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Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
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Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
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2
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Sharov AA, Nakatake Y, Wang W. Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells. BMC Bioinformatics 2022; 23:377. [PMID: 36114445 PMCID: PMC9479252 DOI: 10.1186/s12859-022-04924-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/12/2022] [Indexed: 12/26/2022] Open
Abstract
Background Transcription factors (TFs) play central roles in maintaining “stemness” of embryonic stem (ES) cells and their differentiation into several hundreds of adult cell types. The regulatory competence of TFs is routinely assessed by detecting target genes to which they bind. However, these data do not indicate which target genes are activated, repressed, or not affected by the change of TF abundance. There is a lack of large-scale studies that compare the genome binding of TFs with the expression change of target genes after manipulation of each TF. Results In this paper we associated human TFs with their target genes by two criteria: binding to genes, evaluated from published ChIP-seq data (n = 1868); and change of target gene expression shortly after induction of each TF in human ES cells. Lists of direction- and strength-specific regulated target genes are generated for 311 TFs (out of 351 TFs tested) with expected proportion of false positives less than or equal to 0.30, including 63 new TFs not present in four existing databases of target genes. Our lists of direction-specific targets for 152 TFs (80.0%) are larger that in the TRRUST database. In average, 30.9% of genes that respond greater than or equal to twofold to the induction of TFs are regulated targets. Regulated target genes indicate that the majority of TFs are either strong activators or strong repressors, whereas sets of genes that responded greater than or equal to twofold to the induction of TFs did not show strong asymmetry in the direction of expression change. The majority of human TFs (82.1%) regulated their target genes primarily via binding to enhancers. Repression of target genes is more often mediated by promoter-binding than activation of target genes. Enhancer-promoter loops are more abundant among strong activator and repressor TFs. Conclusions We developed an atlas of regulated targets of TFs (ART-TF) in human ES cells by combining data on TF binding with data on gene expression change after manipulation of individual TFs. Sets of regulated gene targets were identified with a controlled rate of false positives. This approach contributes to the understanding of biological functions of TFs and organization of gene regulatory networks. This atlas should be a valuable resource for ES cell-based regenerative medicine studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04924-3.
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Su XJ, Shen BD, Wang K, Song QX, Yang X, Wu DS, Shen HX, Zhu C. Roles of the Neuron-Restrictive Silencer Factor in the Pathophysiological Process of the Central Nervous System. Front Cell Dev Biol 2022; 10:834620. [PMID: 35300407 PMCID: PMC8921553 DOI: 10.3389/fcell.2022.834620] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
The neuron-restrictive silencer factor (NRSF), also known as repressor element 1 (RE-1) silencing transcription factor (REST) or X2 box repressor (XBR), is a zinc finger transcription factor that is widely expressed in neuronal and non-neuronal cells. It is a master regulator of the nervous system, and the function of NRSF is the basis of neuronal differentiation, diversity, plasticity, and survival. NRSF can bind to the neuron-restrictive silencer element (NRSE), recruit some co-repressors, and then inhibit transcription of NRSE downstream genes through epigenetic mechanisms. In neurogenesis, NRSF functions not only as a transcriptional silencer that can mediate the transcriptional inhibition of neuron-specific genes in non-neuronal cells and thus give neuron cells specificity, but also as a transcriptional activator to induce neuronal differentiation. Many studies have confirmed the association between NRSF and brain disorders, such as brain injury and neurodegenerative diseases. Overexpression, underexpression, or mutation may lead to neurological disorders. In tumorigenesis, NRSF functions as an oncogene in neuronal tumors, such as neuroblastomas, medulloblastomas, and pheochromocytomas, stimulating their proliferation, which results in poor prognosis. Additionally, NRSF-mediated selective targets gene repression plays an important role in the development and maintenance of neuropathic pain caused by nerve injury, cancer, and diabetes. At present, several compounds that target NRSF or its co-repressors, such as REST-VP16 and X5050, have been shown to be clinically effective against many brain diseases, such as seizures, implying that NRSF and its co-repressors may be potential and promising therapeutic targets for neural disorders. In the present review, we introduced the biological characteristics of NRSF; reviewed the progress to date in understanding the roles of NRSF in the pathophysiological processes of the nervous system, such as neurogenesis, brain disorders, neural tumorigenesis, and neuropathic pain; and suggested new therapeutic approaches to such brain diseases.
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Affiliation(s)
- Xin-Jin Su
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bei-Duo Shen
- Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Kun Wang
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Xin Song
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xue Yang
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - De-Sheng Wu
- Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Hong-Xing Shen
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhu
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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Kamgar-Dayhoff P, Brelidze TI. Multifaceted effect of chlorpromazine in cancer: implications for cancer treatment. Oncotarget 2021; 12:1406-1426. [PMID: 34262651 PMCID: PMC8274723 DOI: 10.18632/oncotarget.28010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Since its discovery in 1951, chlorpromazine (CPZ) has been one of the most widely used antipsychotic medications for treating schizophrenia and other psychiatric disorders. In addition to its antipsychotic effect, many studies in the last several decades have found that CPZ has a potent antitumorigenic effect. These studies have shown that CPZ affects a number of molecular oncogenic targets through multiple pathways, including the regulation of cell cycle, cancer growth and metastasis, chemo-resistance and stemness of cancer cells. Here we review studies on molecular mechanisms of CPZ’s action on key proteins involved in cancer, including p53, YAP, Ras protein, ion channels, and MAPKs. We discuss common and overlapping signaling pathways of CPZ’s action, its cancer-type specificity, antitumorigenic effects of CPZ reported in animal models and population studies on the rate of cancer in psychiatric patients. We also discuss the potential benefits and limitations of repurposing CPZ for cancer treatment.
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Affiliation(s)
- Pareesa Kamgar-Dayhoff
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D.C., USA
| | - Tinatin I Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D.C., USA
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Liu M, Zhang SB, Luo YX, Yang YL, Zhang XZ, Li B, Meng Y, Chen YJ, Guo RX, Xiong YC, Xin WJ, Li D. NFATc2-dependent epigenetic upregulation of CXCL14 is involved in the development of neuropathic pain induced by paclitaxel. J Neuroinflammation 2020; 17:310. [PMID: 33070779 PMCID: PMC7570122 DOI: 10.1186/s12974-020-01992-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022] Open
Abstract
Background The major dose-limiting toxicity of paclitaxel, one of the most commonly used drugs to treat solid tumor, is painful neuropathy. However, the molecular mechanisms underlying paclitaxel-induced painful neuropathy are largely unclarified. Methods Paw withdrawal threshold was measured in the rats following intraperitoneal injection of paclitaxel. The qPCR, western blotting, protein or chromatin immunoprecipitation, ChIP-seq identification of NFATc2 binding sites, and microarray analysis were performed to explore the molecular mechanism. Results We found that paclitaxel treatment increased the nuclear expression of NFATc2 in the spinal dorsal horn, and knockdown of NFATc2 with NFATc2 siRNA significantly attenuated the mechanical allodynia induced by paclitaxel. Further binding site analysis utilizing ChIP-seq assay combining with gene expression profile revealed a shift of NFATc2 binding site closer to TTS of target genes in dorsal horn after paclitaxel treatment. We further found that NFATc2 occupancy may directly upregulate the chemokine CXCL14 expression in dorsal horn, which was mediated by enhanced interaction between NFATc2 and p300 and consequently increased acetylation of histone H4 in CXCL14 promoter region. Also, knockdown of CXCL14 in dorsal horn significantly attenuated mechanical allodynia induced by paclitaxel. Conclusion These results suggested that enhanced interaction between p300 and NFATc2 mediated the epigenetic upregulation of CXCL14 in the spinal dorsal horn, which contributed to the chemotherapeutic paclitaxel-induced chronic pain. Supplementary information The online version contains supplementary material available at 10.1186/s12974-020-01992-1.
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Affiliation(s)
- Meng Liu
- Neuroscience Program, The Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Su-Bo Zhang
- Neuroscience Program, The Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yu-Xuan Luo
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yan-Ling Yang
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xiang-Zhong Zhang
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, China
| | - Bo Li
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Yan Meng
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Yuan-Jie Chen
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Rui-Xian Guo
- Neuroscience Program, The Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, Guangzhou, 510080, China. .,Department of Physiology and Pain Research Center, Zhongshan Medical School, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China.
| | - Yuan-Chang Xiong
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Wen-Jun Xin
- Neuroscience Program, The Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Dai Li
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
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Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep 2020; 26:2465-2476.e4. [PMID: 30811994 PMCID: PMC6582983 DOI: 10.1016/j.celrep.2019.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/ Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data. Ramani et al. describe MNase-SSP, a single-stranded DNA sequencing library preparation method for profiling chromatin structure. MNase-SSP libraries harbor diminished sequence bias and capture shorter DNA fragments compared to traditional MNase-seq libraries. Applying MNase-SSP to murine embryonic stem cells enables simultaneous analysis of nucleosomal, subnucleosomal, and transcription factor-DNA interactions genome-wide.
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Affiliation(s)
- Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
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7
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More than a Corepressor: The Role of CoREST Proteins in Neurodevelopment. eNeuro 2020; 7:ENEURO.0337-19.2020. [PMID: 32075869 PMCID: PMC7070449 DOI: 10.1523/eneuro.0337-19.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/19/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The molecular mechanisms governing normal neurodevelopment are tightly regulated by the action of transcription factors. Repressor element 1 (RE1) silencing transcription factor (REST) is widely documented as a regulator of neurogenesis that acts by recruiting corepressor proteins and repressing neuronal gene expression in non-neuronal cells. The REST corepressor 1 (CoREST1), CoREST2, and CoREST3 are best described for their role as part of the REST complex. However, recent evidence has shown the proteins have the ability to repress expression of distinct target genes in a REST-independent manner. These findings indicate that each CoREST paralogue may have distinct and critical roles in regulating neurodevelopment and are more than simply “REST corepressors,” whereby they act as independent repressors orchestrating biological processes during neurodevelopment.
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8
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Mampay M, Sheridan GK. REST: An epigenetic regulator of neuronal stress responses in the young and ageing brain. Front Neuroendocrinol 2019; 53:100744. [PMID: 31004616 DOI: 10.1016/j.yfrne.2019.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/03/2019] [Accepted: 04/11/2019] [Indexed: 12/27/2022]
Abstract
The transcriptional repressor REST (Repressor Element-1 Silencing Transcription factor) is a key modulator of the neuronal epigenome and targets genes involved in neuronal differentiation, axonal growth, vesicular transport, ion channel conductance and synaptic plasticity. Whilst its gene expression-modifying properties have been examined extensively in neuronal development, REST's response towards stress-induced neuronal insults has only recently been explored. Overall, REST appears to be an ideal candidate to fine-tune neuronal gene expression following different forms of cellular, neuropathological, psychological and physical stressors. Upregulation of REST is reportedly protective against premature neural stem cell depletion, neuronal hyperexcitability, oxidative stress, neuroendocrine system dysfunction and neuropathology. In contrast, neuronal REST activation has also been linked to neuronal dysfunction and neurodegeneration. Here, we highlight key findings and discrepancies surrounding our current understanding of REST's function in neuronal adaptation to stress and explore its potential role in neuronal stress resilience in the young and ageing brain.
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Affiliation(s)
- Myrthe Mampay
- Neuroimmunology & Neurotherapeutics Laboratory, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK
| | - Graham K Sheridan
- Neuroimmunology & Neurotherapeutics Laboratory, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
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9
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Jung HG, Hwang YS, Park YH, Cho HY, Rengaraj D, Han JY. Role of Epigenetic Regulation by the REST/CoREST/HDAC Corepressor Complex of Moderate NANOG Expression in Chicken Primordial Germ Cells. Stem Cells Dev 2018; 27:1215-1225. [DOI: 10.1089/scd.2018.0059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Hyun Gyo Jung
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Young Sun Hwang
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Young Hyun Park
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Ho Yeon Cho
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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10
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Sollinger C, Lillis J, Malik J, Getman M, Proschel C, Steiner L. Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells. Sci Rep 2017; 7:14381. [PMID: 29084993 PMCID: PMC5662632 DOI: 10.1038/s41598-017-14366-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022] Open
Abstract
Erythropoietin (EPO) and its receptor are highly expressed in the developing nervous system, and exogenous EPO therapy is potentially neuroprotective, however the epigenetic and transcriptional changes downstream of EPO signaling in neural cells are not well understood. To delineate epigenetic changes associated with EPO signaling, we compared histone H3 lysine 4 dimethylation (H3K4me2) in EPO treated and control fetal neural progenitor cells, identifying 1,150 differentially bound regions. These regions were highly enriched near protein coding genes and had significant overlap with H4Acetylation, a mark of active regulatory elements. Motif analyses and co-occupancy studies revealed a complex regulatory network underlying the differentially bound regions, including previously identified mediators of EPO signaling (STAT5, STAT3), and novel factors such as REST, an epigenetic modifier central to neural differentiation and plasticity, and NRF1, a key regulator of antioxidant response and mitochondrial biogenesis. Global transcriptome analyses on neural tubes isolated from E9.0 EpoR-null and littermate control embryos validated our in vitro findings, further suggesting a role for REST and NRF1 downstream of EPO signaling. These data support a role for EPO in regulating the survival, proliferation, and differentiation of neural progenitor cells, and suggest a basis for its function in neural development and neuroprotection.
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Affiliation(s)
| | - Jacquelyn Lillis
- Functional Genomic Center, University of Rochester, Rochester, New York, USA
| | - Jeffrey Malik
- Department of Pediatrics, University of Rochester, Rochester, New York, USA
| | - Michael Getman
- Department of Pediatrics, University of Rochester, Rochester, New York, USA
| | - Chris Proschel
- Department of Pediatrics, University of Rochester, Rochester, New York, USA.,Department of Biomedical Genetics, University of Rochester, Rochester, New York, USA
| | - Laurie Steiner
- Department of Pediatrics, University of Rochester, Rochester, New York, USA.
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11
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Xu M, Zhang D, Luo R, Wu Y, Zhou H, Kong L, Bi R, Yao Y. A systematic integrated analysis of brain expression profiles reveals
YAP1
and other prioritized hub genes as important upstream regulators in Alzheimer's disease. Alzheimers Dement 2017; 14:215-229. [DOI: 10.1016/j.jalz.2017.08.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Deng‐Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Rongcan Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Hejiang Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Li‐Li Kong
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Institute of Health Science Anhui University Hefei Anhui China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Yong‐Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences Shanghai China
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12
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Wang P, Zhao D, Rockowitz S, Zheng D. Divergence and rewiring of regulatory networks for neural development between human and other species. NEUROGENESIS 2016; 3:e1231495. [PMID: 27900343 DOI: 10.1080/23262133.2016.1231495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/11/2016] [Accepted: 08/27/2016] [Indexed: 10/21/2022]
Abstract
Neural and brain development in human and other mammalian species are largely similar, but distinct features exist at the levels of macrostructure and underlying genetic control. Comparative studies of epigenetic regulation and transcription factor (TF) binding in humans, chimpanzees, rodents, and other species have found large differences in gene regulatory networks. A recent analysis of the cistromes of REST/NRSF, a critical transcriptional regulator for the nervous system, demonstrated that REST binding to syntenic genomic regions (i.e., conserved binding) represents only a small percentage of the total binding events in human and mouse embryonic stem cells. While conserved binding is significantly associated with functional features (e.g., co-factor recruitment) and enriched at genes important for neural development and function, >3000 genes, including many related to brain and neural functions, either contain extra REST-bound sites (e.g., NRXN1) or are targeted by REST only (e.g. PSEN2) in humans. Surprisingly, several genes known to have critical roles in learning and memory, or brain disorders (e.g., APP and HTT) exhibit characteristics of human specific REST regulation. These findings indicate that more systematic studies are needed to better understand the divergent wiring of regulatory networks in humans, mice, and other mammals and their functional implications.
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Affiliation(s)
- Ping Wang
- Department of Neurology, Albert Einstein College of Medicine , Bronx, New York, NY, USA
| | - Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine , Bronx, New York, NY, USA
| | - Shira Rockowitz
- Department of Neuroscience, Albert Einstein College of Medicine , Bronx, New York, NY, USA
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY, USA; Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY, USA
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13
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Swift J, Coruzzi GM. A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:75-83. [PMID: 27546191 DOI: 10.1016/j.bbagrm.2016.08.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/06/2016] [Accepted: 08/10/2016] [Indexed: 12/16/2022]
Abstract
Dynamic reprogramming of transcriptional networks enables cells to adapt to a changing environment. Thus, it is crucial not only to understand what gene targets are regulated by a transcription factor (TF) but also when. This review explores the way TFs function with respect to time, paying particular attention to discoveries made in plants - where coordinated, genome-wide responses to environmental change is crucial to the survival of these sessile organisms. We investigate the molecular mechanisms that mediate transient TF-DNA binding, and assess how these rapid and dynamic interactions translate to long-term temporal regulation of genomes. We also discuss how current molecular techniques can catch, and sometimes miss, transient TF-target interactions that underlie dynamic cellular responses. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA.
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA
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14
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Aksoy I, Marcy G, Chen J, Divakar U, Kumar V, John-Sanchez D, Rahmani M, Buckley NJ, Stanton LW. A Role for RE-1-Silencing Transcription Factor in Embryonic Stem Cells Cardiac Lineage Specification. Stem Cells 2016; 34:860-72. [PMID: 26864965 DOI: 10.1002/stem.2304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 11/09/2022]
Abstract
During development, lineage specification is controlled by several signaling pathways involving various transcription factors (TFs). Here, we studied the RE-1-silencing transcription factor (REST) and identified an important role of this TF in cardiac differentiation. Using mouse embryonic stem cells (ESC) to model development, we found that REST knockout cells lost the ability to differentiate into the cardiac lineage. Detailed analysis of specific lineage markers expression showed selective downregulation of endoderm markers in REST-null cells, thus contributing to a loss of cardiogenic signals. REST regulates cardiac differentiation of ESCs by negatively regulating the Wnt/β-catenin signaling pathway and positively regulating the cardiogenic TF Gata4. We propose here a new role for REST in cell fate specification besides its well-known repressive role of neuronal differentiation.
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Affiliation(s)
- Irene Aksoy
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore.,Stem Cell and Brain Research Institute, INSERM U1208, 69500 Bron, France.,University of Lyon, University of Lyon I, 69003 Lyon, France
| | - Guillaume Marcy
- Stem Cell and Brain Research Institute, INSERM U1208, 69500 Bron, France.,University of Lyon, University of Lyon I, 69003 Lyon, France
| | - Jiaxuan Chen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Ushashree Divakar
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Vibhor Kumar
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Daniel John-Sanchez
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Mehran Rahmani
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, UK
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
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15
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Aguilo F, Zhang F, Sancho A, Fidalgo M, Di Cecilia S, Vashisht A, Lee DF, Chen CH, Rengasamy M, Andino B, Jahouh F, Roman A, Krig SR, Wang R, Zhang W, Wohlschlegel JA, Wang J, Walsh MJ. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming. Cell Stem Cell 2015; 17:689-704. [PMID: 26526723 DOI: 10.1016/j.stem.2015.09.005] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/24/2015] [Accepted: 09/11/2015] [Indexed: 12/15/2022]
Abstract
Epigenetic and epitranscriptomic networks have important functions in maintaining the pluripotency of embryonic stem cells (ESCs) and somatic cell reprogramming. However, the mechanisms integrating the actions of these distinct networks are only partially understood. Here we show that the chromatin-associated zinc finger protein 217 (ZFP217) coordinates epigenetic and epitranscriptomic regulation. ZFP217 interacts with several epigenetic regulators, activates the transcription of key pluripotency genes, and modulates N6-methyladenosine (m(6)A) deposition on their transcripts by sequestering the enzyme m(6)A methyltransferase-like 3 (METTL3). Consistently, Zfp217 depletion compromises ESC self-renewal and somatic cell reprogramming, globally increases m(6)A RNA levels, and enhances m(6)A modification of the Nanog, Sox2, Klf4, and c-Myc mRNAs, promoting their degradation. ZFP217 binds its own target gene mRNAs, which are also METTL3 associated, and is enriched at promoters of m(6)A-modified transcripts. Collectively, these findings shed light on how a transcription factor can tightly couple gene transcription to m(6)A RNA modification to ensure ESC identity.
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Affiliation(s)
- Francesca Aguilo
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Fan Zhang
- Bioinformatics Laboratory, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Sancho
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fidalgo
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Serena Di Cecilia
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ajay Vashisht
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dung-Fang Lee
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chih-Hung Chen
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhumitha Rengasamy
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Blanca Andino
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Farid Jahouh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angel Roman
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid 28002, Spain
| | - Sheryl R Krig
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA
| | - Rong Wang
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijia Zhang
- Bioinformatics Laboratory, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jianlong Wang
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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16
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Keilwagen J, Grau J. Varying levels of complexity in transcription factor binding motifs. Nucleic Acids Res 2015; 43:e119. [PMID: 26116565 PMCID: PMC4605289 DOI: 10.1093/nar/gkv577] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 11/17/2022] Open
Abstract
Binding of transcription factors to DNA is one of the keystones of gene regulation. The existence of statistical dependencies between binding site positions is widely accepted, while their relevance for computational predictions has been debated. Building probabilistic models of binding sites that may capture dependencies is still challenging, since the most successful motif discovery approaches require numerical optimization techniques, which are not suited for selecting dependency structures. To overcome this issue, we propose sparse local inhomogeneous mixture (Slim) models that combine putative dependency structures in a weighted manner allowing for numerical optimization of dependency structure and model parameters simultaneously. We find that Slim models yield a substantially better prediction performance than previous models on genomic context protein binding microarray data sets and on ChIP-seq data sets. To elucidate the reasons for the improved performance, we develop dependency logos, which allow for visual inspection of dependency structures within binding sites. We find that the dependency structures discovered by Slim models are highly diverse and highly transcription factor-specific, which emphasizes the need for flexible dependency models. The observed dependency structures range from broad heterogeneities to sparse dependencies between neighboring and non-neighboring binding site positions.
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Affiliation(s)
- Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, D-06484 Quedlinburg, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, D-06099 Halle (Saale), Germany
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17
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Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs. Sci Bull (Beijing) 2015; 60:1722-1733. [PMID: 26543668 PMCID: PMC4624819 DOI: 10.1007/s11434-015-0905-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/18/2015] [Indexed: 12/19/2022]
Abstract
Transposable elements (TEs) are mobile genomic sequences of DNA capable of autonomous and non-autonomous duplication. TEs have been highly successful, and nearly half of the human genome now consists of various families of TEs. Originally thought to be non-functional, these elements have been co-opted by animal genomes to perform a variety of physiological functions ranging from TE-derived proteins acting directly in normal biological functions, to innovations in transcription factor logic and influence on epigenetic control of gene expression. During embryonic development, when the genome is epigenetically reprogrammed and DNA-demethylated, TEs are released from repression and show embryonic stage-specific expression, and in human and mouse embryos, intact TE-derived endogenous viral particles can even be detected. A similar process occurs during the reprogramming of somatic cells to pluripotent cells: When the somatic DNA is demethylated, TEs are released from repression. In embryonic stem cells (ESCs), where DNA is hypomethylated, an elaborate system of epigenetic control is employed to suppress TEs, a system that often overlaps with normal epigenetic control of ESC gene expression. Finally, many long non-coding RNAs (lncRNAs) involved in normal ESC function and those assisting or impairing reprogramming contain multiple TEs in their RNA. These TEs may act as regulatory units to recruit RNA-binding proteins and epigenetic modifiers. This review covers how TEs are interlinked with the epigenetic machinery and lncRNAs, and how these links influence each other to modulate aspects of ESCs, embryogenesis, and somatic cell reprogramming.
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18
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Zelante T, Wong A, Ping T, Chen J, Sumatoh H, Viganò E, Hong Bing Y, Lee B, Zolezzi F, Fric J, Newell E, Mortellaro A, Poidinger M, Puccetti P, Ricciardi-Castagnoli P. CD103+ Dendritic Cells Control Th17 Cell Function in the Lung. Cell Rep 2015; 12:1789-801. [DOI: 10.1016/j.celrep.2015.08.030] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/17/2015] [Accepted: 08/07/2015] [Indexed: 11/29/2022] Open
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19
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Rockowitz S, Zheng D. Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. Nucleic Acids Res 2015; 43:5730-43. [PMID: 25990720 PMCID: PMC4499139 DOI: 10.1093/nar/gkv514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Abstract
Recent studies have employed cross-species comparisons of transcription factor binding, reporting significant regulatory network 'rewiring' between species. Here, we address how a transcriptional repressor targets and regulates neural genes differentially between human and mouse embryonic stem cells (ESCs). We find that the transcription factor, Repressor Element 1 Silencing Transcription factor (REST; also called neuron restrictive silencer factor) binds to a core group of ∼1200 syntenic genomic regions in both species, with these conserved sites highly enriched with co-factors, selective histone modifications and DNA hypomethylation. Genes with conserved REST binding are enriched with neural functions and more likely to be upregulated upon REST depletion. Interestingly, we identified twice as many REST peaks in human ESCs compared to mouse ESCs. Human REST cistrome expansion involves additional peaks in genes targeted by REST in both species and human-specific gene targets. Genes with expanded REST occupancy in humans are enriched for learning or memory functions. Analysis of neurological disorder associated genes reveals that Amyotrophic Lateral Sclerosis and oxidative stress genes are particularly enriched with human-specific REST binding. Overall, our results demonstrate that there is substantial rewiring of human and mouse REST cistromes, and that REST may have human-specific roles in brain development and functions.
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Affiliation(s)
- Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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20
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Monaco SA, Gulchina Y, Gao WJ. NR2B subunit in the prefrontal cortex: A double-edged sword for working memory function and psychiatric disorders. Neurosci Biobehav Rev 2015; 56:127-38. [PMID: 26143512 DOI: 10.1016/j.neubiorev.2015.06.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/27/2015] [Accepted: 06/29/2015] [Indexed: 12/23/2022]
Abstract
The prefrontal cortex (PFC) is a brain region featured with working memory function. The exact mechanism of how working memory operates within the PFC circuitry is unknown, but persistent neuronal firing recorded from prefrontal neurons during a working memory task is proposed to be the neural correlate of this mnemonic encoding. The PFC appears to be specialized for sustaining persistent firing, with N-methyl-D-aspartate (NMDA) receptors, especially slow-decay NR2B subunits, playing an essential role in the maintenance of sustained activity and normal working memory function. However, the NR2B subunit serves as a double-edged sword for PFC function. Because of its slow kinetics, NR2B endows the PFC with not only "neural psychic" properties, but also susceptibilities for neuroexcitotoxicity and psychiatric disorders. This review aims to clarify the interplay among working memory, the PFC, and NMDA receptors; demonstrate the importance of NR2B in the maintenance of persistent activity; understand the risks and vulnerabilities of how NR2B is related to the development of neuropsychiatric disorders; identify gaps that currently exist in our understanding of these processes; and provide insights regarding future directions that may clarify these issues. We conclude that the PFC is a specialized brain region with distinct delayed maturation, unique neuronal circuitry, and characteristic NMDA receptor function. The unique properties and development of NMDA receptors, especially enrichment of NR2B subunits, endow the PFC with not only the capability to generate sustained activity for working memory, but also serves as a major vulnerability to environmental insults and risk factors for psychiatric disorders.
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Affiliation(s)
- Sarah A Monaco
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Room 243, Philadelphia, PA 19129, United States
| | - Yelena Gulchina
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Room 243, Philadelphia, PA 19129, United States
| | - Wen-Jun Gao
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Room 243, Philadelphia, PA 19129, United States.
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21
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MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A 2015; 112:E3457-65. [PMID: 26080409 DOI: 10.1073/pnas.1424804112] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The analysis of chromatin structure is essential for the understanding of transcriptional regulation in eukaryotes. Here we describe methidiumpropyl-EDTA sequencing (MPE-seq), a method for the genome-wide characterization of chromatin that involves the digestion of nuclei withMPE-Fe(II) followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. However, there are differences in the cleavage of nuclear chromatin by MPE-Fe(II) relative to MNase. Most notably, immediately upstream of the transcription start site of active promoters, we frequently observed nucleosome-sized (141-190 bp) and subnucleosome-sized (such as 101-140 bp) peaks of digested chromatin fragments with MPE-seq but not with MNase-seq. These peaks also correlate with the presence of core histones and could thus be due, at least in part, to noncanonical chromatin structures such as labile nucleosome-like particles that have been observed in other contexts. The subnucleosome-sized MPE-seq peaks exhibit a particularly distinct association with active promoters. In addition, unlike MNase, MPE-Fe(II) cleaves nuclear DNA with little sequence bias. In this regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase but not by MPE-Fe(II). This phenomenon may have affected the analysis of nucleosome occupancy over exons. These findings collectively indicate that MPE-seq provides a unique and straightforward means for the genome-wide analysis of chromatin structure with minimal DNA sequence bias. In particular, the combined use of MPE-seq and MNase-seq enables the identification of noncanonical chromatin structures that are likely to be important for the regulation of gene expression.
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22
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Saritas-Yildirim B, Childers CP, Elsik CG, Silva EM. Identification of REST targets in the Xenopus tropicalis genome. BMC Genomics 2015; 16:380. [PMID: 25971704 PMCID: PMC4430910 DOI: 10.1186/s12864-015-1591-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 04/28/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A major role of REST (repressor element-1 silencing transcription factor) is to inhibit the expression of neuronal genes in neural stem cells and non-neuronal cells by binding to a 21 bp consensus sequence and recruiting epigenetic and regulatory cofactors to gene regulatory regions. In neural stem cells, REST silences differentiation-promoting genes to prevent their premature expression and is central to the regulation of neurogenesis and the balance of neural stem cells and neurons. RESULTS To understand the role of REST in vertebrate neurogenesis, we performed a genome-wide screen for REST targets in Xenopus tropicalis. We identified 742 neuron-restrictive silencer elements (NRSE) associated with 1396 genes that are enriched in neuronal function. Comparative analyses revealed that characteristics of NRSE motifs in frog are similar to those in mammals in terms of the distance to target genes, frequency of motifs and the repertoire of putative target genes. In addition, we identified four F-box ubiquitin ligases as putative REST targets and determined that they are expressed in neuronal tissues during Xenopus development. CONCLUSION We identified a conserved core of putative target genes in human, mouse and frog that may be fundamental to REST function in vertebrates. We demonstrate that NRSE sites are associated with both protein-coding genes and lncRNAs in the human genome. Furthermore, we demonstrate that REST binding sites are abundant in low gene-occupancy regions of the human genome but this is not due to an increased association with non-coding RNAs. Our findings identify novel targets of REST and broaden the known mechanism of REST-mediated silencing in neurogenesis.
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Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
| | - Christopher P Childers
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Christine G Elsik
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. .,Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
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23
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Yu HB, Yurieva M, Balachander A, Foo I, Leong X, Zelante T, Zolezzi F, Poidinger M, Ricciardi-Castagnoli P. NFATc2 mediates epigenetic modification of dendritic cell cytokine and chemokine responses to dectin-1 stimulation. Nucleic Acids Res 2015; 43:836-47. [PMID: 25550437 PMCID: PMC4333412 DOI: 10.1093/nar/gku1369] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/03/2014] [Accepted: 12/18/2014] [Indexed: 01/03/2023] Open
Abstract
The transcription factor NFATc2 regulates dendritic cell (DC) responses to microbial stimulation through the C-type lectin receptor dectin-1. But the genetic targets of NFATc2 and their effects on DC function remain largely unknown. Therefore we used ChIP-seq to conduct genome-wide mapping of NFATc2 target sites in dectin-1-activated DCs. By combining binding-site data with a comprehensive gene expression profile, we found that NFATc2 occupancy regulates the expression of a subset of dectin-1-activated genes. Surprisingly, NFATc2 targeted an extensive range of DC-derived cytokines and chemokines, including regulatory cytokines such as IL2, IL23a and IL12b. Furthermore, we demonstrated that NFATc2 binding is required to induce the histone 3 lysine 4 trimethylation (H3K4me3) epigenetic mark, which is associated with enhanced gene expression. Together, these data show that the transcription factor NFATc2 mediates epigenetic modification of DC cytokine and chemokine genes leading to activation of their expression.
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Affiliation(s)
- Hong-Bing Yu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Marina Yurieva
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Akhila Balachander
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Ivy Foo
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Xiangrong Leong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Teresa Zelante
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
| | - Paola Ricciardi-Castagnoli
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*Star), Biopolis, Singapore
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24
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NRSF: an Angel or a Devil in Neurogenesis and Neurological Diseases. J Mol Neurosci 2014; 56:131-44. [DOI: 10.1007/s12031-014-0474-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 12/12/2022]
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25
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McGann JC, Oyer JA, Garg S, Yao H, Liu J, Feng X, Liao L, Yates JR, Mandel G. Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype. eLife 2014; 3:e04235. [PMID: 25250711 PMCID: PMC4371837 DOI: 10.7554/elife.04235] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022] Open
Abstract
The bivalent hypothesis posits that genes encoding developmental regulators required
for early lineage decisions are poised in stem/progenitor cells by the balance
between a repressor histone modification (H3K27me3), mediated by the Polycomb
Repressor Complex 2 (PRC2), and an activator modification (H3K4me3). In this study,
we test whether this mechanism applies equally to genes that are not required until
terminal differentiation. We focus on the RE1 Silencing Transcription Factor (REST)
because it is expressed highly in stem cells and is an established global repressor
of terminal neuronal genes. Elucidation of the REST complex, and comparison of
chromatin marks and gene expression levels in control and REST-deficient stem cells,
shows that REST target genes are poised by a mechanism independent of Polycomb, even
at promoters which bear the H3K27me3 mark. Specifically, genes under REST control are
actively repressed in stem cells by a balance of the H3K4me3 mark and a repressor
complex that relies on histone deacetylase activity. Thus, chromatin distinctions
between pro-neural and terminal neuronal genes are established at the embryonic stem
cell stage by two parallel, but distinct, repressor pathways. DOI:http://dx.doi.org/10.7554/eLife.04235.001 When an embryo is developing, genes are switched on or off at different times, for
many different reasons. Many of these genes are switched off, or repressed, by making
the DNA inaccessible to the various proteins and molecules that control gene
activity. This is achieved by altering the way that the DNA is packaged into a
compacted structure called chromatin. A host of proteins modify the structure of
chromatin: it can be made more tightly packaged, which keeps genes switched off; or
it can be made more loosely packaged, which allows the genes within to be accessed
and switched on. The stem cells in an embryo are able to give rise to many different types of
specialized cell. Genes that determine which cell type a stem cell will eventually
become are often kept in a so-called ‘poised’ state, and have chromatin modifications
that encourage genes to be switch on, as well as modifications that switch genes off.
Current thinking is that this poised state allows these genes to be switched on or
off rapidly in response to the signals that the cell receives during development. The only known protein complex that causes the chromatin to become more compacted in
this poised state is the Polycomb complex. This complex binds to specific regions of
DNA and is thought to allow stem cells to remain able to become different cell types
by repressing the genes required for adopting a specialized cell fate. However, it is
unclear if this poised state also regulates those genes that control the final stages
of a cell becoming a specific cell type. McGann et al. investigated genes that are involved in the final stages of a nerve
cell's development. These genes are regulated by another protein called REST, which
acts to repress the genes in non-neuronal cells. McGann et al. found that the genes
that are regulated by REST in embryonic stem cells from mice also have their
chromatin modified in two contrasting ways. Some of the modifications are linked to
switching genes on, while others are linked to keeping genes switched off. Thus these
genes are also in a poised state. However, for these genes, this state is acquired
without the activity of the Polycomb complex. The results of McGann et al. show that two similar, but distinct, mechanisms keep the
genes required for the early and the late stages of nerve cell development in a
poised state. If this poised state aids the development of other cell types (for
example muscle or fat cells), uncovering how it is achieved could improve our ability
to direct stem cells to develop into specific cell types and tissues. DOI:http://dx.doi.org/10.7554/eLife.04235.002
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Affiliation(s)
- James C McGann
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jon A Oyer
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Saurabh Garg
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Huilan Yao
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jun Liu
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Xin Feng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Lujian Liao
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, Portland, United States
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Rockowitz S, Lien WH, Pedrosa E, Wei G, Lin M, Zhao K, Lachman HM, Fuchs E, Zheng D. Comparison of REST cistromes across human cell types reveals common and context-specific functions. PLoS Comput Biol 2014; 10:e1003671. [PMID: 24922058 PMCID: PMC4055426 DOI: 10.1371/journal.pcbi.1003671] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 05/01/2014] [Indexed: 11/18/2022] Open
Abstract
Recent studies have shown that the transcriptional functions of REST are much broader than repressing neuronal genes in non-neuronal systems. Whether REST occupies similar chromatin regions in different cell types and how it interacts with other transcriptional regulators to execute its functions in a context-dependent manner has not been adequately investigated. We have applied ChIP-seq analysis to identify the REST cistrome in human CD4+ T cells and compared it with published data from 15 other cell types. We found that REST cistromes were distinct among cell types, with REST binding to several tumor suppressors specifically in cancer cells, whereas 7% of the REST peaks in non-neuronal cells were ubiquitously called and <25% were identified for ≥ 5 cell types. Nevertheless, using a quantitative metric directly comparing raw ChIP-seq signals, we found the majority (∼80%) was shared by ≥ 2 cell types. Integration with RNA-seq data showed that REST binding was generally correlated with low gene expression. Close examination revealed that multiple contexts were correlated with reduced expression of REST targets, e.g., the presence of a cognate RE1 motif and cellular specificity of REST binding. These contexts were shown to play a role in differential corepressor recruitment. Furthermore, transcriptional outcome was highly influenced by REST cofactors, e.g., SIN3 and EZH2 co-occupancy marked higher and lower expression of REST targets, respectively. Unexpectedly, the REST cistrome in differentiated neurons exhibited unique features not observed in non-neuronal cells, e.g., the lack of RE1 motifs and an association with active gene expression. Finally, our analysis demonstrated how REST could differentially regulate a transcription network constituted of miRNAs, REST complex and neuronal factors. Overall, our findings of contexts playing critical roles in REST occupancy and regulatory outcome provide insights into the molecular interactions underlying REST's diverse functions, and point to novel roles of REST in differentiated neurons.
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Affiliation(s)
- Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Wen-Hui Lien
- Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology & Development, The Rockefeller University, New York, New York, United States of America
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Gang Wei
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology & Development, The Rockefeller University, New York, New York, United States of America
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- * E-mail:
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Sharov AA, Nishiyama A, Qian Y, Dudekula DB, Longo DL, Schlessinger D, Ko MSH. Chromatin properties of regulatory DNA probed by manipulation of transcription factors. J Comput Biol 2014; 21:569-77. [PMID: 24918633 DOI: 10.1089/cmb.2013.0126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) bind to DNA and regulate the transcription of nearby genes. However, only a small fraction of TF binding sites have such regulatory effects. Here we search for the predictors of functional binding sites by carrying out a systematic computational screening of a variety of contextual factors (histone modifications, nuclear lamin-bindings, and cofactor bindings). We used regression analysis to test if contextual factors are associated with upregulation or downregulation of neighboring genes following the induction or knockdown of the 9 TFs in mouse embryonic stem (ES) cells. Functional TF binding sites appeared to be either active (i.e., bound by P300, CHD7, mediator, cohesin, and SWI/SNF) or repressed (i.e., with H3K27me3 histone marks and bound by Polycomb factors). Active binding sites mediated the downregulation of nearby genes upon knocking down the activating TFs or inducing repressors. Repressed TF binding sites mediated the upregulation of nearby genes (e.g., poised developmental regulators) upon inducing TFs. In addition, repressed binding sites mediated repressive effects of TFs, identified by the downregulation of target genes after the induction of TFs or by the upregulation of target genes after the knockdown of TFs. The contextual factors associated with functions of DNA-bound TFs were used to improve the identification of candidate target genes regulated by TFs.
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Affiliation(s)
- Alexei A Sharov
- 1 National Institute on Aging, National Institutes of Health , Baltimore, Maryland
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Seki M, Masaki H, Arauchi T, Nakauchi H, Sugano S, Suzuki Y. A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells. PLoS One 2014; 9:e95374. [PMID: 24752154 PMCID: PMC3994037 DOI: 10.1371/journal.pone.0095374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/26/2014] [Indexed: 10/29/2022] Open
Abstract
We detected and characterized the binding sites of the representative Rest complex components Rest, Sin3A, and Lsd1. We compared their binding patterns in mouse embryonic stem (ES) cells and epiblast stem (EpiS) cells. We found few Rest sites unique to the EpiS cells. The ES-unique site features were distinct from those of the common sites, namely, the signal intensities were weaker, and the characteristic gene function categories differed. Our analyses showed that the Rest binding sites do not always overlap with the Sin3A and Lsd1 binding sites. The Sin3A binding pattern differed remarkably between the ES and EpiS cells and was accompanied by significant changes in acetylated-histone patterns in the surrounding regions. A series of transcriptome analyses in the same cell types unexpectedly showed that the putative target gene transcript levels were not dramatically different despite dynamic changes in the Rest complex binding patterns and chromatin statuses, which suggests that Rest is not the sole determinant of repression at its targets. Nevertheless, we identified putative Rest targets with explicitly enhanced transcription upon Rest knock-down in 143 and 60 common and ES-unique Rest target genes, respectively. Among such sites, several genes are involved in ES cell proliferation. In addition, we also found that long, intergenic non-coding RNAs were apparent Rest targets and shared similar features with the protein-coding target genes. Interestingly, such non-coding target genes showed less conservation through evolution than protein-coding targets. As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells.
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Affiliation(s)
- Masahide Seki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Hideki Masaki
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
| | - Takako Arauchi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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29
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Satoh JI, Kawana N, Yamamoto Y. ChIP-Seq Data Mining: Remarkable Differences in NRSF/REST Target Genes between Human ESC and ESC-Derived Neurons. Bioinform Biol Insights 2013; 7:357-68. [PMID: 24324330 PMCID: PMC3855043 DOI: 10.4137/bbi.s13279] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The neuron-restrictive silencer factor (NRSF) is a zinc finger transcription factor that represses neuronal gene transcription in non-neuronal cells by binding to the consensus repressor element-1 (RE1) located in regulatory regions of target genes. NRSF silences the expression of a wide range of target genes involved in neuron-specific functions. Previous studies showed that aberrant regulation of NRSF plays a key role in the pathological process of human neurodegenerative diseases. However, a comprehensive set of NRSF target genes relevant to human neuronal functions has not yet been characterized. We performed genome-wide data mining from chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) datasets of NRSF binding sites in human embryonic stem cells (ESC) and the corresponding ESC-derived neurons, retrieved from the database of the ENCODE/HAIB project. Using bioinformatics tools such as Avadis NGS and MACS, we identified 2,172 NRSF target genes in ESC and 308 genes in ESC-derived neurons based on stringent criteria. Only 40 NRSF target genes overlapped between both data sets. According to motif analysis, binding regions showed an enrichment of the consensus RE1 sites in ESC, whereas they were mainly located in poorly defined non-RE1 sites in ESC-derived neurons. Molecular pathways of NRSF target genes were linked with various neuronal functions in ESC, such as neuroactive ligand-receptor interaction, CREB signaling, and axonal guidance signaling, while they were not directed to neuron-specific functions in ESC-derived neurons. Remarkable differences in ChIP-Seq-based NRSF target genes and pathways between ESC and ESC-derived neurons suggested that NRSF-mediated silencing of target genes is highly effective in human ESC but not in ESC-derived neurons.
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Affiliation(s)
- Jun-Ichi Satoh
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
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31
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Giannopoulou EG, Elemento O. Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res 2013; 23:1295-306. [PMID: 23554462 PMCID: PMC3730103 DOI: 10.1101/gr.149419.112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Genome-wide binding assays can determine where individual transcription factors bind in the genome. However, these factors rarely bind chromatin alone, but instead frequently bind to cis-regulatory elements (CREs) together with other factors thus forming protein complexes. Currently there are no integrative analytical approaches that can predict which complexes are formed on chromatin. Here, we describe a computational methodology to systematically capture protein complexes and infer their impact on gene expression. We applied our method to three human cell types, identified thousands of CREs, inferred known and undescribed complexes recruited to these CREs, and determined the role of the complexes as activators or repressors. Importantly, we found that the predicted complexes have a higher number of physical interactions between their members than expected by chance. Our work provides a mechanism for developing hypotheses about gene regulation via binding partners, and deciphering the interplay between combinatorial binding and gene expression.
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Affiliation(s)
- Eugenia G Giannopoulou
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10021, USA
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32
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Negrini S, Prada I, D'Alessandro R, Meldolesi J. REST: an oncogene or a tumor suppressor? Trends Cell Biol 2013; 23:289-95. [PMID: 23414932 DOI: 10.1016/j.tcb.2013.01.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 12/21/2022]
Abstract
The Repressor Element-1 (RE-1) Silencing Transcription (REST) factor, which is highly expressed in stem cells and non-neural cells, with low expression in neurons and other neural cells, orchestrates neural differentiation and preserves the unique neural phenotype. REST also plays a role in proliferation, although its effect differs depending on the cell type. It acts as an oncogene in neural cells and tumors (medulloblastomas, neuroblastomas, glioblastomas) and as a tumor suppressor in carcinomas of the lung, breast, and colon. The mechanisms underlying this duality have started to emerge recently and new therapeutic approaches based on these findings are being developed. Here, we present the mechanisms proposed to account for the oncogenic and antioncogenic roles of REST and discuss the therapeutic perspective of recent advances, particularly for small-cell lung cancer.
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Affiliation(s)
- Sara Negrini
- San Raffaele Scientific Institute and Vita Salute San Raffaele University, Milan, Italy
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33
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Abstract
Epigenetic remodeling and modifications of chromatin structure by DNA methylation and histone modifications represent central mechanisms for the regulation of neuronal gene expression during brain development, higher-order processing, and memory formation. Emerging evidence implicates epigenetic modifications not only in normal brain function, but also in neuropsychiatric disorders. This review focuses on recent findings that disruption of chromatin modifications have a major role in the neurodegeneration associated with ischemic stroke and epilepsy. Although these disorders differ in their underlying causes and pathophysiology, they share a common feature, in that each disorder activates the gene silencing transcription factor REST (repressor element 1 silencing transcription factor), which orchestrates epigenetic remodeling of a subset of 'transcriptionally responsive targets' implicated in neuronal death. Although ischemic insults activate REST in selectively vulnerable neurons in the hippocampal CA1, seizures activate REST in CA3 neurons destined to die. Profiling the array of genes that are epigenetically dysregulated in response to neuronal insults is likely to advance our understanding of the mechanisms underlying the pathophysiology of these disorders and may lead to the identification of novel therapeutic strategies for the amelioration of these serious human conditions.
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34
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DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A 2012; 109:21330-5. [PMID: 23236164 DOI: 10.1073/pnas.1209589110] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In animals, each sequence-specific transcription factor typically binds to thousands of genomic regions in vivo. Our previous studies of 20 transcription factors show that most genomic regions bound at high levels in Drosophila blastoderm embryos are known or probable functional targets, but genomic regions occupied only at low levels have characteristics suggesting that most are not involved in the cis-regulation of transcription. Here we use transgenic reporter gene assays to directly test the transcriptional activity of 104 genomic regions bound at different levels by the 20 transcription factors. Fifteen genomic regions were selected based solely on the DNA occupancy level of the transcription factor Kruppel. Five of the six most highly bound regions drive blastoderm patterns of reporter transcription. In contrast, only one of the nine lowly bound regions drives transcription at this stage and four of them are not detectably active at any stage of embryogenesis. A larger set of 89 genomic regions chosen using criteria designed to identify functional cis-regulatory regions supports the same trend: genomic regions occupied at high levels by transcription factors in vivo drive patterned gene expression, whereas those occupied only at lower levels mostly do not. These results support studies that indicate that the high cellular concentrations of sequence-specific transcription factors drive extensive, low-occupancy, nonfunctional interactions within the accessible portions of the genome.
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35
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Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 2012; 41:D177-87. [PMID: 23161675 PMCID: PMC3531181 DOI: 10.1093/nar/gks1060] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity. In this study, we describe ChIPBase (http://deepbase.sysu.edu.cn/chipbase/), a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. The current release of ChIPBase includes high-throughput sequencing data that were generated by 543 ChIP-Seq experiments in diverse tissues and cell lines from six organisms. By analysing millions of TFBSs, we identified tens of thousands of TF-lncRNA and TF-miRNA regulatory relationships. Furthermore, two web-based servers were developed to annotate and discover transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. In addition, we developed two genome browsers, deepView and genomeView, to provide integrated views of multidimensional data. Moreover, our web implementation supports diverse query types and the exploration of TFs, lncRNAs, miRNAs, gene ontologies and pathways.
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Affiliation(s)
- Jian-Hua Yang
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China
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36
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Zhang J, Wang S, Yuan L, Yang Y, Zhang B, Liu Q, Chen L, Yue W, Li Y, Pei X. Neuron-restrictive silencer factor (NRSF) represses cocaine- and amphetamine-regulated transcript (CART) transcription and antagonizes cAMP-response element-binding protein signaling through a dual NRSE mechanism. J Biol Chem 2012; 287:42574-87. [PMID: 23086924 DOI: 10.1074/jbc.m112.376590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cocaine- and amphetamine-regulated transcript (CART) peptide plays a pivotal role in neuroprotection against stroke-related brain injury. However, the regulatory mechanism on CART transcription, especially the repression mechanism, is not fully understood. Here, we show that the transcriptional repressor neuron-restrictive silencer elements (NRSF, also known as REST) represses CART expression through direct binding to two NRSF-binding elements (NRSEs) in the CART promoter and intron 1 (named pNRSE and iNRSE, respectively). EMSA show that NRSF binds to pNRSE and iNRSE directly in vitro. ChIP assays show that NRSF recruits differential co-repressor complexes including CoREST and HDAC1 to these NRSEs. The presence of both NRSEs is required for efficient repression of CART transcription as indicated by reporter gene assays. NRSF overexpression antagonizes forskolin-mediated up-regulation of CART mRNA and protein. Ischemia insult triggered by oxygen-glucose deprivation (OGD) enhances NRSF mRNA levels and then NRSF antagonizes the CREB signaling on CART activation, leading to augmented cell death. Depletion of NRSF in combination with forskolin treatment increases neuronal survival after ischemic insult. These findings reveal a novel dual NRSE mechanism by which NRSF represses CART expression and suggest that NRSF may serve as a therapeutic target for stroke treatment.
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Affiliation(s)
- Jing Zhang
- Stem Cell and Regenerative Medicine Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China
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Rodenas-Ruano A, Chávez AE, Cossio MJ, Castillo PE, Zukin RS. REST-dependent epigenetic remodeling promotes the developmental switch in synaptic NMDA receptors. Nat Neurosci 2012; 15:1382-90. [PMID: 22960932 PMCID: PMC3501125 DOI: 10.1038/nn.3214] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/13/2012] [Indexed: 11/20/2022]
Abstract
N-methyl-D-aspartate receptors (NMDARs) are critical to synaptogenesis, neural circuitry and higher cognitive functions such as learning and memory. A hallmark feature of NMDARs is an early postnatal developmental switch from primarily GluN2B- to GluN2A-containing. Although the switch in phenotype has been an area of intense interest for two decades, the mechanisms that trigger it, and the link between experience and the switch are unclear. Here we show a novel role for the transcriptional repressor REST in the developmental switch of synaptic NMDARs. REST is activated at a critical window of time and acts via epigenetic remodeling to repress grin2b expression and properties at rat hippocampal synapses. Knockdown of REST in vivo prevented the decline in GluN2B and developmental switch in NMDARs. Notably, maternal deprivation impaired REST activation and acquisition of the mature NMDAR phenotype. Thus, REST is essential for experience-dependent fine-tuning of genes involved in synaptic plasticity.
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Affiliation(s)
- Alma Rodenas-Ruano
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
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Maston GA, Landt SG, Snyder M, Green MR. Characterization of enhancer function from genome-wide analyses. Annu Rev Genomics Hum Genet 2012; 13:29-57. [PMID: 22703170 DOI: 10.1146/annurev-genom-090711-163723] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There has been a recent surge in the use of genome-wide methodologies to identify and annotate the transcriptional regulatory elements in the human genome. Here we review some of these methodologies and the conceptual insights about transcription regulation that have been gained from the use of genome-wide studies. It has become clear that the binding of transcription factors is itself a highly regulated process, and binding does not always appear to have functional consequences. Numerous properties have now been associated with regulatory elements that may be useful in their identification. Several aspects of enhancer function have been shown to be more widespread than was previously appreciated, including the highly combinatorial nature of transcription factor binding, the postinitiation regulation of many target genes, and the binding of enhancers at early stages to maintain their competence during development. Going forward, the integration of multiple genome-wide data sets should become a standard approach to elucidate higher-order regulatory interactions.
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Affiliation(s)
- Glenn A Maston
- Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Gao Z, Ding P, Hsieh J. Profiling of REST-Dependent microRNAs Reveals Dynamic Modes of Expression. Front Neurosci 2012; 6:67. [PMID: 22590451 PMCID: PMC3349273 DOI: 10.3389/fnins.2012.00067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/19/2012] [Indexed: 12/20/2022] Open
Abstract
Multipotent neural stem cells (NSCs) possess the ability to self-renew and differentiate into both neurons and glia. However, the detailed mechanisms underlying NSC fate decisions are not well understood. Recent work suggests that the interaction between cell type specific transcription factors and microRNAs (miRNAs) is important as resident neural stem/progenitor cells give rise to functionally mature neurons. Recently, we demonstrated that the transcriptional repressor REST (RE1-silencing transcription factor) is essential to prevent precocious neuronal differentiation and maintain NSC self-renewal in the adult hippocampus. Here we show that REST is required for orchestrating the expression of distinct subsets of miRNAs in primary mouse NSC cultures, a physiologically relevant cell type. Using miRNA array profiling, we identified known REST-regulated miRNA genes, as well as previously uncharacterized REST-dependent miRNAs. Interestingly, in response to proliferation and differentiation stimuli, REST-regulated miRNAs formed distinct clusters and displayed variable expression dynamics. These results suggest that REST functions in a context-dependent manner through its target miRNAs for mediating neuronal production.
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Affiliation(s)
- Zhengliang Gao
- Department of Molecular Biology, UT Southwestern Medical Center Dallas, TX, USA
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40
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Gascon E, Gao FB. Cause or Effect: Misregulation of microRNA Pathways in Neurodegeneration. Front Neurosci 2012; 6:48. [PMID: 22509148 PMCID: PMC3321503 DOI: 10.3389/fnins.2012.00048] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/23/2012] [Indexed: 12/12/2022] Open
Abstract
During normal aging or neurodegenerative diseases, neuronal survival and function depend on protein homeostasis, which is regulated by multiple mechanisms, including the microRNA (miRNA) pathway. In different cells types, the absence of Dicer, a key miRNA processing enzyme, leads to neurodegeneration through cell-autonomous and non-cell-autonomous mechanisms. Loss of certain miRNAs also causes neurodegeneration in some model organisms. On the other hand, miRNA expression is misregulated in patients with different neurodegenerative diseases. Thus, the miRNA pathway appears to be essential in the pathogenesis of several age-dependent neurodegenerative conditions; however, our understanding of the underlying mechanism remains rudimentary. The precise causal relationships between specific miRNAs and neurodegeneration in humans need to be further investigated.
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Affiliation(s)
- Eduardo Gascon
- Department of Neurology, University of Massachusetts Medical School Worcester, MA, USA
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41
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Soldati C, Bithell A, Johnston C, Wong KY, Teng SW, Beglopoulos V, Stanton LW, Buckley NJ. Repressor Element 1 Silencing Transcription Factor Couples Loss of Pluripotency with Neural Induction and Neural Differentiation. Stem Cells 2012; 30:425-34. [DOI: 10.1002/stem.1004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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42
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Johnson R. Long non-coding RNAs in Huntington's disease neurodegeneration. Neurobiol Dis 2011; 46:245-54. [PMID: 22202438 DOI: 10.1016/j.nbd.2011.12.006] [Citation(s) in RCA: 313] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 12/04/2011] [Indexed: 01/04/2023] Open
Abstract
Neurodegeneration in the brains of Huntington's disease patients is accompanied by widespread changes in gene regulatory networks. Recent studies have found that these changes are not restricted to protein-coding genes, but also include non-coding RNAs (ncRNAs). One particularly abundant but poorly understood class of ncRNAs is the long non-coding RNAs (lncRNAs), of which at least ten thousand have been identified in the human genome. Although we presently know little about their function, lncRNAs are widely expressed in the mammalian nervous system, and many are likely to play critical roles in neuronal development and activity. LncRNAs are now being implicated in neurodegenerative processes, including Alzheimer's (AD) and Huntington's disease (HD). In the present study, I discuss the potential significance of lncRNAs in HD. To support this, I have mined existing microarray data to discover seven new lncRNAs that are dysregulated in HD brains. Interestingly, several of these contain genomic binding sites for the transcriptional repressor REST, a key mediator of transcriptional changes in HD, including the known REST target lncRNA, DGCR5. Previously described lncRNAs TUG1 (necessary for retinal development) and NEAT1 (a structural component of nuclear paraspeckles) are upregulated in HD caudate, while the brain-specific tumour-suppressor MEG3 is downregulated. Three other lncRNAs of unknown function are also significantly changed in HD brains. Many lncRNAs regulate gene expression through formation of epigenetic ribonucleoprotein complexes, including TUG1 and MEG3. These findings lead me to propose that lncRNA expression changes in HD are widespread, that many of these result in altered epigenetic gene regulation in diseased neurons, and that contributes to neurodegeneration. Therefore, elucidating lncRNA network changes in HD may be important in understanding and treating this and other neurodegenerative processes.
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Affiliation(s)
- Rory Johnson
- Bioinformatics and Genomics Group, Centre for Genomic Regulation and UPF, C Dr Aiguader, 88 Barcelona 08003, Catalonia, Spain.
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Buckley NJ, Johnson R. New insights into non-coding RNA networks in Huntington's disease. Exp Neurol 2011; 231:191-4. [DOI: 10.1016/j.expneurol.2011.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 07/11/2011] [Accepted: 07/16/2011] [Indexed: 10/17/2022]
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