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Zhan Y, Yin A, Su X, Tang N, Zhang Z, Chen Y, Wang W, Wang J. Interpreting the molecular mechanisms of RBBP4/7 and their roles in human diseases (Review). Int J Mol Med 2024; 53:48. [PMID: 38577935 PMCID: PMC10999228 DOI: 10.3892/ijmm.2024.5372] [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: 10/18/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
Histone chaperones serve a pivotal role in maintaining human physiological processes. They interact with histones in a stable manner, ensuring the accurate and efficient execution of DNA replication, repair and transcription. Retinoblastoma binding protein (RBBP)4 and RBBP7 represent a crucial pair of histone chaperones, which not only govern the molecular behavior of histones H3 and H4, but also participate in the functions of several protein complexes, such as polycomb repressive complex 2 and nucleosome remodeling and deacetylase, thereby regulating the cell cycle, histone modifications, DNA damage and cell fate. A strong association has been indicated between RBBP4/7 and some major human diseases, such as cancer, age‑related memory loss and infectious diseases. The present review assesses the molecular mechanisms of RBBP4/7 in regulating cellular biological processes, and focuses on the variations in RBBP4/7 expression and their potential mechanisms in various human diseases, thus providing new insights for their diagnosis and treatment.
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Affiliation(s)
- Yajing Zhan
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, P.R. China
| | - Ankang Yin
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, P.R. China
| | - Xiyang Su
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Nan Tang
- Department of Clinical Laboratory, Wangcheng District People's Hospital, Changsha, Hunan 410000, P.R. China
| | - Zebin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, P.R. China
| | - Yi Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, P.R. China
| | - Wei Wang
- Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Hangzhou, Zhejiang 310012, P.R. China
- Department of Clinical Laboratory, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310012, P.R. China
| | - Juan Wang
- Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Hangzhou, Zhejiang 310012, P.R. China
- Department of Clinical Laboratory, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310012, P.R. China
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Cai L, Liu B, Cao Y, Sun T, Li Y. Unveiling the molecular structure and role of RBBP4/7: implications for epigenetic regulation and cancer research. Front Mol Biosci 2023; 10:1276612. [PMID: 38028543 PMCID: PMC10679446 DOI: 10.3389/fmolb.2023.1276612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Retinoblastoma-binding protein (RBBP) family is a class of proteins that can interact with tumor suppressor retinoblastoma protein (pRb). RBBP4 and RBBP7 are the only pair of homologous proteins in this family, serving as scaffold proteins whose main function is to offer a platform to indirectly connect two proteins. This characteristic allows them to extensively participate in the binding of various proteins and epigenetic complexes, indirectly influencing the function of effector proteins. As a result, they are often highlighted in organism activities involving active epigenetic modifications, such as embryonic development and cancer activation. In this review, we summarize the structural characteristics of RBBP4/7, the complexes they are involved in, their roles in embryonic development and cancer, as well as potential future research directions, which we hope to inspire the field of epigenetic research in the future.
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Affiliation(s)
- Lize Cai
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Bin Liu
- Department of Neurosurgery, Qinghai Provincial People’s Hospital, Xining, China
| | - Yufei Cao
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Ting Sun
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Yanyan Li
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
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New Biomarkers Based on Dendritic Cells for Breast Cancer Treatment and Prognosis Diagnosis. Int J Mol Sci 2023; 24:ijms24044058. [PMID: 36835467 PMCID: PMC9963148 DOI: 10.3390/ijms24044058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Dendritic cells(DCs) play a protective role in the antitumor immunity of most cancers, which can be divided into conventional dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs). Most current studies are only based on either cDCs or pDCs for the study of the relationship between DCs and breast cancer prognosis, without combining the two together. We aimed to select new biomarkers from pDCs and cDCs. In this paper, the xCell algorithm was first used to calculate the cellular abundance of 64 types of immune cells and stromal cells in tumor samples from the TCGA database, and the high-abundance pDC group and cDC group were divided according to the results of a survival analysis. Then, we looked for the co-expressed gene module of highly infiltrating pDC and cDC patients with a weighted correlation network analysis (WGCNA) and screened out the hub genes, including RBBP5, HNRNPU, PEX19, TPR, and BCL9. Finally, we analyzed the biological functions of the hub genes, and the results showed that RBBP5, TPR, and BCL9 were significantly related to the immune cells and prognosis of patients, and RBBP5 and BCL9 were involved in responding to TCF-related instructions of the Wnt pathway. In addition, we also evaluated the response of pDCs and cDCs with different abundances to chemotherapy, and the results showed that the higher the abundance of pDCs and cDCs, the higher their sensitivity to drugs. This paper revealed new biomarkers related to DCs-among them, BCL9, TPR, and RBBP5 were proven to be closely related to dendritic cells in cancer. For the first time, this paper puts forward that HNRNPU and PEX19 are related to the prognosis of dendritic cells in cancer, which also provides new possibilities for finding new targets for breast cancer immunotherapy.
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Scarrow M, Wang Y, Sun G. Molecular regulatory mechanisms underlying the adaptability of polyploid plants. Biol Rev Camb Philos Soc 2020; 96:394-407. [PMID: 33098261 DOI: 10.1111/brv.12661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Polyploidization influences the genetic composition and gene expression of an organism. This multi-level genetic change allows the formation of new regulatory pathways leading to increased adaptability. Although both forms of polyploidization provide advantages, autopolyploids were long thought to have little impact on plant divergence compared to allopolyploids due to their formation through genome duplication only, rather than in combination with hybridization. Recent advances have begun to clarify the molecular regulatory mechanisms such as microRNAs, alternative splicing, RNA-binding proteins, histone modifications, chromatin remodelling, DNA methylation, and N6 -methyladenosine (m6A) RNA methylation underlying the evolutionary success of polyploids. Such research is expanding our understanding of the evolutionary adaptability of polyploids and the regulatory pathways that allow adaptive plasticity in a variety of plant species. Herein we review the roles of individual molecular regulatory mechanisms and their potential synergistic pathways underlying plant evolution and adaptation. Notably, increasing interest in m6A methylation has provided a new component in potential mechanistic coordination that is still predominantly unexplored. Future research should attempt to identify and functionally characterize the evolutionary impact of both individual and synergistic pathways in polyploid plant species.
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Affiliation(s)
- Margaret Scarrow
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041000, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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5
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Wang JK, Wang Z, Li G. MicroRNA-125 in immunity and cancer. Cancer Lett 2019; 454:134-145. [PMID: 30981762 DOI: 10.1016/j.canlet.2019.04.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a wide variety of critical roles in different biological processes by post-transcriptionally regulating gene expression. They access diverse regulatory pathways during various stages of cellular differentiation, growth, and apoptosis, and can contribute to both normal and diseased functions. One important family of miRNAs involved in these functions is the miR-125 family (miR-125a and miR-125b). Investigations have been made to increasingly uncover the mechanisms by which the miR-125 family regulates normal homeostasis and growth in a variety of cell types including immune cells, and how dysregulation of miR-125a and miR-125b can lead to disease pathogenesis and tumorigenesis. In this review, we summarize what is currently known about miR-125a and miR-125b, mainly focusing on their roles in immune cell development and function as well as tumor suppression and promotion.
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Affiliation(s)
- Jessica K Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Zhe Wang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Guideng Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States; Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
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Malhotra S, Villar LM, Costa C, Midaglia L, Cubedo M, Medina S, Fissolo N, Río J, Castilló J, Álvarez-Cermeño JC, Sánchez A, Montalban X, Comabella M. Circulating EZH2-positive T cells are decreased in multiple sclerosis patients. J Neuroinflammation 2018; 15:296. [PMID: 30367633 PMCID: PMC6202809 DOI: 10.1186/s12974-018-1336-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies in experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis (MS), suggest an involvement of the histone methyltransferase enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) in important processes such as cell adhesion and migration. METHODS Here, we aimed to expand these initial observations by investigating the role of EZH2 in MS. mRNA expression levels for EZH2 were measured by real-time PCR in peripheral blood mononuclear cells (PBMC) from 121 MS patients (62 untreated and 59 receiving treatment) and 24 healthy controls. RESULTS EZH2 expression levels were decreased in PBMC from untreated patients compared to that from controls, and treatment significantly upregulated EZH2 expression. Expression of miR-124 was increased in MS patients compared to controls. Blood immunophenotyping revealed EZH2 expression mostly restricted to CD4+ and CD8+ T cells, and circulating EZH2+ CD4+ and CD8+ T cells were decreased in untreated MS patients compared to controls. CD8+ T cells expressing EZH2 exhibited a predominant central memory phenotype, whereas EZH2+ CD4+ T cells were of effector memory nature, and both T cell subsets produced TNF-α. EZH2+ T cells were enriched in the cerebrospinal fluid compartment compared to blood and were found in chronic active lesions from MS patients. EZH2 inhibition and microarray analysis in PBMC was associated with significant downregulation of key T cell adhesion molecules. CONCLUSION These findings suggest a role of EZH2 in the migration of T cells in MS patients. The observation of TNF-α expression by CD4+ and CD8+ T cells expressing EZH2 warrants additional studies to explore more in depth the pathogenic potential of EZH2+-positive cells in MS.
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Affiliation(s)
- Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Luisa M Villar
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - Carme Costa
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luciana Midaglia
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Cubedo
- Departament d'Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Silvia Medina
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - Nicolás Fissolo
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Río
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquín Castilló
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José C Álvarez-Cermeño
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - Alex Sánchez
- Unitat d'Estadística i Bioinformàtica, Institut de Recerca, HUVH, Barcelona, Spain.,Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Spain
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.
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Czimmerer Z, Horvath A, Daniel B, Nagy G, Cuaranta-Monroy I, Kiss M, Kolostyak Z, Poliska S, Steiner L, Giannakis N, Varga T, Nagy L. Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:14-28. [DOI: 10.1016/j.bbagrm.2017.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/23/2017] [Accepted: 11/09/2017] [Indexed: 12/26/2022]
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Fujino T, Hasebe N. Alteration of histone H3K4 methylation in glomerular podocytes associated with proteinuria in patients with membranous nephropathy. BMC Nephrol 2016; 17:179. [PMID: 27855638 PMCID: PMC5114780 DOI: 10.1186/s12882-016-0390-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/03/2016] [Indexed: 01/06/2023] Open
Abstract
Background Histone H3K4 trimethylation (H3K4 me3) is found in active euchromatic regions and plays an important role in podocyte function in which actin filaments are abundant in the foot processes. The pathogenesis of membranous nephropathy (MN), the most prevalent cause of primary nephrotic syndrome in the middle-aged and elderly, is podocyte dysfunction. Methods We investigated the role of H3K4 me3 in podocyte dysfunction in nephrotic syndrome using cultured podocytes and a mouse proteinuria model induced by LPS. We examined renal biopsy specimens from six patients with nephrotic syndrome caused by Phospholipase-A2-Receptor-positive primary MN. Results H3K4 me3 exhibited a pattern of nuclear expression in podocytes of the kidneys from patients with MN. The overlapping expression of H3K4 me3 and cathepsin L (a potent endoprotease causing the breakdown of actin-associated protein within lysosomal compartments in kidney podocytes) were higher in patients with MN compared with the controls. Histone H3K4 me3 in kidney podocytes was negatively correlated with synaptopodin, an actin-associated protein in podocytes, and the expression was positively correlated with the proteinuria levels in patients with MN. Histone H3K4 me3 levels were elevated in podocytes of LPS-treated mice, combined with an increase in podocyte swelling, an elevation of serum creatinine and urine albumin, increased cathepsin L, and decreased synaptopodin expression. Histone H3K4 me3 levels at the cathepsin L promoter were elevated in LPS-exposed mouse kidneys. The administration of shRNA against MLL3 (an H3K4 methyltransferase) to LPS-treated mice and cultured podocytes co-cultured with LPS-stimulated macrophages ameliorated podocyte swelling, an elevation in the serum creatinine and urine albumin levels and an increased expression of histone H3K4 me3 and cathepsin L, and a decreased expression of synaptopodin and increase in histone H3K4 me3 levels at the cathepsin L promoter. Conclusions Histone H3K4 me3 upregulation may be involved in podocyte dysfunction and the pathophysiology of MN. Targeting this epigenetic signature of histone H3K4 me3 followed by modulating the actin dynamics may be an effective strategy to ameliorate the consequences of MN.
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Affiliation(s)
- Takayuki Fujino
- Department of Internal Medicine, Cardiovascular Respiratory and Neurology and Nephrology Division, Asahikawa Medical University, Midorigaoka Higashi 2-1-1-1, Asahikawa, 078-8510, Japan.
| | - Naoyuki Hasebe
- Department of Internal Medicine, Cardiovascular Respiratory and Neurology and Nephrology Division, Asahikawa Medical University, Midorigaoka Higashi 2-1-1-1, Asahikawa, 078-8510, Japan
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Olbromski M, Grzegrzolka J, Jankowska-Konsur A, Witkiewicz W, Podhorska-Okolow M, Dziegiel P. MicroRNAs modulate the expression of the SOX18 transcript in lung squamous cell carcinoma. Oncol Rep 2016; 36:2884-2892. [DOI: 10.3892/or.2016.5102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/11/2016] [Indexed: 11/06/2022] Open
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Darcq E, Warnault V, Phamluong K, Besserer GM, Liu F, Ron D. MicroRNA-30a-5p in the prefrontal cortex controls the transition from moderate to excessive alcohol consumption. Mol Psychiatry 2015; 20:1219-31. [PMID: 25330738 PMCID: PMC4437888 DOI: 10.1038/mp.2014.120] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 08/11/2014] [Accepted: 08/25/2014] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) induce messenger RNA (mRNA) degradation and repress mRNA translation. Several miRNAs control the expression of the brain-derived neurotrophic factor (BDNF) in the prefrontal cortex (PFC). The BDNF signaling pathway is activated by moderate intake of alcohol to prevent escalation to excessive drinking. Here, we present data to suggest that the transition from moderate to uncontrolled alcohol intake occurs, in part, upon a breakdown of this endogenous protective pathway via a miRNA-dependent mechanism. Specifically, a mouse paradigm that mimics binge alcohol drinking in humans produced a robust reduction in BDNF mRNA levels in the medial PFC (mPFC), which was associated with increased expression of several miRNAs including miR-30a-5p. We show that miR-30a-5p binds the 3' untranslated region of BDNF, and that overexpression of miR-30a-5p in the mPFC decreased BDNF expression. Importantly, overexpression of miR-30a-5p in the mPFC produced an escalation of alcohol intake and a preference over water. Conversely, inhibition of miR-30a-5p in the mPFC using a Locked Nucleic Acid sequence that targets miR-30a-5p restored BDNF levels and decreased excessive alcohol intake. Together, our results indicate that miR-30a-5p plays a key role in the transition from moderate to excessive alcohol intake.
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Epigenetic dynamics in immunity and autoimmunity. Int J Biochem Cell Biol 2015; 67:65-74. [DOI: 10.1016/j.biocel.2015.05.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 02/01/2023]
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Liu Y, Liang X, Yang R. Identification of peculiar and common effects of histone modifications on transcription. J Theor Biol 2015; 380:24-39. [PMID: 26002420 DOI: 10.1016/j.jtbi.2015.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/05/2015] [Accepted: 04/29/2015] [Indexed: 11/16/2022]
Abstract
Histone modifications (HMs) play an important role in controlling eukaryotic gene expression and next generation sequencing (NGS) has greatly advanced the research on this topic with generating many high-resolution maps for HMs. Here, we use these maps to analyze the relationship between HMs and transcription. By incorporating various segments of genes into analysis without restricting the scope only in the promoter region, we have collected more comprehensive data and captured some details of this process. A position effect of gene regions has been revealed and it can even inverse the property of some HMs from activating to repressing genes such as the cases of H3K4me3, H3K36me3 and H3K14ac. Especially H3K36me3, its dual character on gene transcription makes it able to serve as a criterion to distinguish high and low expressed genes. We also study the general property of different HMs based on the comprehensive data. Using exploratory factor analysis (EFA), we have extracted 4 latent structures underlying the HMs, which are able to represent their activating and repressing effects concisely. These 4 factors have fine properties in the aspects of distinguishing high and low expressed genes, predicting transcription level and identifying genes with unique attributes such as stable RNA generating genes found to have a close relationship with lifespan of organisms here. In summary, while the position effect associated HM peculiarities demonstrate some details of the complex HM regulation network divergently, the common factors catch the nature of the network convergently. This deepens our understanding on the HM-transcription relationship.
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Affiliation(s)
- Yu Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, PR China
| | - Xue Liang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, PR China
| | - Rongcun Yang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, PR China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, PR China.
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Mei S, Liu Y, Wu X, He Q, Min S, Li L, Zhang Y, Yang R. TNF-α-mediated microRNA-136 induces differentiation of myeloid cells by targeting NFIA. J Leukoc Biol 2015; 99:301-10. [PMID: 26329426 DOI: 10.1189/jlb.1a0115-032rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 08/19/2015] [Indexed: 01/05/2023] Open
Abstract
Immune cell-lineage specification and function are influenced by progenitor origin and environmental factors. The mechanism of differentiation of immune cells, such as neutrophils, monocytes, and myeloid-derived suppressor cells, in inflammatory environments has not been elucidated completely. In this study, we have identified human microRNA-136 as a positive regulator of the differentiation of granulocytes and monocytes. Ectopic microRNA-136 induced cells to express higher levels of CD11b, CD14, and C/EBPε, secrete more cytokines, and synthesize higher levels of reactive oxygen species and H(2)O(2). microRNA-136 was shown to target and degrade multiple differentiation-associated molecules, such as the transcription factor NFIA, which induced the release of another microRNA, microRNA-223, with the ability to promote CD11b expression. Furthermore, microRNA-136 expression was remarkably increased by TNF-α, which activated NF-κB to bind to the DNA-promoter region controlling microRNA-136 expression. Additionally, TNF-α may alter NFIA expression through its modulation of microRNA-136 expression. Thus, TNF-α-mediated microRNA-136 may play a critical role in the generation and differentiation of inflammatory immune cells.
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Affiliation(s)
- Shiyue Mei
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Yu Liu
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Xue Wu
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Qingsheng He
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Siping Min
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Ling Li
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Yuan Zhang
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
| | - Rongcun Yang
- *Department of Immunology, School of Medicine, State Key Laboratory of Medicinal Chemical Biology, and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, P. R. China
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