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Xu L, Zheng S, Witzel K, Van De Slijke E, Baekelandt A, Mylle E, Van Damme D, Cheng J, De Jaeger G, Inzé D, Jiang H. Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana. Nat Commun 2024; 15:1286. [PMID: 38346986 PMCID: PMC10861482 DOI: 10.1038/s41467-024-45577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
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Affiliation(s)
- Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Shiwei Zheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, 14979, Germany
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany.
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Li H, Zheng C, Han J, Zhu J, Liu S, Jin T. PD-1/PD-L1 Axis as a Potential Therapeutic Target for Multiple Sclerosis: A T Cell Perspective. Front Cell Neurosci 2021; 15:716747. [PMID: 34381337 PMCID: PMC8350166 DOI: 10.3389/fncel.2021.716747] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/22/2021] [Indexed: 12/19/2022] Open
Abstract
The programmed cell death protein-1/programmed death ligand-1 (PD-1/PD-L1) axis is a widely studied immune checkpoint that modulates signaling pathways related to T cell activation. The use of PD-1/PD-L1 inhibitors is a promising immune therapy strategy for cancer patients. However, individuals treated with PD-1/PD-L1 inhibitors may develop immune-related adverse events due to excessive immune reactions. Multiple sclerosis (MS) is a chronic demyelinating and neurodegenerative disease of the central nervous system. T cells and the PD-1/PD-L1 axis play vital roles in the pathogenesis of MS. A better understanding of the complex relationship between the PD-1/PD-L1 axis and T cells may extend our knowledge of the molecular mechanisms and therapeutic approaches for MS. In this review, we summarize the most recent findings regarding the role of the PD-1/PD-L1 axis in MS and discuss the potential therapeutic strategies to modulate the expression of PD-1/PD-L1 in MS.
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Affiliation(s)
- HaiXia Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Chao Zheng
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Jinming Han
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jie Zhu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Shan Liu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Tao Jin
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
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3
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Huang YA, Hu P, Chan KCC, You ZH. Graph convolution for predicting associations between miRNA and drug resistance. Bioinformatics 2020; 36:851-858. [PMID: 31397851 DOI: 10.1093/bioinformatics/btz621] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 07/17/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION MicroRNA (miRNA) therapeutics is becoming increasingly important. However, aberrant expression of miRNAs is known to cause drug resistance and can become an obstacle for miRNA-based therapeutics. At present, little is known about associations between miRNA and drug resistance and there is no computational tool available for predicting such association relationship. Since it is known that miRNAs can regulate genes that encode specific proteins that are keys for drug efficacy, we propose here a computational approach, called GCMDR, for finding a three-layer latent factor model that can be used to predict miRNA-drug resistance associations. RESULTS In this paper, we discuss how the problem of predicting such associations can be formulated as a link prediction problem involving a bipartite attributed graph. GCMDR makes use of the technique of graph convolution to build a latent factor model, which can effectively utilize information of high-dimensional attributes of miRNA/drug in an end-to-end learning scheme. In addition, GCMDR also learns graph embedding features for miRNAs and drugs. We leveraged the data from multiple databases storing miRNA expression profile, drug substructure fingerprints, gene ontology and disease ontology. The test for performance shows that the GCMDR prediction model can achieve AUCs of 0.9301 ± 0.0005, 0.9359 ± 0.0006 and 0.9369 ± 0.0003 based on 2-fold, 5-fold and 10-fold cross validation, respectively. Using this model, we show that the associations between miRNA and drug resistance can be reliably predicted by properly introducing useful side information like miRNA expression profile and drug structure fingerprints. AVAILABILITY AND IMPLEMENTATION Python codes and dataset are available at https://github.com/yahuang1991polyu/GCMDR/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yu-An Huang
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China
| | - Pengwei Hu
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China
| | - Keith C C Chan
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China
| | - Zhu-Hong You
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China.,Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Urumqi 830011, China
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4
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Bhat AA, Younes SN, Raza SS, Zarif L, Nisar S, Ahmed I, Mir R, Kumar S, Sharawat SK, Hashem S, Elfaki I, Kulinski M, Kuttikrishnan S, Prabhu KS, Khan AQ, Yadav SK, El-Rifai W, Zargar MA, Zayed H, Haris M, Uddin S. Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance. Mol Cancer 2020; 19:57. [PMID: 32164715 PMCID: PMC7069174 DOI: 10.1186/s12943-020-01175-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Early-stage detection of leukemia is a critical determinant for successful treatment of the disease and can increase the survival rate of leukemia patients. The factors limiting the current screening approaches to leukemia include low sensitivity and specificity, high costs, and a low participation rate. An approach based on novel and innovative biomarkers with high accuracy from peripheral blood offers a comfortable and appealing alternative to patients, potentially leading to a higher participation rate. Recently, non-coding RNAs due to their involvement in vital oncogenic processes such as differentiation, proliferation, migration, angiogenesis and apoptosis have attracted much attention as potential diagnostic and prognostic biomarkers in leukemia. Emerging lines of evidence have shown that the mutational spectrum and dysregulated expression of non-coding RNA genes are closely associated with the development and progression of various cancers, including leukemia. In this review, we highlight the expression and functional roles of different types of non-coding RNAs in leukemia and discuss their potential clinical applications as diagnostic or prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Ajaz A Bhat
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Salma N Younes
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Era's Lucknow Medical College and Hospital, Lucknow, Uttar Pradesh, India
| | - Lubna Zarif
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Sabah Nisar
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ikhlak Ahmed
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Rashid Mir
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Sachin Kumar
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Surender K Sharawat
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Santosh K Yadav
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami, Miami, Florida, USA
| | - Mohammad A Zargar
- Department of Biotechnology, Central University of Kashmir, Ganderbal, Jammu and Kashmir, India
| | - Hatem Zayed
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar
| | - Mohammad Haris
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Laboratory Animal Research Center, Qatar University, Doha, Qatar.
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar.
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5
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Fu F, Wang T, Wu Z, Feng Y, Wang W, Zhou S, Ma X, Wang S. HMGA1 exacerbates tumor growth through regulating the cell cycle and accelerates migration/invasion via targeting miR-221/222 in cervical cancer. Cell Death Dis 2018; 9:594. [PMID: 29789601 PMCID: PMC5964147 DOI: 10.1038/s41419-018-0683-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/11/2018] [Accepted: 05/03/2018] [Indexed: 12/17/2022]
Abstract
High-mobility group AT-hook1 (HMGA1, formerly HMG-I/Y), an architectural transcription factor, participates in a number of tumor biological processes. However, its effect on cervical cancer remains largely indistinct. In this study, we found that HMGA1 was generally overexpressed in cervical cancer tissues and was positively correlated with lymph node metastasis and advanced clinical stage. Via exogenously increasing or decreasing the expression of HMGA1, we showed that HMGA1 affected the proliferation, colony formation, migration and invasion of cervical cancer cells in vitro. Rescue experiments suggested that miR-221/222 could partly reverse HMGA1-mediated migration and invasion processes. Mechanistically, we discovered that HMGA1 accelerated the G1/S phase transition by regulating the expression of cyclin D1 and cyclin E1, which was consistent with the results of the in vivo experiment. Furthermore, we found that HMGA1 regulated the expression of the miR-221/222 cluster at the transcriptional level and that miR-221/222 targeted the 3'UTR of tissue inhibitor of metalloproteinases 3(TIMP3). We propose a fresh perspective that HMGA1 participates in the migration and invasion process via the miR-221/222-TIMP3-MMP2/MMP9 axis in cervical cancer. In summary, our study identified a critical role played by HMGA1 in the progression of cervical cancer and the potential mechanisms by which exerts its effects, suggesting that targeting HMGA1-related pathways could be conducive to the therapies for cervical cancer.
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Affiliation(s)
- Fangfang Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Tian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Zhangying Wu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, 55000, Guiyang, Guizhou, China
| | - Yourong Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Wenwen Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Su Zhou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
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6
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Gabra MM, Salmena L. microRNAs and Acute Myeloid Leukemia Chemoresistance: A Mechanistic Overview. Front Oncol 2017; 7:255. [PMID: 29164055 PMCID: PMC5674931 DOI: 10.3389/fonc.2017.00255] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022] Open
Abstract
Up until the early 2000s, a functional role for microRNAs (miRNAs) was yet to be elucidated. With the advent of increasingly high-throughput and precise RNA-sequencing techniques within the last two decades, it has become well established that miRNAs can regulate almost all cellular processes through their ability to post-transcriptionally regulate a majority of protein-coding genes and countless other non-coding genes. In cancer, miRNAs have been demonstrated to play critical roles by modifying or controlling all major hallmarks including cell division, self-renewal, invasion, and DNA damage among others. Before the introduction of anthracyclines and cytarabine in the 1960s, acute myeloid leukemia (AML) was considered a fatal disease. In decades since, prognosis has improved substantially; however, long-term survival with AML remains poor. Resistance to chemotherapy, whether it is present at diagnosis or induced during treatment is a major therapeutic challenge in the treatment of this disease. Certain mechanisms such as DNA damage response and drug targeting, cell cycling, cell death, and drug trafficking pathways have been shown to be further dysregulated in treatment resistant cancers. miRNAs playing key roles in the emergence of these drug resistance phenotypes have recently emerged and replacement or inhibition of these miRNAs may be a viable treatment option. Herein, we describe the roles miRNAs can play in drug resistant AML and we describe miRNA-transcript interactions found within other cancer states which may be present within drug resistant AML. We describe the mechanisms of action of these miRNAs and how they can contribute to a poor overall survival and outcome as well. With the precision of miRNA mimic- or antagomir-based therapies, miRNAs provide an avenue for exquisite targeting in the therapy of drug resistant cancers.
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Affiliation(s)
- Martino Marco Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Leonardo Salmena
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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7
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MicroRNA-20b promotes the accumulation of CD11b+Ly6G+Ly6C low myeloid-derived suppressor cells in asthmatic mice. Cent Eur J Immunol 2017; 42:30-38. [PMID: 28680329 PMCID: PMC5470612 DOI: 10.5114/ceji.2017.67316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
miR-20b is a member of the miR-106a-363 gene cluster, which has been shown to play an important role in a variety of diseases, including cancer, inflammation, and autoimmune diseases. Our previous study indicated that miR-20b has an inhibitory effect on airway inflammation in asthmatic mice, but the exact mechanism is unclear. In this study, we report that the ratio of CD11b+Ly6G+Ly6Clow cells, but not the amount of CD11b+Ly6C+Ly6G– cells, was increased in the lung tissue of asthmatic mice after intranasal instillation with miR-20b mimics, while Th2-type cytokines (interleukin (IL)-4 and IL-13) were significantly decreased in the bronchoalveolar lavage fluid. In addition, the transcription factor CREB regulated the expression of miR-20b. Our findings suggest that miR-20b can induce the accumulation of myeloid-derived suppressor cells in the lungs of asthmatic mice, which may be a mechanism by which miR-20b inhibits airway inflammation in asthmatic mice. Thus, miR-20b may be used as a target for the effective treatment of asthma in the future.
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8
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Dumler JS, Sinclair SH, Pappas-Brown V, Shetty AC. Genome-Wide Anaplasma phagocytophilum AnkA-DNA Interactions Are Enriched in Intergenic Regions and Gene Promoters and Correlate with Infection-Induced Differential Gene Expression. Front Cell Infect Microbiol 2016; 6:97. [PMID: 27703927 PMCID: PMC5028410 DOI: 10.3389/fcimb.2016.00097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils, and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR)-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains. We hypothesize that identification of additional AnkA binding sites will better delineate how A. phagocytophilum infection results in reprogramming of the neutrophil genome. Using AnkA-binding ChIP-seq, we showed that AnkA binds broadly throughout all chromosomes in a reproducible pattern, especially at: (i) intergenic regions predicted to be MARs; (ii) within predicted lamina-associated domains; and (iii) at promoters ≤ 3000 bp upstream of transcriptional start sites. These findings provide genome-wide support for AnkA as a regulator of cis-gene transcription. Moreover, the dominant mark of AnkA in distal intergenic regions known to be AT-enriched, coupled with frequent enrichment in the nuclear lamina, provides strong support for its role as a MAR-binding protein and genome “re-organizer.” AnkA must be considered a prime candidate to promote neutrophil reprogramming and subsequent functional changes that belie improved microbial fitness and pathogenicity.
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Affiliation(s)
- J Stephen Dumler
- Department of Pathology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences Bethesda, MD, USA
| | | | - Valeria Pappas-Brown
- Department of Pathology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences Bethesda, MD, USA
| | - Amol C Shetty
- Informatics Resource Center, Institute for Genome Sciences, University of Maryland Baltimore, MD, USA
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9
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A novel HMGA1-CCNE2-YAP axis regulates breast cancer aggressiveness. Oncotarget 2016; 6:19087-101. [PMID: 26265440 PMCID: PMC4662477 DOI: 10.18632/oncotarget.4236] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/12/2015] [Indexed: 12/23/2022] Open
Abstract
High Mobility Group A1 (HMGA1) is an architectural chromatin factor that promotes neoplastic transformation and progression. However, the mechanism by which HMGA1 exerts its oncogenic function is not fully understood. Here, we show that cyclin E2 (CCNE2) acts downstream of HMGA1 to regulate the motility and invasiveness of basal-like breast cancer cells by promoting the nuclear localization and activity of YAP, the downstream mediator of the Hippo pathway. Mechanistically, the activity of MST1/2 and LATS1/2, the core kinases of the Hippo pathway, are required for the HMGA1- and CCNE2-mediated regulation of YAP localization. In breast cancer patients, high levels of HMGA1 and CCNE2 expression are associated with the YAP/TAZ signature, supporting this connection. Moreover, we provide evidence that CDK inhibitors induce the translocation of YAP from the nucleus to the cytoplasm, resulting in a decrease in its activity. These findings reveal an association between HMGA1 and the Hippo pathway that is relevant to stem cell biology, tissue homeostasis, and cancer.
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10
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Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M. High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. BMC Genomics 2016; 17:341. [PMID: 27161480 PMCID: PMC4862039 DOI: 10.1186/s12864-016-2468-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/12/2016] [Indexed: 12/15/2022] Open
Abstract
Background Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA sequencing, FAIRE-seq, is emerging as a powerful new high-throughput tool for global CRE discovery. FAIRE results in the preferential recovery of open chromatin DNA fragments that are not bound by nucleosomes, an evolutionarily conserved indicator of regulatory activity, which are then sequenced. Despite the power of the approach, FAIRE-seq has not yet been applied to the study of non-model insects. In this investigation, we utilized FAIRE-seq to profile open chromatin and identify likely regulatory elements throughout the genome of the human disease vector mosquito Aedes aegypti. We then assessed genetic variation in the regulatory elements of dengue virus susceptible (Moyo-S) and refractory (Moyo-R) mosquito strains. Results Analysis of sequence data obtained through next generation sequencing of FAIRE DNA isolated from A. aegypti embryos revealed >121,000 FAIRE peaks (FPs), many of which clustered in the 1 kb 5’ upstream flanking regions of genes known to be expressed at this stage. As expected, known transcription factor consensus binding sites were enriched in the FPs, and of these FoxA1, Hunchback, Gfi, Klf4, MYB/ph3 and Sox9 are most predominant. All of the elements tested in vivo were confirmed to drive gene expression in transgenic Drosophila reporter assays. Of the >13,000 single nucleotide polymorphisms (SNPs) recently identified in dengue virus-susceptible and refractory mosquito strains, 3365 were found to map to FPs. Conclusion FAIRE-seq analysis of open chromatin in A. aegypti permitted genome-wide discovery of CREs. The results of this investigation indicate that FAIRE-seq is a powerful tool for identification of regulatory DNA in the genomes of non-model organisms, including human disease vector mosquitoes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2468-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Joseph Sarro
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - Ping Li
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - Keshava Mysore
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - David W Severson
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Molly Duman-Scheel
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.
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11
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Miyaji M, Furuta R, Sano K, Tsutsui KM, Tsutsui K. Genomic regions targeted by DNA topoisomerase IIβ frequently interact with a nuclear scaffold/matrix protein hnRNP U/SAF-A/SP120. J Cell Biochem 2016; 116:677-85. [PMID: 25418483 PMCID: PMC5024068 DOI: 10.1002/jcb.25024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/18/2014] [Indexed: 11/16/2022]
Abstract
Type II DNA topoisomerases (topo II) play critical roles in some cellular events through repeated cleavage/rejoining of nuclear DNA. The β isoform (topo IIβ) is essential for the transcriptional induction of neuronal genes in terminal differentiation. Genomic sites targeted by the enzyme are nonrandom. Although previous studies have claimed that topo II cleavage sites are close to the nuclear scaffold/matrix attachment region (S/MAR), it is still unclear whether this view can be generalized. We report here that a library of cloned genomic DNA fragments targeted by topo IIβ in vivo frequently contains S/MAR and binding sites for hnRNP U/SAF‐A/SP120. Binding assays in vitro showed that a large proportion of the target DNAs bound to SP120 but their affinity to the nuclear scaffold/matrix varied significantly. Topo IIβ targets were extremely AT‐rich and often located in gene‐poor long intergenic regions (so‐called gene desert) that are juxtaposed to long genes expressed in neurons under differentiation. Sequence analysis revealed that topo IIβ targets are not just AT‐rich but are enriched with short tracts of A's and T's (termed A/T‐patches). Their affinity to the nuclear scaffold/matrix showed a moderate positive correlation with the coverage rate of A/T‐patches. The results suggest that the interaction of topo IIβ/SP120 with target regions modulates their proximity to the nuclear scaffold/matrix in a dynamic fashion and that A/T‐patch is a sequence motif assisting this process. J. Cell. Biochem. 116: 677–685, 2015. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Mary Miyaji
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
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Hamid SM, Akgül B. Master regulators of posttranscriptional gene expression are subject to regulation. Methods Mol Biol 2014; 1107:303-10. [PMID: 24272445 DOI: 10.1007/978-1-62703-748-8_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs of 17-25 nt in length that control gene expression posttranscriptionally. As master regulators of posttranscriptional gene expression, miRNAs themselves are subject to tight regulation at multiple steps. The most common mechanisms include miRNA transcription, processing, and localization. Additionally, intricate feedback loops between miRNAs and transcription factors result in unidirectional, reciprocal, or self-directed elegant control mechanisms. In this chapter, we focus on the posttranscriptional regulatory mechanisms that generate miRNAs whose sequence might be slightly different from the miRNA-coding sequences. Hopefully, this information will be helpful in the discovery of novel miRNAs as well as in the analysis of deep-sequencing data and ab initio prediction of miRNAs.
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Affiliation(s)
- Syed Muhammad Hamid
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
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Epigenetic deregulation of microRNAs in rhabdomyosarcoma and neuroblastoma and translational perspectives. Int J Mol Sci 2012; 13:16554-79. [PMID: 23443118 PMCID: PMC3546707 DOI: 10.3390/ijms131216554] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 11/21/2012] [Accepted: 11/21/2012] [Indexed: 12/21/2022] Open
Abstract
Gene expression control mediated by microRNAs and epigenetic remodeling of chromatin are interconnected processes often involved in feedback regulatory loops, which strictly guide proper tissue differentiation during embryonal development. Altered expression of microRNAs is one of the mechanisms leading to pathologic conditions, such as cancer. Several lines of evidence pointed to epigenetic alterations as responsible for aberrant microRNA expression in human cancers. Rhabdomyosarcoma and neuroblastoma are pediatric cancers derived from cells presenting features of skeletal muscle and neuronal precursors, respectively, blocked at different stages of differentiation. Consistently, tumor cells express tissue markers of origin but are unable to terminally differentiate. Several microRNAs playing a key role during tissue differentiation are often epigenetically downregulated in rhabdomyosarcoma and neuroblastoma and behave as tumor suppressors when re-expressed. Recently, inhibition of epigenetic modulators in adult tumors has provided encouraging results causing re-expression of anti-tumor master gene pathways. Thus, a similar approach could be used to correct the aberrant epigenetic regulation of microRNAs in rhabdomyosarcoma and neuroblastoma. The present review highlights the current insights on epigenetically deregulated microRNAs in rhabdomyosarcoma and neuroblastoma and their role in tumorigenesis and developmental pathways. The translational clinical implications and challenges regarding modulation of epigenetic chromatin remodeling/microRNAs interconnections are also discussed.
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Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs of ~22nt in length which are involved in the regulation of gene expression at the posttranscriptional level by degrading their target mRNAs and/or inhibiting their translation. Expressed ubiquitously or in a tissue-specific manner, miRNAs are involved in the regulation of many biological processes such as cell proliferation, differentiation, apoptosis, and the maintenance of normal cellular physiology. Many miRNAs are expressed in embryonic, postnatal, and adult hearts. Aberrant expression or genetic deletion of miRNAs is associated with abnormal cardiac cell differentiation, disruption of heart development, and cardiac dysfunction. This chapter will summarize the history, biogenesis, and processing of miRNAs as well as their function in heart development, remodeling, and disease.
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Affiliation(s)
- Ramón A Espinoza-Lewis
- Cardiovascular Research Division, Department of Cardiology, Children’s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
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