AND BIOCHEMICAL PARASITOLOGY 2005年第2期144卷 149-158页

作者： Upadhyay, R Bawankar, P Malhotra, D Patankar, S Indian Inst Technol Sch Biosci & Bioengn Bombay 400076 Maharashtra India

noncoding rnas (ncrnas) such as snrnas, snornas and micrornas play important roles in transcription and translation control. These ncrnas have yet to be discovered in the malarial parasite Plasmodium falciparum, an organism in which these basic biological processes are poorly understood. Inspired by a report by Klein et al., we initiated a bioinformatics screen to uncover several candidate ncrnas from the parasite genome using two simple criteria: first, elevated GC content in the highly A-T rich intergenic regions of the P. falciparum genome and second, conservation of sequence homology between malaria parasite species. We show that all the annotated trnas can be successfully identified in our screen as well as several new candidates that show homology to snrnas and snornas, and ten candidate ncrnas of unknown function. Three of the candidate snrnas, a predicted selenocysteine trna and two candidates of unknown function are expressed in asexual stage parasites, further validating the screen. With these results, the biological processes underlying rna-mediated regulation of transcription, translation and splicing can be studied in an important human pathogen. (c) 2005 Elsevier B.V. All rights reserved.

关键词： Plasmodium malaria noncoding rna bioinformatics GC content

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Functional Classification and Experimental Dissection of Long noncoding rnas

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CELL 2018年第3期172卷 393-407页

作者： Kopp, Florian Mendell, Joshua T. Univ Texas Southwestern Med Ctr Dallas Dept Mol Biol Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Harold C Simmons Comprehens Canc Ctr Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Hamon Ctr Regenerat Sci & Med Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Howard Hughes Med Inst Dallas TX 75390 USA

Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding rnas (lncrnas). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncrna field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncrna function. We categorize lncrna loci into those that regulate gene expression in cis versus those that perform functions in trans and propose an experimental approach to dissect lncrna activity based on these classifications. These strategies to further understand lncrnas promise to reveal new and unanticipated biology with great potential to advance our understanding of normal physiology and disease.

关键词： lncrna noncoding rna

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The promising role of noncoding rnas in cancer-associated fibroblasts: an overview of current status and future perspectives

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JOUrnaL OF HEMATOLOGY & ONCOLOGY 2020年第1期13卷 1-21页

作者： Fang, Zengli Xu, Jin Zhang, Bo Wang, Wei Liu, Jiang Liang, Chen Hua, Jie Meng, Qingcai Yu, Xianjun Shi, Si Fudan Univ Shanghai Canc Ctr Dept Pancreat Surg 270 Dong An Rd Shanghai 200032 Peoples R China Fudan Univ Shanghai Med Coll Dept Oncol Shanghai 200032 Peoples R China Shanghai Pancreat Canc Inst Shanghai 200032 Peoples R China Fudan Univ Pancreat Canc Inst Shanghai 200032 Peoples R China

As the most important component of the stromal cell population in the tumor microenvironment (TME), cancer-associated fibroblasts (CAFs) are crucial players in tumor initiation and progression. The interaction between CAFs and tumor cells, as well as the resulting effect, is much greater than initially expected. Numerous studies have shown that noncoding rnas (ncrnas) play an irreplaceable role in this interplay, and related evidence continues to emerge and advance. Under the action of ncrnas, normal fibroblasts are directly or indirectly activated into CAFs, and their metabolic characteristics are changed;thus, CAFs can more effectively promote tumor progression. Moreover, via ncrnas, activated CAFs can affect the gene expression and secretory characteristics of cells, alter the TME and enhance malignant biological processes in tumor cells to contribute to tumor promotion. Previously, ncrna dysregulation was considered the main mechanism by which ncrnas participate in the crosstalk between CAFs and tumor cells. Recently, however, exosomes containing ncrnas have been identified as another vital mode of interaction between these two types of cells, with a more direct and clear function. Gaining an in-depth understanding of ncrnas in CAFs and the complex regulatory network connecting CAFs with tumor cells might help us to establish more effective and safer approaches for cancer therapies targeting ncrnas and CAFs and offer new hope for cancer patients.

关键词： noncoding rna Microrna Long noncoding rna Cancer-associated fibroblasts Tumor microenvironment Cancer Exosome Cell– cell interaction

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Emerging role of long noncoding rnas in autoimmune diseases

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AUTOIMMUNITY REVIEWS 2015年第9期14卷 798-805页

作者： Wu, Guo-Cui Pan, Hai-Feng Leng, Rui-Xue Wang, De-Guang Li, Xiang-Pei Li, Xiao-Mei Ye, Dong-Qing Anhui Med Univ Sch Publ Hlth Dept Epidemiol & Biostat Hefei 230032 Anhui Peoples R China Anhui Med Univ Anhui Prov Lab Populat Hlth & Major Dis Screening Hefei 230032 Anhui Peoples R China Anhui Med Univ Affiliated Hosp 2 Dept Nephrol Hefei 230601 Anhui Peoples R China Anhui Med Univ Anhui Prov Hosp Dept Rheumatol & Immunol Hefei 230001 Anhui Peoples R China

Long noncoding rna (lncrna), with size larger than 200 nucleotides, is a new class of noncoding rna. Emerging evidence has revealed that lncrnas play a key role in the regulation of immunological functions and autoimmunity. Herein, we review the recent findings of lncrna regulation in immune functions and in the development of autoimmunity and autoimmune disease. In addition, we focus on the involvement of lncrna regulation in innate and adaptive immune responses, immune cell development, and differential expression of lncrnas in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), type 1 diabetes mellitus (T1DM), multiple sclerosis (MS), autoimmune thyroid disease (AITD), psoriasis, polymyositis/dermatomyositis (PM/DM) and Crohn's disease (CD). (C) 2015 Elsevier B.V. All rights reserved.

关键词： lncrna noncoding rna Immune function Autoimmunity Autoimmune disease

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Predicting the Organelle Location of noncoding rnas Using Pseudo Nucleotide Compositions

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INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES 2017年第4期9卷 540-544页

作者： Feng, Pengmian Zhang, Jidong Tang, Hua Chen, Wei Lin, Hao North China Univ Sci & Technol Sch Publ Hlth Tangshan 063000 Peoples R China Zunyi Med Coll Dept Immunol Zunyi 563000 Peoples R China Sichuan Med Univ Dept Pathophysiol Luzhou 646000 Peoples R China North China Univ Sci & Technol Sch Sci Dept Phys Tangshan 063000 Peoples R China North China Univ Sci & Technol Ctr Genom & Computat Biol Tangshan 063000 Peoples R China Univ Elect Sci & Technol China Key Lab Neuroinformat Minist Educ Chengdu 610054 Sichuan Peoples R China Univ Elect Sci & Technol China Ctr Informat Biomed Sch Life Sci & Technol Chengdu 610054 Sichuan Peoples R China

noncoding rnas (ncrnas) are implicated in various biological processes. Recent findings have demonstrated that the function of ncrnas correlates with their provenance. Therefore, the recognition of ncrnas from different organelle genomes will be helpful to understand their molecular functions. However, the weakness of experimental techniques limits the progress toward studying organellar ncrnas and their functional relevance. As a complement of experiments, computational method provides an important choice to identify ncrna in different organelles. Thus, a computational model was developed to identify ncrnas from kinetoplast and mitochondrion organelle genomes. In this model, rna sequences are encoded by "pseudo dinucleotide composition." It was observed by the jackknife test that the overall success rate achieved by the proposed model was 90.08 %. We hope that the proposed method will be helpful in predicting ncrna organellar locations.

关键词： noncoding rna Organelle Support vector machine Pseudo nucleotide composition rna structural property

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Probing the function of long noncoding rnas in the nucleus

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CHROMOSOME RESEARCH 2020年第1期28卷 87-110页

作者： Akkipeddi, Sajal Medha K. Velleca, Anthony J. Carone, Dawn M. Swarthmore Coll Dept Biol Swarthmore PA 19081 USA Mem Sloan Kettering Canc Ctr Dept Mol Phamacol 1275 York Ave New York NY 10021 USA

The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding rnas have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding rna (lncrna), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other rna molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncrnas, along with the ways in which those techniques have revealed insights into their mechanisms of action. Foundational observations into lncrna function have been gleaned from molecular cytology-based, single-cell approaches to illuminate both the localization and abundance of lncrnas in addition to their potential binding partners. Biochemical, extraction-based approaches have revealed the molecular contacts between lncrnas and other molecules within the nuclear environment and how those interactions may contribute to nuclear organization and regulation. Using examples of well-studied nuclear lncrnas, we demonstrate that the emerging functions of individual lncrnas have been most clearly deduced from combined cytology and biochemical approaches tailored to study specific lncrnas. As more functional nuclear lncrnas continue to emerge, the development of additional technologies to study their interactions and mechanisms of action promise to continually expand our understanding of nuclear organization, chromosome architecture, genome regulation, and disease states.

关键词： noncoding rna Nuclear organization Genome regulation Molecular cytology Microscopy Biochemical methods

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The Connection between the Growth Dynamics of Transplanted Lewis Carcinoma in Mice and Changes in the Activity of Genes and noncoding rnas after Low-Dose Irradiation

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BIOLOGY BULLETIN 2022年第12期49卷 2266-2278页

作者： Mikhailov, V. F. Saleeva, D. V. Shulenina, L. V. Raeva, N. F. Rozhdestvensky, L. M. Zasukhina, G. D. Fed Med Biol Agcy Burnasyan Fed Med Biophys Ctr Moscow Russia Russian Acad Sci Vavilov Inst Gen Genet Moscow Russia

The effect of low-dose radiation was studied on the growth dynamics of transfused Lewis carcinoma cells in female C57Bl/6 mice. Fourfold total fractionated irradiation was conducted at a dose of 75 mGy (at a dose rate of 0.154 Gy/min and a voltage of 200 kV), starting from day 10 after the transplantation with a four-day interval. On days 14 and 22, a group of mice was euthanized to study the expression levels of genes and noncoding rnas (micrornas and long noncoding rnas) in tumor cells, as well as in normal tissues (bone marrow, liver, spleen, thymus). The total rna was obtained, and complementary DNA was synthesized according to the manufacturer's protocol. After that, a real-time PCR reaction was performed using the SYBR Green I dye (Thermo Scientific, United States) or a TaqMan probe and specific primers. Genes and noncoding rnas were divided into groups of oncogenes and oncosuppressors according to scientific research. In the group of irradiated mice, a decrease in the tumor growth rate was observed, mainly from day 20, accompanied by a change in the activity of the studied genes. The ratio of the activity of oncosuppressors to oncogenes was calculated for the obtained tissues. These fractions were 0.5 for the tumor, 10.7 for the bone marrow, and 2.4 for the spleen and thymus. Thus, it can be stated that in the tumor there was a particularly pronounced activation of oncogenes compared to the activity of oncosuppressors, while the opposite effect was observed in normal tissues.

关键词： low-dose radiation Lewis lung carcinoma genes noncoding rna oncogenes oncosuppressors P53 NFkB

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Analysis of autophagy-related genes and associated noncoding rnas and transcription factors in digestive system tumors

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FUTURE ONCOLOGY 2019年第36期15卷 4141-4154页

作者： Lin, Liewen Xia, Ligang Tang, Donge Dai, Yong Chen, Wenbiao Zhejiang Univ Affiliated Hosp 1 Collaborat Innovat Ctr Diag & Treatment Infect Di Coll MedNatl Clin Res Ctr Infect DisState Key L Hangzhou Zhejiang Peoples R China Southern Univ Sci & Technol Jinan Univ Shenzhen Peoples Hosp Clin Med Coll 2Affiliated Hosp 1Dept Clin Med R Shenzhen 518020 Guangdong Peoples R China Southern Univ Sci & Technol Affiliated Hosp 1 Jinan Univ Clin Med Coll 2Shenzhen Peoples HospDept Gastro Shenzhen 518020 Guangdong Peoples R China

Aim: To investigate the autophagy-related gene (ATG) expression and the associated noncoding rnas (ncrna) and transcription factors (TF) in digestive system tumors (DST). Methods: We systematically investigated the ATG expression in DST by weighted gene correlation network analysis, crosstalk connection, functional analysis and Pivot analysis. Results: ATGs were clustered into six modules with co-expression in DST. Functional analysis revealed that six ATG-related modules were enriched in biological pathways involved in tumorigenesis. Pivot analysis identified key ncrnas and TFs, which are essential for the pathogenesis, clinical diagnosis and treatment of DST. Conclusion: Our study highlights the crucial roles of ncrna and TFs in the identification of potential biomarkers or therapeutic targets for DST.

关键词： autophagy-related gene digestive system tumor noncoding rna pan-cancer transcription factor

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First Transcriptome Analysis of Hepatoblastoma in Brazil: Unraveling the Pivotal Role of noncoding rnas and Metabolic Pathways

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BIOCHEMICAL GENETICS 2024年 1-34页

作者： Aguiar, Talita Ferreira Marques Rivas, Maria Prates Silva, Edson Mario de Andrade Pires, Sara Ferreira Dangoni, Gustavo Dib Macedo, Taiany Curdulino Defelicibus, Alexandre Barros, Bruna Duraes de Figueiredo Novak, Estela Cristofani, Lilian Maria Odone, Vicente Cypriano, Monica de Toledo, Silvia Regina Caminada da Cunha, Isabela Werneck da Costa, Cecilia Maria Lima Carraro, Dirce Maria Tojal, Israel Mendes, Tiago Antonio de Oliveira Krepischi, Ana Cristina Victorino Univ Sao Paulo Inst Biosci Human Genome & Stem Cell Res Ctr Dept Genet & Evolutionary Biol So Paulo Brazil Columbia Univ Irving Med Ctr New York NY USA Univ Fed Vicosa Dept Biochem & Mol Biol Vicosa MG Brazil Int Ctr Res AC Camargo Canc Ctr So Paulo Brazil So Paulo Univ Pediat Canc Inst ITACI Med Sch Pediat Dept So Paulo Brazil Fed Univ So Paulo Dept Pediat Adolescent & Child Canc Support Grp GRAACC So Paulo Brazil Rede DOR So Luiz Rede OR Sao Luiz So Paulo Brazil Dept Pediat Oncol AC Camargo Canc Ctr So Paulo Brazil Univ Florida Hort Sci Dept Gainesville FL USA

Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues. The analysis unveiled 1,492 differentially expressed genes (1,031 upregulated and 461 downregulated), including 920 protein-coding genes (62%). Upregulated biological processes were linked to cell differentiation, signaling, morphogenesis, and development, involving known hepatoblastoma-associated genes (DLK1, MEG3, HDAC2, TET1, HMGA2, DKK1, DKK4), alongside with novel findings (GYNG4, CDH3, and TNFRSF19). Downregulated processes predominantly centered around oxidation and metabolism, affecting amines, nicotinamides, and lipids, featuring novel discoveries like the repression of SYT7, TTC36, THRSP, CCND1, GCK and CAMK2B. Two genes, which displayed a concordant pattern of DNA methylation alteration in their promoter regions and dysregulation in the transcriptome, were further validated by RT-qPCR: the upregulated TNFRSF19, a key gene in the embryonic development, and the repressed THRSP, connected to lipid metabolism. Furthermore, based on protein-protein interaction analysis, we identified genes holding central positions in the network, such as HDAC2, CCND1, GCK, and CAMK2B, among others, that emerged as prime candidates warranting functional validation in future studies. Notably, a significant dysregulation of non-coding rnas (ncrnas), predominantly upregulated transcripts, was observed, with 42% of the top 50 highly expressed genes being ncrnas. An integrative mirna-mrna analysis revealed crucial biological processe

关键词： Hepatoblastoma rna-seq Transcriptome noncoding rna Lipid Metabolism

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