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Fan T, Huang Y. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis. Sci Rep 2021; 11:7896. [PMID: 33846424 PMCID: PMC8042068 DOI: 10.1038/s41598-021-86919-3] [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: 08/17/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
This study was conducted to investigate epigenetic landscape across multiple species and identify transcription factors (TFs) and their roles in controlling cell fate decision events during early embryogenesis. We made a comprehensively joint-research of chromatin accessibility of five species during embryogenesis by integration of ATAC-seq and RNA-seq datasets. Regulatory roles of candidate early embryonic TFs were investigated. Widespread accessible chromatin in early embryos overlapped with putative cis-regulatory sequences. Sets of cell-fate-determining TFs were identified. YOX1, a key cell cycle regulator, were found to homologous to clusters of TFs that are involved in neuron and epidermal cell-fate determination. Our research provides an intriguing insight into evolution of cell-fate decision during early embryogenesis among organisms.
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Affiliation(s)
- Tongqiang Fan
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
| | - Youjun Huang
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
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2
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Wu J, Chen X, Pan N, Chen B, Zhang J, Liu Z. 3β-Hydroxycholest-5-en-7-one from seahorse alleviates lipopolysaccharide-induced inflammatory responses by downregulating miR-98-5p. Life Sci 2020; 258:118176. [PMID: 32771556 DOI: 10.1016/j.lfs.2020.118176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/09/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
AIMS We investigated the anti-inflammatory activity of 3β-hydroxycholest-5-en-7-one from Hippocampus trimaculatus leach and provided a theoretical basis for identifying its therapeutic targets. MAIN METHODS Small-RNA libraries were constructed for untreated control RAW 264.7 cells and cells treated with lipopolysaccharide (LPS; 1.0 μg/mL) or 10 μM 3β-hydroxycholest-5-en-7-one +1.0 μg/mL LPS. We constructed and tested a miR-98-5p-interfering lentivirus to evaluate the role of miR-98-5p in the 3β-hydroxycholest-5-en-7-one-dependent regulation of inflammatory responses in LPS-induced macrophage and murine inflammation models. The small-RNA libraries were analyzed using high-throughput sequencing. KEY FINDINGS Among the differentially expressed microRNAs, miR-98-5p showed the most significant difference. Bioinformatics tools were used to identify the potential regulatory targets of miR-98-5p, which were tested using dual-luciferase reporter assays. Our results demonstrated that 3β-hydroxycholest-5-en-7-one exerted an anti-inflammatory effect via miR-98-5p, which negatively regulated the expression of its target gene TNFAIP3. The results indicate that miR-98-5p interference and 3β-hydroxycholest-5-en-7-one treatment significantly upregulated the low TNFAIP3 expression induced by LPS stimulation, thereby inhibiting TRAF6, RIP, NF-κB, IL-1β, and TNF-α secretion. SIGNIFICANCE 3β-Hydroxycholest-5-en-7-one alleviates inflammation by downregulating miR-98-5p and upregulating TNFAIP3, thereby blocking NF-κB pathway activation. These results reveal the specific anti-inflammatory mechanism of 3β-hydroxycholest-5-en-7-one, providing a foundation for developing new drugs and identifying drug targets.
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Affiliation(s)
- Jingna Wu
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medical College, Xiamen 361023, PR China; Fujian Universities and Colleges Engineering Research Center of Marine Biopharmaceutical Resources, Xiamen Medical College, Xiamen 361023, PR China.
| | - Xiaoting Chen
- Fisheries Research Institute of Fujian, Xiamen 361013, PR China
| | - Nan Pan
- Fisheries Research Institute of Fujian, Xiamen 361013, PR China
| | - Bei Chen
- Fisheries Research Institute of Fujian, Xiamen 361013, PR China
| | - Jinhua Zhang
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medical College, Xiamen 361023, PR China; Fujian Universities and Colleges Engineering Research Center of Marine Biopharmaceutical Resources, Xiamen Medical College, Xiamen 361023, PR China
| | - Zhiyu Liu
- Fisheries Research Institute of Fujian, Xiamen 361013, PR China.
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Bai Z, Wei J, Yu C, Han X, Qin X, Zhang C, Liao W, Li L, Huang W. Non-viral nanocarriers for intracellular delivery of microRNA therapeutics. J Mater Chem B 2019; 7:1209-1225. [DOI: 10.1039/c8tb02946f] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs are small regulatory noncoding RNAs that regulate various biological processes. Herein, we will present the development of the strategies for intracellular miRNAs delivery, and specially focus on the rational designed routes, their mechanisms of action, as well as potential therapeutics used in the host cells orin vivostudies.
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Affiliation(s)
- Zhiman Bai
- School of Physics and Materials Science
- Anhui University
- Hefei 230601
- China
| | - Jing Wei
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
| | - Changmin Yu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
| | - Xisi Han
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
| | - Xiaofei Qin
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
| | - Chengwu Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
| | - Wenzhen Liao
- Department of Nutrition and Food Hygiene
- Guangdong Provincial Key Laboratory of Tropical Disease Research
- School of Public Health
- Southern Medical University
- Guangzhou 510515
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University (NanjingTech)
- Nanjing 211816
- China
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Chen X, Guan NN, Sun YZ, Li JQ, Qu J. MicroRNA-small molecule association identification: from experimental results to computational models. Brief Bioinform 2018; 21:47-61. [PMID: 30325405 DOI: 10.1093/bib/bby098] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Small molecule is a kind of low molecular weight organic compound with variety of biological functions. Studies have indicated that small molecules can inhibit a specific function of a multifunctional protein or disrupt protein-protein interactions and may have beneficial or detrimental effect against diseases. MicroRNAs (miRNAs) play crucial roles in cellular biology, which makes it possible to develop miRNA as diagnostics and therapeutic targets. Several drug-like compound libraries were screened successfully against different miRNAs in cellular assays further demonstrating the possibility of targeting miRNAs with small molecules. In this review, we summarized the concept and functions of small molecule and miRNAs. Especially, five aspects of miRNA functions were exhibited in detail with individual examples. In addition, four disease states that have been linked to miRNA alterations were summed up. Then, small molecules related to four important miRNAs miR-21, 122, 4644 and 27 were selected for introduction. Some important publicly accessible databases and web servers of the experimentally validated or potential small molecule-miRNA associations were discussed. Identifying small molecule targeting miRNAs has become an important goal of biomedical research. Thus, several experimental and computational models have been developed and implemented to identify novel small molecule-miRNA associations. Here, we reviewed four experimental techniques used in the past few years to search for small-molecule inhibitors of miRNAs, as well as three types of models of predicting small molecule-miRNA associations from different perspectives. Finally, we summarized the limitations of existing methods and discussed the future directions for further development of computational models.
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Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Na-Na Guan
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
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Li X, Lian L, Zhang D, Qu L, Yang N. gga-miR-26a targets NEK6 and suppresses Marek's disease lymphoma cell proliferation. Poult Sci 2014; 93:1097-105. [PMID: 24795301 DOI: 10.3382/ps.2013-03656] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNA (miRNA) are a class of highly conserved, small noncoding RNA that emerge as key posttranscriptional regulators in various neoplastic transformations. Our previous study profiling the miRNA transcriptome in Marek's disease virus (MDV)-induced lymphoma revealed many novel and differentially expressed miRNA, including gga-miR-26a, which was downregulated in MDV-infected spleens of chickens. In this study, differential expression of gga-miR-26a between MDV-infected and noninfected spleens at 4, 7, 14, 21, and 28 d postinfection was analyzed by real-time PCR. The results showed gga-miR-26a were downregulated in MDV-infected spleens at cytolytic infection, latency, and tumor transformation phases. Subsequent cell proliferation assay revealed cell viability was lower in gga-miR-26a mimic transfection group than that in negative controls. Target genes of gga-miR-26a were identified by luciferase reporter gene assay. The results showed significant interaction between gga-miR-26a and Never In Mitosis Gene A (NIMA)-related kinase 6 (NEK6) gene. Subsequent gain of function experiment and Western blot assay showed that mRNA and protein levels of NEK6 were downregulated after gga-miR-26 mimic was transfected into MDV-transformed lymphoid cell line (MSB-1), indicating that NEK6 was modulated by gga-miR-26a. The expression of NEK6 showed a higher trend in MDV-infected samples including tumorous spleen and MD lymphoma from liver than that in noninfected controls. The results suggested that gga-miR-26a inhibited MSB-1 cell proliferation. Gga-miR-26a and its direct target, NEK6, might play important roles in MDV infection.
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Affiliation(s)
- Xin Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X. MicroRNA: Function, Detection, and Bioanalysis. Chem Rev 2013; 113:6207-33. [PMID: 23697835 DOI: 10.1021/cr300362f] [Citation(s) in RCA: 836] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Lin Ding
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Yongqiang Wen
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
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Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics 2013; 14 Suppl 6:S1. [PMID: 23734902 PMCID: PMC3633009 DOI: 10.1186/1471-2105-14-s6-s1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background H1N1 influenza viruses were responsible for the 1918 pandemic that caused millions of deaths worldwide and the 2009 pandemic that caused approximately twenty thousand deaths. The cellular response to such virus infections involves extensive genetic reprogramming resulting in an antiviral state that is critical to infection control. Identifying the underlying transcriptional network driving these changes, and how this program is altered by virally-encoded immune antagonists, is a fundamental challenge in systems immunology. Results Genome-wide gene expression patterns were measured in human monocyte-derived dendritic cells (DCs) infected in vitro with seasonal H1N1 influenza A/New Caledonia/20/1999. To provide a mechanistic explanation for the timing of gene expression changes over the first 12 hours post-infection, we developed a statistically rigorous enrichment approach integrating genome-wide expression kinetics and time-dependent promoter analysis. Our approach, TIme-Dependent Activity Linker (TIDAL), generates a regulatory network that connects transcription factors associated with each temporal phase of the response into a coherent linked cascade. TIDAL infers 12 transcription factors and 32 regulatory connections that drive the antiviral response to influenza. To demonstrate the generality of this approach, TIDAL was also used to generate a network for the DC response to measles infection. The software implementation of TIDAL is freely available at http://tsb.mssm.edu/primeportal/?q=tidal_prog. Conclusions We apply TIDAL to reconstruct the transcriptional programs activated in monocyte-derived human dendritic cells in response to influenza and measles infections. The application of this time-centric network reconstruction method in each case produces a single transcriptional cascade that recapitulates the known biology of the response with high precision and recall, in addition to identifying potentially novel antiviral factors. The ability to reconstruct antiviral networks with TIDAL enables comparative analysis of antiviral responses, such as the differences between pandemic and seasonal influenza infections.
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Affiliation(s)
- Elena Zaslavsky
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA.
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Rana T, Misra S, Mittal MK, Farrow AL, Wilson KT, Linton MF, Fazio S, Willis IM, Chaudhuri G. Mechanism of down-regulation of RNA polymerase III-transcribed non-coding RNA genes in macrophages by Leishmania. J Biol Chem 2010; 286:6614-26. [PMID: 21149457 DOI: 10.1074/jbc.m110.181735] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The parasitic protozoan Leishmania invades mammalian macrophages to establish infection. We reported previously that Leishmania manipulates the expression of several non-coding RNA genes (e.g. Alu RNA, B1 RNA, and signal recognition particle RNA) in macrophages to favor the establishment of their infection in the phagolysosomes of these cells (Ueda, Y., and Chaudhuri, G. (2000) J. Biol. Chem. 275, 19428-19432; Misra, S., Tripathi, M. K., and Chaudhuri, G. (2005) J. Biol. Chem. 280, 29364-29373). We report here the mechanism of this down-regulation. We found that the non-coding RNA (ncRNA) genes that are repressed by Leishmania infection in macrophages contain a "B-box" in their promoters and thus require the polymerase III transcription factor TFIIIC for their expression. We also found that Leishmania promastigotes through their surface protease (leishmanolysin or gp63) activate the thrombin receptor PAR1 in the macrophages. This activation of PAR1 raised the cytosolic concentration of Ca(2+) into the micromolar range, thereby activating the Ca(2+)-dependent protease μ-calpain. μ-Calpain then degraded TFIIIC110 to inhibit the expression of the selected ncRNA genes. Avirulent stocks of Leishmania not expressing surface gp63 failed to down-regulate ncRNAs in the exposed macrophages. Inhibition of PAR1 or calpain 1 in macrophages made them resistant to Leishmania infection. These data suggest that macrophage PAR1 and calpain 1 are potential drug targets against leishmaniasis.
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Affiliation(s)
- Tanu Rana
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208, USA
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Li T, Morgan MJ, Choksi S, Zhang Y, Kim YS, Liu ZG. MicroRNAs modulate the noncanonical transcription factor NF-kappaB pathway by regulating expression of the kinase IKKalpha during macrophage differentiation. Nat Immunol 2010; 11:799-805. [PMID: 20711193 PMCID: PMC2926307 DOI: 10.1038/ni.1918] [Citation(s) in RCA: 270] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 07/13/2010] [Indexed: 02/06/2023]
Abstract
MicroRNAs are key regulators of many biological processes, including cell differentiation. Here we show that during human monocyte-macrophage differentiation, expression of the microRNAs miR-223, miR-15a and miR-16 decreased considerably, which led to higher expression of the serine-threonine kinase IKKalpha in macrophages. In macrophages, higher IKKalpha expression in conjunction with stabilization of the kinase NIK induced larger amounts of p52. Because of low expression of the transcription factor RelB in untreated macrophages, high p52 expression repressed basal transcription of both canonical and noncanonical NF-kappaB target genes. However, proinflammatory stimuli in macrophages resulted in greater induction of noncanonical NF-kappaB target genes. Thus, a decrease in certain microRNAs probably prevents macrophage hyperactivation yet primes the macrophage for certain responses to proinflammatory stimuli.
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Affiliation(s)
- Tao Li
- Cell and Cancer Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892
| | - Michael J. Morgan
- Cell and Cancer Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892
| | - Swati Choksi
- Cell and Cancer Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892
| | - Yan Zhang
- Cell and Cancer Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892
| | - You-Sun Kim
- Institute for Medical Sciences, Ajou University School of Medicine, Suwon, 443-749 Korea
| | - Zheng-gang Liu
- Cell and Cancer Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892
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Xu H, Yao Y, Smith LP, Nair V. MicroRNA-26a-mediated regulation of interleukin-2 expression in transformed avian lymphocyte lines. Cancer Cell Int 2010; 10:15. [PMID: 20441582 PMCID: PMC2873332 DOI: 10.1186/1475-2867-10-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 05/04/2010] [Indexed: 12/15/2022] Open
Abstract
Background Micro(mi)RNAs are a class of small non-coding RNAs that play critical roles in the induction of various cancers, including lymphomas induced by oncogenic viruses. While some of the miRNAs are oncogenic, miRNAs such as miR-26a are consistently downregulated in a number of cancers, demonstrating their potential tumor suppressor functions. Global miRNA expression profiles of a number of virus-transformed avian lymphoma cell lines have shown downregulation of gga-miR-26a expression, irrespective of molecular mechanisms of transformation or the viral aetiology. The neoplastic transformation of lymphocytes by many viruses accompanies high levels of proliferative responses, mostly mediated through cytokines such as IL-2. Chicken IL-2 can modulate T-cell proliferation and cytotoxicity in vitro and in vivo and dysregulation of IL-2 expression is observed in diseases such as leukaemia. Results The expression levels of gga-miR-26a in chicken lymphoma cells transformed by 3 distinct avian oncogenic viruses, viz Marek's disease virus (MDV), avian leukosis virus (ALV) and Reticuloendotheliosis virus (REV) were consistently downregulated compared to the levels in the normal lymphocytes. This downregulation of miR-26a regardless of the viral etiology and molecular mechanisms of transformation was consistent with the tumor suppressor role of this miRNA. Notwithstanding this well-established role in cancer, we demonstrate the additional role of this miRNA in directly targeting chicken IL-2 through reporter and biochemical assays. The downregulation of miR-26a can relieve the suppressive effect of this miRNA on IL-2 expression. Conclusions We show that miR-26a is globally downregulated in a number of avian lymphoma cells irrespective of the mechanisms of transformation, reiterating the highly conserved tumor suppressor function of this miRNA. However, with the potential for directly targeting chicken IL-2, the downregulation of miR-26a in these tumor cells could relieve the inhibitory effect on IL-2 expression assisting in the proliferative features of the transformed lymphocyte lines.
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Affiliation(s)
- Hongtao Xu
- Avian Oncogenic Virus Group, Avian Infectious Diseases Programme, Institute for Animal Health, Compton, Berkshire, UK RG20 7NN.
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Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, Tenoever BR, Sealfon SC, Kleinstein SH. Antiviral response dictated by choreographed cascade of transcription factors. THE JOURNAL OF IMMUNOLOGY 2010; 184:2908-17. [PMID: 20164420 DOI: 10.4049/jimmunol.0903453] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. To isolate and identify this network, we studied DCs infected with Newcastle disease virus, which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human IFN response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell-state transition during the first 18 h postinfection could be explained by a single convergent regulatory network. Gene expression changes were driven by a stepwise multifactor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes were regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell-state transitions.
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Affiliation(s)
- Elena Zaslavsky
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
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12
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Teng G, Papavasiliou FN. Long noncoding RNAs: implications for antigen receptor diversification. Adv Immunol 2009; 104:25-50. [PMID: 20457115 DOI: 10.1016/s0065-2776(08)04002-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Noncoding RNAs (ncRNAs), both small and large, have recently risen to prominence as surprisingly versatile regulators of gene expression. In fact, eukaryotic transcriptomes are rife with RNAs that do not code for protein, though the majority of these species remains wholly uncharacterized. The functional diversity among the mere handful of validated ncRNAs hints at the vast regulatory potential of these silent biomolecules. Though the act of noncoding transcription and the resultant ncRNAs do not directly produce proteins, they represent powerful means of gene control. Here we survey the accumulating literature on the myriad functions of long ncRNAs and emphasize one curious case of noncoding transcription at antigen receptor loci in lymphocytes.
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Affiliation(s)
- Grace Teng
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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13
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Li C, Feng Y, Coukos G, Zhang L. Therapeutic microRNA strategies in human cancer. AAPS JOURNAL 2009; 11:747-57. [PMID: 19876744 DOI: 10.1208/s12248-009-9145-9] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 09/21/2009] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are approximately 22 nucleotide long, noncoding, endogenous RNA molecules which exert their functions by base pairing with messenger RNAs (mRNAs), thereby regulate protein-coding gene expression. In eukaryotic cells, miRNAs play important roles in regulating biological processes such as proliferation, differentiation, apoptosis, and stem cell self-renewal. The human genome may contain as many as 1,000 miRNAs, and more than 700 of them have been identified. miRNAs are predicted to target up to one third of mRNAs. Each miRNA can target hundreds of transcripts directly or indirectly, while more than one miRNA can converge on a single transcript target. Therefore, the potential regulatory circuitry afforded by miRNA is enormous. Recently, mounting evidence implicates miRNAs as a new class of modulator for human tumor initiation and progression. Therefore, it has been proposed that manipulating miRNA activity and miRNA biogenesis may be a novel avenue for developing efficient therapies against cancer.
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Affiliation(s)
- Chunsheng Li
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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