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Shaykevich A, Chae D, Silverman I, Bassali J, Louloueian N, Siegman A, Bandyopadhyaya G, Goel S, Maitra R. Impact of carbamazepine on SMARCA4 (BRG1) expression in colorectal cancer: modulation by KRAS mutation status. Invest New Drugs 2024; 42:229-239. [PMID: 38446332 PMCID: PMC10944448 DOI: 10.1007/s10637-024-01418-2] [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: 12/23/2023] [Accepted: 01/07/2024] [Indexed: 03/07/2024]
Abstract
SMARCA4 is a gene traditionally considered a tumor suppressor. Recent research has however found that SMARCA4 likely promotes cancer growth and is a good target for cancer treatment. The drug carbamazepine, an autophagy inducer, was used on colorectal cancer cell lines, HCT1116 and Hke3 (KRAS mutant and wildtype). Our study finds that Carbamazepine affects SMARCA4 levels and that this effect is different depending on the KRAS mutation status. This study analyzes the effect of carbamazepine on early-stage autophagy via ULK1 as well as simulates the docking of carbamazepine on KRAS, depending on the mutation status. Our study highlights the therapeutic uses of carbamazepine on cancer, and we propose that carbamazepine in conjunction with other chemotherapies may prove useful in targeting KRAS-mutated colorectal cancer.
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Affiliation(s)
- Aaron Shaykevich
- Department of Biology, Yeshiva University, New York, NY, 10033, USA
| | - Danbee Chae
- Department of Biology, Yeshiva University, New York, NY, 10033, USA
| | - Isaac Silverman
- Department of Biology, Yeshiva University, New York, NY, 10033, USA
| | - Jeremy Bassali
- Department of Biology, Yeshiva University, New York, NY, 10033, USA
| | | | | | | | - Sanjay Goel
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Radhashree Maitra
- Department of Biology, Yeshiva University, New York, NY, 10033, USA.
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2
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Bertzbach LD, Seddar L, von Stromberg K, Ip WH, Dobner T, Hidalgo P. The adenovirus DNA-binding protein DBP. J Virol 2024; 98:e0188523. [PMID: 38197632 PMCID: PMC10878046 DOI: 10.1128/jvi.01885-23] [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] [Indexed: 01/11/2024] Open
Abstract
Adenoviruses are a group of double-stranded DNA viruses that can mainly cause respiratory, gastrointestinal, and eye infections in humans. In addition, adenoviruses are employed as vector vaccines for combatting viral infections, including SARS-CoV-2, and serve as excellent gene therapy vectors. These viruses have the ability to modulate the host cell machinery to their advantage and trigger significant restructuring of the nuclei of infected cells through the activity of viral proteins. One of those, the adenovirus DNA-binding protein (DBP), is a multifunctional non-structural protein that is integral to the reorganization processes. DBP is encoded in the E2A transcriptional unit and is highly abundant in infected cells. Its activity is unequivocally linked to the formation, structure, and integrity of virus-induced replication compartments, molecular hubs for the regulation of viral processes, and control of the infected cell. DBP also plays key roles in viral DNA replication, transcription, viral gene expression, and even host range specificity. Notably, post-translational modifications of DBP, such as SUMOylation and extensive phosphorylation, regulate its biological functions. DBP was first investigated in the 1970s, pioneering research on viral DNA-binding proteins. In this literature review, we provide an overview of DBP and specifically summarize key findings related to its complex structure, diverse functions, and significant role in the context of viral replication. Finally, we address novel insights and perspectives for future research.
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Affiliation(s)
- Luca D. Bertzbach
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Laura Seddar
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Wing-Hang Ip
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Thomas Dobner
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Paloma Hidalgo
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
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3
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Chu L, Xie D, Xu D. Epigenetic Regulation of Fibroblasts and Crosstalk between Cardiomyocytes and Non-Myocyte Cells in Cardiac Fibrosis. Biomolecules 2023; 13:1382. [PMID: 37759781 PMCID: PMC10526373 DOI: 10.3390/biom13091382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/10/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetic mechanisms and cell crosstalk have been shown to play important roles in the initiation and progression of cardiac fibrosis. This review article aims to provide a thorough overview of the epigenetic mechanisms involved in fibroblast regulation. During fibrosis, fibroblast epigenetic regulation encompasses a multitude of mechanisms, including DNA methylation, histone acetylation and methylation, and chromatin remodeling. These mechanisms regulate the phenotype of fibroblasts and the extracellular matrix composition by modulating gene expression, thereby orchestrating the progression of cardiac fibrosis. Moreover, cardiac fibrosis disrupts normal cardiac function by imposing myocardial mechanical stress and compromising cardiac electrical conduction. This review article also delves into the intricate crosstalk between cardiomyocytes and non-cardiomyocytes in the heart. A comprehensive understanding of the mechanisms governing epigenetic regulation and cell crosstalk in cardiac fibrosis is critical for the development of effective therapeutic strategies. Further research is warranted to unravel the precise molecular mechanisms underpinning these processes and to identify potential therapeutic targets.
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Affiliation(s)
| | | | - Dachun Xu
- Department of Cardiology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, 315 Yanchang Middle Road, Shanghai 200072, China; (L.C.); (D.X.)
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4
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Singh A, Modak SB, Chaturvedi MM, Purohit JS. SWI/SNF Chromatin Remodelers: Structural, Functional and Mechanistic Implications. Cell Biochem Biophys 2023:10.1007/s12013-023-01140-5. [PMID: 37119511 DOI: 10.1007/s12013-023-01140-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
The nuclear events of a eukaryotic cell, such as replication, transcription, recombination and repair etc. require the transition of the compactly arranged chromatin into an uncompacted state and vice-versa. This is mediated by post-translational modification of the histones, exchange of histone variants and ATP-dependent chromatin remodeling. The SWI/SNF chromatin remodeling complexes are one of the most well characterized families of chromatin remodelers. In addition to their role in modulating chromatin, they have also been assigned roles in cancer and health-related anomalies such as developmental, neurocognitive, and intellectual disabilities. Owing to their vital cellular and medical connotations, developing an understanding of the structural and functional aspects of the complex becomes imperative. However, due to the intricate nature of higher-order chromatin as well as compositional heterogeneity of the SWI/SNF complex, intra-species isoforms and inter-species homologs, this often becomes challenging. To this end, the present review attempts to present an amalgamated perspective on the discovery, structure, function, and regulation of the SWI/SNF complex.
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Affiliation(s)
- Abhilasha Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Madan M Chaturvedi
- Department of Zoology, University of Delhi, Delhi, 110007, India
- SGT University, Gurugram (Delhi-NCR), Haryana, 122505, India
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5
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BRG1: Promoter or Suppressor of Cancer? The Outcome of BRG1's Interaction with Specific Cellular Pathways. Int J Mol Sci 2023; 24:ijms24032869. [PMID: 36769189 PMCID: PMC9917617 DOI: 10.3390/ijms24032869] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
BRG1 is one of two catalytic subunits of the SWI/SNF ATP-dependent chromatin-remodeling complex. In cancer, it has been hypothesized that BRG1 acts as a tumor suppressor. Further study has shown that, under certain circumstances, BRG1 acts as an oncogene. Targeted knockout of BRG1 has proven successful in most cancers in suppressing tumor growth and proliferation. Furthermore, BRG1 effects cancer proliferation in oncogenic KRAS mutated cancers, with varying directionality. Thus, dissecting BRG1's interaction with various cellular pathways can highlight possible intermediates that can facilitate the design of different treatment methods, including BRG1 inhibition. Autophagy and apoptosis are two important cellular responses to stress. BRG1 plays a direct role in autophagy and apoptosis and likely promotes autophagy and suppresses apoptosis, supporting unfettered cancer growth. PRMT5 inhibits transcription by interacting with ATP-dependent chromatin remodeling complexes, such as SWI/SNF. When PRMT5 associates with the SWI/SNF complex, including BRG1, it represses tumor suppressor genes. The Ras/Raf/MAPK/ERK1/2 pathway in cancers is a signal transduction pathway involved in the transcription of genes related to cancer survival. BRG1 has been shown to effect KRAS-driven cancer growth. BRG1 associates with several proteins within the signal transduction pathway. In this review, we analyze BRG1 as a promising target for cancer inhibition and possible synergy with other cancer treatments.
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Cobos SN, Janani C, Cruz G, Rana N, Son E, Frederic R, Paredes Casado J, Khan M, Bennett SA, Torrente MP. [PRION +] States Are Associated with Specific Histone H3 Post-Translational Modification Changes. Pathogens 2022; 11:pathogens11121436. [PMID: 36558770 PMCID: PMC9786042 DOI: 10.3390/pathogens11121436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Prions are proteins able to take on alternative conformations and propagate them in a self-templating process. In Saccharomyces cerevisiae, prions enable heritable responses to environmental conditions through bet-hedging mechanisms. Hence, [PRION+] states may serve as an atypical form of epigenetic control, producing heritable phenotypic change via protein folding. However, the connections between prion states and the epigenome remain unknown. Do [PRION+] states link to canonical epigenetic channels, such as histone post-translational modifications? Here, we map out the histone H3 modification landscape in the context of the [SWI+] and [PIN+] prion states. [SWI+] is propagated by Swi1, a subunit of the SWI/SNF chromatin remodeling complex, while [PIN+] is propagated by Rnq1, a protein of unknown function. We find [SWI+] yeast display decreases in the levels of H3K36me2 and H3K56ac compared to [swi-] yeast. In contrast, decreases in H3K4me3, H3K36me2, H3K36me3 and H3K79me3 are connected to the [PIN+] state. Curing of the prion state by treatment with guanidine hydrochloride restored histone PTM to [prion-] state levels. We find histone PTMs in the [PRION+] state do not match those in loss-of-function models. Our findings shed light into the link between prion states and histone modifications, revealing novel insight into prion function in yeast.
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Affiliation(s)
- Samantha N. Cobos
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Chaim Janani
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Gabriel Cruz
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Navin Rana
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Elizaveta Son
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Rania Frederic
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | | | - Maliha Khan
- Biology Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Seth A. Bennett
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Mariana P. Torrente
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence:
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7
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Al-Farsi H, Al-Azwani I, Malek JA, Chouchane L, Rafii A, Halabi NM. Discovery of new therapeutic targets in ovarian cancer through identifying significantly non-mutated genes. J Transl Med 2022; 20:244. [PMID: 35619151 PMCID: PMC9134657 DOI: 10.1186/s12967-022-03440-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutated and non-mutated genes interact to drive cancer growth and metastasis. While research has focused on understanding the impact of mutated genes on cancer biology, understanding non-mutated genes that are essential to tumor development could lead to new therapeutic strategies. The recent advent of high-throughput whole genome sequencing being applied to many different samples has made it possible to calculate if genes are significantly non-mutated in a specific cancer patient cohort. METHODS We carried out random mutagenesis simulations of the human genome approximating the regions sequenced in the publicly available Cancer Growth Atlas Project for ovarian cancer (TCGA-OV). Simulated mutations were compared to the observed mutations in the TCGA-OV cohort and genes with the largest deviations from simulation were identified. Pathway analysis was performed on the non-mutated genes to better understand their biological function. We then compared gene expression, methylation and copy number distributions of non-mutated and mutated genes in cell lines and patient data from the TCGA-OV project. To directly test if non-mutated genes can affect cell proliferation, we carried out proof-of-concept RNAi silencing experiments of a panel of nine selected non-mutated genes in three ovarian cancer cell lines and one primary ovarian epithelial cell line. RESULTS We identified a set of genes that were mutated less than expected (non-mutated genes) and mutated more than expected (mutated genes). Pathway analysis revealed that non-mutated genes interact in cancer associated pathways. We found that non-mutated genes are expressed significantly more than mutated genes while also having lower methylation and higher copy number states indicating that they could be functionally important. RNAi silencing of the panel of non-mutated genes resulted in a greater significant reduction of cell viability in the cancer cell lines than in the non-cancer cell line. Finally, as a test case, silencing ANKLE2, a significantly non-mutated gene, affected the morphology, reduced migration, and increased the chemotherapeutic response of SKOV3 cells. CONCLUSION We show that we can identify significantly non-mutated genes in a large ovarian cancer cohort that are well-expressed in patient and cell line data and whose RNAi-induced silencing reduces viability in three ovarian cancer cell lines. Targeting non-mutated genes that are important for tumor growth and metastasis is a promising approach to expand cancer therapeutic options.
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Affiliation(s)
| | | | - Joel A Malek
- Genomics Core, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Arash Rafii
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar.
| | - Najeeb M Halabi
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar.
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8
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Wang Z, Cao H, Zhang C, Chen F, Liu Y. The SNF5-type protein BUSHY regulates seed germination via the gibberellin pathway and is dependent on HUB1 in Arabidopsis. PLANTA 2022; 255:34. [PMID: 35006338 DOI: 10.1007/s00425-021-03767-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
The SNF5-type protein BUSHY plays a role in the regulation of seed germination via the gibberellin pathway dependent on HUB1 in Arabidopsis thaliana. SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complexes play diverse roles in plant development. Some components have roles in embryo development and seed maturation, however, whether the SNF5-type protein BUSHY (BSH), one of the components, plays a role in Arabidopsis seed related traits is presently unclear. In our study, we show that a loss-of-function mutation in BSH causes increased seed germination in Arabidopsis. BSH transcription was induced by the gibberellin (GA) inhibitor paclobutrazol (PAC) in the seed, and BSH regulates the expression of GA pathway genes, such as Gibberellin 3-Oxidase 1 (GA3OX1), Gibberellic Acid-Stimulated Arabidopsis 4 (GASA4), and GASA6 during seed germination. A genetic analysis showed that seed germination was distinctly improved in the bshga3ox1ga3ox2 triple mutant, indicating that BSH acts partially downstream of GA3OX1 and GA3OX2. Moreover, the regulation of seed germination by BSH in response to PAC is dependent on HUB1. These results provide new insights and clues to understand the mechanisms of phytohormones in the regulation of seed germination.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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9
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Enríquez P, Krajewski K, Strahl BD, Rothbart SB, Dowen RH, Rose RB. Binding specificity and function of the SWI/SNF subunit SMARCA4 bromodomain interaction with acetylated histone H3K14. J Biol Chem 2021; 297:101145. [PMID: 34473995 PMCID: PMC8506967 DOI: 10.1016/j.jbc.2021.101145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
Bromodomains (BD) are conserved reader modules that bind acetylated lysine residues on histones. Although much has been learned regarding the in vitro properties of these domains, less is known about their function within chromatin complexes. SWI/SNF chromatin-remodeling complexes modulate transcription and contribute to DNA damage repair. Mutations in SWI/SNF subunits have been implicated in many cancers. Here we demonstrate that the BD of Caenorhabditis elegans SMARCA4/BRG1, a core SWI/SNF subunit, recognizes acetylated lysine 14 of histone H3 (H3K14ac), similar to its Homo sapiens ortholog. We identify the interactions of SMARCA4 with the acetylated histone peptide from a 1.29 Å-resolution crystal structure of the CeSMARCA4 BD-H3K14ac complex. Significantly, most of the SMARCA4 BD residues in contact with the histone peptide are conserved with other proteins containing family VIII bromodomains. Based on the premise that binding specificity is conserved among bromodomain orthologs, we propose that loop residues outside of the binding pocket position contact residues to recognize the H3K14ac sequence. CRISPR-Cas9-mediated mutations in the SMARCA4 BD that abolish H3K14ac binding in vitro had little or no effect on C. elegans viability or physiological function in vivo. However, combining SMARCA4 BD mutations with knockdown of the SWI/SNF accessory subunit PBRM-1 resulted in severe developmental defects in animals. In conclusion, we demonstrated an essential function for the SWI/SNF bromodomain in vivo and detected potential redundancy in epigenetic readers in regulating chromatin remodeling. These findings have implications for the development of small-molecule BD inhibitors to treat cancers and other diseases.
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Affiliation(s)
- Paul Enríquez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Robert H Dowen
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Robert B Rose
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA.
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Lin X, Yuan C, Zhu B, Yuan T, Li X, Yuan S, Cui S, Zhao H. LFR Physically and Genetically Interacts With SWI/SNF Component SWI3B to Regulate Leaf Blade Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:717649. [PMID: 34456957 PMCID: PMC8385146 DOI: 10.3389/fpls.2021.717649] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/14/2021] [Indexed: 05/26/2023]
Abstract
Leaves start to develop at the peripheral zone of the shoot apical meristem. Thereafter, symmetric and flattened leaf laminae are formed. These events are simultaneously regulated by auxin, transcription factors, and epigenetic regulatory factors. However, the relationships among these factors are not well known. In this study, we conducted protein-protein interaction assays to show that our previously reported Leaf and Flower Related (LFR) physically interacted with SWI3B, a component of the ATP-dependent chromatin remodeling SWI/SNF complex in Arabidopsis. The results of truncated analysis and transgenic complementation showed that the N-terminal domain (25-60 amino acids) of LFR was necessary for its interaction with SWI3B and was crucial for LFR functions in Arabidopsis leaf development. Genetic results showed that the artificial microRNA knockdown lines of SWI3B (SWI3B-amic) had a similar upward-curling leaf phenotype with that of LFR loss-of-function mutants. ChIP-qPCR assay was conducted to show that LFR and SWI3B co-targeted the promoters of YABBY1/FILAMENTOUS FLOWER (YAB1/FIL) and IAA carboxyl methyltransferase 1 (IAMT1), which were misexpressed in lfr and SWI3B-amic mutants. In addition, the association between LFR and the FIL and IAMT1 loci was partly hampered by the knockdown of SWI3B. These data suggest that LFR interacts with the chromatin-remodeling complex component, SWI3B, and influences the transcriptional expression of the important transcription factor, FIL, and the auxin metabolism enzyme, IAMT1, in flattened leaf lamina development.
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Affiliation(s)
- Xiaowei Lin
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Can Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Bonan Zhu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Tingting Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaorong Li
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shan Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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11
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Structure and Function of Chromatin Remodelers. J Mol Biol 2021; 433:166929. [PMID: 33711345 PMCID: PMC8184634 DOI: 10.1016/j.jmb.2021.166929] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 12/25/2022]
Abstract
Chromatin remodelers act to regulate multiple cellular processes, such as transcription and DNA repair, by controlling access to genomic DNA. Four families of chromatin remodelers have been identified in yeast, each with non-redundant roles within the cell. There has been a recent surge in structural models of chromatin remodelers in complex with their nucleosomal substrate. These structural studies provide new insight into the mechanism of action for individual chromatin remodelers. In this review, we summarize available data for the structure and mechanism of action of the four chromatin remodeling complex families.
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12
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Golson ML. Islet Epigenetic Impacts on β-Cell Identity and Function. Compr Physiol 2021; 11:1961-1978. [PMID: 34061978 DOI: 10.1002/cphy.c200004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The development and maintenance of differentiation is vital to the function of mature cells. Terminal differentiation is achieved by locking in the expression of genes essential for the function of those cells. Gene expression and its memory through generations of cell division is controlled by transcription factors and a host of epigenetic marks. In type 2 diabetes, β cells have altered gene expression compared to controls, accompanied by altered chromatin marks. Mutations, diet, and environment can all disrupt the implementation and preservation of the distinctive β-cell transcriptional signature. Understanding of the full complement of genomic control in β cells is still nascent. This article describes the known effects of histone marks and variants, DNA methylation, how they are regulated in the β cell, and how they affect cell-fate specification, maintenance, and lineage propagation. © 2021 American Physiological Society. Compr Physiol 11:1-18, 2021.
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Affiliation(s)
- Maria L Golson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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13
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Sarker H, Haimour A, Toor R, Fernandez-Patron C. The Emerging Role of Epigenetic Mechanisms in the Causation of Aberrant MMP Activity during Human Pathologies and the Use of Medicinal Drugs. Biomolecules 2021; 11:biom11040578. [PMID: 33920915 PMCID: PMC8071227 DOI: 10.3390/biom11040578] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
Matrix metalloproteinases (MMPs) cleave extracellular matrix proteins, growth factors, cytokines, and receptors to influence organ development, architecture, function, and the systemic and cell-specific responses to diseases and pharmacological drugs. Conversely, many diseases (such as atherosclerosis, arthritis, bacterial infections (tuberculosis), viral infections (COVID-19), and cancer), cholesterol-lowering drugs (such as statins), and tetracycline-class antibiotics (such as doxycycline) alter MMP activity through transcriptional, translational, and post-translational mechanisms. In this review, we summarize evidence that the aforementioned diseases and drugs exert significant epigenetic pressure on genes encoding MMPs, tissue inhibitors of MMPs, and factors that transcriptionally regulate the expression of MMPs. Our understanding of human pathologies associated with alterations in the proteolytic activity of MMPs must consider that these pathologies and their medicinal treatments may impose epigenetic pressure on the expression of MMP genes. Whether the epigenetic mechanisms affecting the activity of MMPs can be therapeutically targeted warrants further research.
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Wolff MR, Schmid A, Korber P, Gerland U. Effective dynamics of nucleosome configurations at the yeast PHO5 promoter. eLife 2021; 10:58394. [PMID: 33666171 PMCID: PMC8004102 DOI: 10.7554/elife.58394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Chromatin dynamics are mediated by remodeling enzymes and play crucial roles in gene regulation, as established in a paradigmatic model, the Saccharomyces cerevisiae PHO5 promoter. However, effective nucleosome dynamics, that is, trajectories of promoter nucleosome configurations, remain elusive. Here, we infer such dynamics from the integration of published single-molecule data capturing multi-nucleosome configurations for repressed to fully active PHO5 promoter states with other existing histone turnover and new chromatin accessibility data. We devised and systematically investigated a new class of 'regulated on-off-slide' models simulating global and local nucleosome (dis)assembly and sliding. Only seven of 68,145 models agreed well with all data. All seven models involve sliding and the known central role of the N-2 nucleosome, but regulate promoter state transitions by modulating just one assembly rather than disassembly process. This is consistent with but challenges common interpretations of previous observations at the PHO5 promoter and suggests chromatin opening by binding competition.
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Affiliation(s)
| | - Andrea Schmid
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Philipp Korber
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ulrich Gerland
- Department of Physics, Technical University of Munich, Garching, Germany
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Abstract
Drosophila melanogaster males reduce courtship behaviour after mating failure. In the lab, such conditioned courtship suppression, aka 'courtship conditioning', serves as a complex learning and memory assay. Interestingly, variations in the courtship conditioning assay can establish different types of memory. Here, we review research investigating the underlying cellular and molecular mechanisms that allow male flies to form memories of previous mating failures.
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Affiliation(s)
- Nicholas Raun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Spencer Jones
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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16
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Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity. Mucosal Immunol 2021; 14:38-52. [PMID: 32612160 PMCID: PMC7790751 DOI: 10.1038/s41385-020-0317-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/10/2020] [Accepted: 06/11/2020] [Indexed: 02/04/2023]
Abstract
Group 3 innate lymphoid cells (ILC3s), a subset of the innate lymphoid cells, are abundantly present in the intestine and are crucial regulators of intestinal inflammation. Brg1 (Brahma-related gene 1), a catalytic subunit of the mammalian SWI-SNF-like chromatin-remodeling BAF complex, regulates the development and function of various immune cells. Here, by genetic deletion of Brg1 in ILC3s (Smarca4ΔILC3), we prove that Brg1 supports the differentiation of NKp46+ILC3s by promoting the T-bet expression in NKp46-ILC3s, which facilitates the conversion of NKp46-ILC3s to NKp46+ILC3s. Strikingly, Smarca4ΔILC3 mice of the Rag1-/- background develop spontaneous colitis accompanied with increased GM-CSF production in ILC3s. By construction of a mixed bone marrow chimeric system, we demonstrate that Brg1 enhances T-bet and inhibits GM-CSF expression in ILC3s through a cell-intrinsic manner. Blockade of GM-CSF ameliorates colitis in Rag1-/-Smarca4ΔILC3 mice, suggesting that the suppression of GM-CSF production from ILC3s by Brg1 serves as a critical mechanism for Brg1 to restrain intestinal inflammation. We have further demonstrated that Brg1 binds to the Tbx21 and Csf2 gene locus in ILC3s, and favors the active and repressive histones modifications on gene locus of Tbx21 and Csf2 respectively. Our work reveals the essential role of Brg1 in intestinal immunity by regulating ILC3s.
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17
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Barish S, Barakat TS, Michel BC, Mashtalir N, Phillips JB, Valencia AM, Ugur B, Wegner J, Scott TM, Bostwick B, Murdock DR, Dai H, Perenthaler E, Nikoncuk A, van Slegtenhorst M, Brooks AS, Keren B, Nava C, Mignot C, Douglas J, Rodan L, Nowak C, Ellard S, Stals K, Lynch SA, Faoucher M, Lesca G, Edery P, Engleman KL, Zhou D, Thiffault I, Herriges J, Gass J, Louie RJ, Stolerman E, Washington C, Vetrini F, Otsubo A, Pratt VM, Conboy E, Treat K, Shannon N, Camacho J, Wakeling E, Yuan B, Chen CA, Rosenfeld JA, Westerfield M, Wangler M, Yamamoto S, Kadoch C, Scott DA, Bellen HJ. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms. Am J Hum Genet 2020; 107:1096-1112. [PMID: 33232675 PMCID: PMC7820627 DOI: 10.1016/j.ajhg.2020.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.
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Affiliation(s)
- Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Brittany C Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nazar Mashtalir
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alfredo M Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology Program, Harvard University, Cambridge, MA 02138, USA
| | - Berrak Ugur
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeremy Wegner
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Tiana M Scott
- Department of Microbiology and Molecular Biology, College of Life Science, Brigham Young University, Provo, UT 84602, USA
| | - Brett Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Anita Nikoncuk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Caroline Nava
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Jessica Douglas
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Lance Rodan
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Catherine Nowak
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK; Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter EX4 4PY, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin D12 N512, Ireland
| | - Marie Faoucher
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Patrick Edery
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Kendra L Engleman
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - John Herriges
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Jennifer Gass
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Raymond J Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Francesco Vetrini
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Aiko Otsubo
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Victoria M Pratt
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Erin Conboy
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Kayla Treat
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Nora Shannon
- Regional Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK
| | - Jose Camacho
- Pediatric Genetics and Metabolism, Loma Linda University Children's Hospital, Loma Linda, CA 92354, USA
| | - Emma Wakeling
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Monte Westerfield
- Department of Biology, University of Oregon, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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18
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Synovial Sarcoma: A Complex Disease with Multifaceted Signaling and Epigenetic Landscapes. Curr Oncol Rep 2020; 22:124. [PMID: 33025259 DOI: 10.1007/s11912-020-00985-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/29/2022]
Abstract
PURPOSE OF REVIEW Aside from a characteristic SS18-SSX translocation identified in almost all cases, no genetic anomalies have been reliably isolated yet to drive the pathogenesis of synovial sarcoma. In the following review, we explore the structural units of wild-type SS18 and SSX, particularly as they relate to the transcriptional alterations and cellular pathway changes imposed by SS18-SSX. RECENT FINDINGS Native SS18 and SSX contribute recognizable domains to the SS18-SSX chimeric proteins, which inflict transcriptional and epigenetic changes through selective protein interactions involving the SWI/SNF and Polycomb chromatin remodeling complexes. Multiple oncogenic and developmental pathways become altered, collectively reprogramming the cellular origin of synovial sarcoma and promoting its malignant transformation. Synovial sarcoma is characterized by complex epigenetic and signaling landscapes. Identifying the operational pathways and concomitant genetic changes induced by SS18-SSX fusions could help develop tailored therapeutic strategies to ultimately improve disease control and patient survivorship.
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Cerasuolo A, Buonaguro L, Buonaguro FM, Tornesello ML. The Role of RNA Splicing Factors in Cancer: Regulation of Viral and Human Gene Expression in Human Papillomavirus-Related Cervical Cancer. Front Cell Dev Biol 2020; 8:474. [PMID: 32596243 PMCID: PMC7303290 DOI: 10.3389/fcell.2020.00474] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
The spliceosomal complex components, together with the heterogeneous nuclear ribonucleoproteins (hnRNPs) and serine/arginine-rich (SR) proteins, regulate the process of constitutive and alternative splicing, the latter leading to the production of mRNA isoforms coding multiple proteins from a single pre-mRNA molecule. The expression of splicing factors is frequently deregulated in different cancer types causing the generation of oncogenic proteins involved in cancer hallmarks. Cervical cancer is caused by persistent infection with oncogenic human papillomaviruses (HPVs) and constitutive expression of viral oncogenes. The aberrant activity of hnRNPs and SR proteins in cervical neoplasia has been shown to trigger the production of oncoproteins through the processing of pre-mRNA transcripts either derived from human genes or HPV genomes. Indeed, hnRNP and SR splicing factors have been shown to regulate the production of viral oncoprotein isoforms necessary for the completion of viral life cycle and for cell transformation. Target-therapy strategies against hnRNPs and SR proteins, causing simultaneous reduction of oncogenic factors and inhibition of HPV replication, are under development. In this review, we describe the current knowledge of the functional link between RNA splicing factors and deregulated cellular as well as viral RNA maturation in cervical cancer and the opportunity of new therapeutic strategies.
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Affiliation(s)
| | | | | | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumouri IRCCS–Fondazione G. Pascale, Naples, Italy
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20
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FitzPatrick DR, Firth HV. Genomically Aided Diagnosis of Severe Developmental Disorders. Annu Rev Genomics Hum Genet 2020; 21:327-349. [PMID: 32421356 DOI: 10.1146/annurev-genom-120919-082329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our ability to make accurate and specific genetic diagnoses in individuals with severe developmental disorders has been transformed by data derived from genomic sequencing technologies. These data reveal both the patterns and rates of different mutational mechanisms and identify regions of the human genome with fewer mutations than would be expected. In outbred populations, the most common identifiable cause of severe developmental disorders is de novo mutation affecting the coding region in one of approximately 500 different genes, almost universally showing constraint. Simply combining the location of a de novo genomic event with its predicted consequence on the gene product gives significant diagnostic power. Our knowledge of the diversity of phenotypic consequences associated with comparable diagnostic genotypes at each locus is improving. Computationally useful phenotype data will improve diagnostic interpretation of ultrarare genetic variants and, in the long run, indicate which specific embryonic processes have been perturbed.
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Affiliation(s)
- David R FitzPatrick
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; .,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom.,Royal Hospital for Children and Young People, Edinburgh EH16 4SF, United Kingdom
| | - Helen V Firth
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; .,Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
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21
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Sanphui P, Kumar Das A, Biswas SC. Forkhead Box O3a requires BAF57, a subunit of chromatin remodeler SWI/SNF complex for induction of p53 up‐regulated modulator of apoptosis (Puma) in a model of Parkinson’s disease. J Neurochem 2020; 154:547-561. [DOI: 10.1111/jnc.14969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Priyankar Sanphui
- Cell Biology and Physiology Division CSIR‐Indian Institute of Chemical Biology Kolkata India
| | - Anoy Kumar Das
- Cell Biology and Physiology Division CSIR‐Indian Institute of Chemical Biology Kolkata India
| | - Subhas C. Biswas
- Cell Biology and Physiology Division CSIR‐Indian Institute of Chemical Biology Kolkata India
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22
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Collings CK, Little DW, Schafer SJ, Anderson JN. HIV chromatin is a preferred target for drugs that bind in the DNA minor groove. PLoS One 2019; 14:e0216515. [PMID: 31887110 PMCID: PMC6936835 DOI: 10.1371/journal.pone.0216515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2022] Open
Abstract
The HIV genome is rich in A but not G or U and deficient in C. This nucleotide bias controls HIV phenotype by determining the highly unusual composition of all major HIV proteins. The bias is also responsible for the high frequency of narrow DNA minor groove sites in the double-stranded HIV genome as compared to cellular protein coding sequences and the bulk of the human genome. Since drugs that bind in the DNA minor groove disrupt nucleosomes on sequences that contain closely spaced oligo-A tracts which are prevalent in HIV DNA because of its bias, it was of interest to determine if these drugs exert this selective inhibitory effect on HIV chromatin. To test this possibility, nucleosomes were reconstituted onto five double-stranded DNA fragments from the HIV-1 pol gene in the presence and in the absence of several minor groove binding drugs (MGBDs). The results demonstrated that the MGBDs inhibited the assembly of nucleosomes onto all of the HIV-1 segments in a manner that was proportional to the A-bias, but had no detectable effect on the formation of nucleosomes on control cloned fragments or genomic DNA from chicken and human. Nucleosomes preassembled onto HIV DNA were also preferentially destabilized by the drugs as evidenced by enhanced nuclease accessibility in physiological ionic strength and by the preferential loss of the histone octamer in hyper-physiological salt solutions. The drugs also selectively disrupted HIV-containing nucleosomes in yeast as revealed by enhanced nuclease accessibility of the in vivo assembled HIV chromatin and reductions in superhelical densities of plasmid chromatin containing HIV sequences. A comparison of these results to the density of A-tracts in the HIV genome indicates that a large fraction of the nucleosomes that make up HIV chromatin should be preferred in vitro targets for the MGBDs. These results show that the MGBDs preferentially disrupt HIV-1 chromatin in vitro and in vivo and raise the possibility that non-toxic derivatives of certain MGBDs might serve as a novel class of anti-HIV agents.
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Affiliation(s)
- Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States of America.,Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Donald W Little
- University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Samuel J Schafer
- Department of Reproductive and Developmental Sciences, University of British Columbia, Vancouver, BC, Canada
| | - John N Anderson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
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23
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Novel Interactions between the Human T-Cell Leukemia Virus Type 1 Antisense Protein HBZ and the SWI/SNF Chromatin Remodeling Family: Implications for Viral Life Cycle. J Virol 2019; 93:JVI.00412-19. [PMID: 31142665 DOI: 10.1128/jvi.00412-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/19/2019] [Indexed: 12/15/2022] Open
Abstract
The human T-cell leukemia virus type 1 (HTLV-1) regulatory proteins Tax and HBZ play indispensable roles in regulating viral and cellular gene expression. BRG1, the ATPase subunit of the SWI/SNF chromatin remodeling complex, has been demonstrated to be essential not only for Tax transactivation but also for viral replication. We sought to investigate the physical interaction between HBZ and BRG1 and to determine the effect of these interactions on Tax-mediated long terminal repeat (LTR) activation. We reveal that HTLV-1 cell lines and adult T-cell leukemia (ATL) cells harbor high levels of BRG1. Using glutathione S-transferase (GST) pulldown and coimmunoprecipitation assays, we have demonstrated physical interactions between BRG1 and HBZ and characterized the protein domains involved. Moreover, we have identified the PBAF signature subunits BAF200 and BAF180 as novel interaction partners of HBZ, suggesting that the PBAF complex may be required for HTLV-1 transcriptional repression by HBZ. Additionally, we found that BRG1 expression translocates HBZ into distinct nuclear foci. We show that HBZ substantially represses HTLV-1 LTR activation by Tax/BRG1. Interestingly, we found that Tax stabilizes the expression of exogenous and endogenous BRG1 and that HBZ reverses this effect. Finally, using a chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay, we illustrate that HBZ facilitates the downregulation of HTLV-1 transcription by deregulating the recruitment of SWI/SNF complexes to the promoter. Overall, we conclude that SWI/SNF complexes, in addition to other cellular transcription factors, are involved in HBZ-mediated suppression of HTLV-1 viral gene expression.IMPORTANCE The pathogenic potential of HTLV-1 is linked to the indispensable multifaceted functions of the viral regulatory proteins Tax and HBZ, encoded by the sense and antisense viral transcripts, respectively. The interaction between Tax and the SWI/SNF family of chromatin remodeling complexes has been associated with HTLV-1 transcriptional activation. To date, the relationship between the SWI/SNF chromatin remodeling family and HBZ, the only viral protein that is consistently expressed in infected cells and ATL cells, has not been elucidated. Here, we have characterized the biological significance of the SWI/SNF family in regard to viral transcriptional repression by HBZ. This is important because it provides a better understanding of the function and role of HBZ in downregulating viral transcription and, hence, its contribution to viral latency and persistence in vivo, a process that may ultimately lead to the development of ATL.
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Cao Y, Zheng F, Zhang W, Meng X, Liu W. Trichoderma reesei XYR1 recruits SWI/SNF to facilitate cellulase gene expression. Mol Microbiol 2019; 112:1145-1162. [PMID: 31309604 DOI: 10.1111/mmi.14352] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
Cellulase gene expression in Trichoderma reesei is highly responsive to environmental cues and is under stringent regulation by multiple transcription factors. XYR1 (Xylanase regulator 1) has been identified as the most important transcriptional activator of cellulase/hemicellulase gene expression although the precise transactivating mechanism remains largely elusive. Here we show that the activation domain of XYR1 interacts with the T. reesei homolog of the TrSNF12 subunit of SWI/SNF complex. Deletion of Trsnf12 markedly impaired the induced cellulase gene expression. Individual loss of other SWI/SNF subunits including the catalytic subunit also severely compromised cellulase gene expression and interfered with loss of histone H4 in the cbh1 and eg1 promoters upon cellulose induction. In addition, we find that the SWI/SNF occupancy on cellulase gene promoters strictly required XYR1 and TrSNF12 but TrSNF12 was dispensable for the XYR1 binding to these promoters. These data suggest a model in which XYR1 recruits SWI/SNF through direct interactions with TrSNF12 to remodel chromatin at cellulase gene promoters, thereby activating cellulase gene expression to initiate the cellulolytic response in T. reesei.
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Affiliation(s)
- Yanli Cao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Fanglin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
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25
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Bell S, Rousseau J, Peng H, Aouabed Z, Priam P, Theroux JF, Jefri M, Tanti A, Wu H, Kolobova I, Silviera H, Manzano-Vargas K, Ehresmann S, Hamdan FF, Hettige N, Zhang X, Antonyan L, Nassif C, Ghaloul-Gonzalez L, Sebastian J, Vockley J, Begtrup AG, Wentzensen IM, Crunk A, Nicholls RD, Herman KC, Deignan JL, Al-Hertani W, Efthymiou S, Salpietro V, Miyake N, Makita Y, Matsumoto N, Østern R, Houge G, Hafström M, Fassi E, Houlden H, Klein Wassink-Ruiter JS, Nelson D, Goldstein A, Dabir T, van Gils J, Bourgeron T, Delorme R, Cooper GM, Martinez JE, Finnila CR, Carmant L, Lortie A, Oegema R, van Gassen K, Mehta SG, Huhle D, Abou Jamra R, Martin S, Brunner HG, Lindhout D, Au M, Graham JM, Coubes C, Turecki G, Gravel S, Mechawar N, Rossignol E, Michaud JL, Lessard J, Ernst C, Campeau PM. Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons. Am J Hum Genet 2019; 104:815-834. [PMID: 31031012 PMCID: PMC6507050 DOI: 10.1016/j.ajhg.2019.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/01/2019] [Indexed: 02/04/2023] Open
Abstract
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Justine Rousseau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Arnaud Tanti
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Ilaria Kolobova
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Heika Silviera
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Karla Manzano-Vargas
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Sophie Ehresmann
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Fadi F Hamdan
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Christina Nassif
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | | | | | - Robert D Nicholls
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Kristin C Herman
- University of California at Davis Medical Center, Section of Medical Genomics, Sacramento, CA 95817, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Walla Al-Hertani
- Departments of Medical Genetics and Paediatrics, Cumming School of Medicine, Alberta Children's Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Rune Østern
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Maria Hafström
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Dominic Nelson
- McGill University, Department of Human Genetics, Montreal, QC H3G 0B1, Canada
| | - Amy Goldstein
- Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, UK
| | - Julien van Gils
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Richard Delorme
- Assistance Publique Hôpitaux de Paris (APHP), Robert Debré Hospital, Child and Adolescent Psychiatry Department, Paris, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Lionel Carmant
- Children's Rehabilitation Service, Mobile, AL 36604, USA
| | - Anne Lortie
- Department of Neurology, University of Montreal, Montreal, QC, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Sarju G Mehta
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Dagmar Huhle
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Sonja Martin
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 GA, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - Dick Lindhout
- Department of Genetics, University Medical Center Utrecht, Utrecht & Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Margaret Au
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - John M Graham
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christine Coubes
- Service de génétique clinique, Département de génétique médicale, Maladies rares et médecine personnalisée, Centre de Référence Anomalies du développement et Syndromes malformatifs du Sud-Ouest Occitanie Réunion, CHU de Montpellier, 34295 Montpellier Cedex 5, France
| | - Gustavo Turecki
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Simon Gravel
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Naguib Mechawar
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Elsa Rossignol
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Jacques L Michaud
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Julie Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Carl Ernst
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada.
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada.
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26
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Chubak MC, Nixon KCJ, Stone MH, Raun N, Rice SL, Sarikahya M, Jones SG, Lyons TA, Jakub TE, Mainland RLM, Knip MJ, Edwards TN, Kramer JM. Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the Drosophila mushroom body. Dis Model Mech 2019; 12:12/3/dmm037325. [PMID: 30923190 PMCID: PMC6451433 DOI: 10.1242/dmm.037325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/23/2019] [Indexed: 12/13/2022] Open
Abstract
Technology has led to rapid progress in the identification of genes involved in neurodevelopmental disorders such as intellectual disability (ID), but our functional understanding of the causative genes is lagging. Here, we show that the SWI/SNF chromatin remodelling complex is one of the most over-represented cellular components disrupted in ID. We investigated the role of individual subunits of this large protein complex using targeted RNA interference in post-mitotic memory-forming neurons of the Drosophila mushroom body (MB). Knockdown flies were tested for defects in MB morphology, short-term memory and long-term memory. Using this approach, we identified distinct roles for individual subunits of the Drosophila SWI/SNF complex. Bap60, Snr1 and E(y)3 are required for pruning of the MBγ neurons during pupal morphogenesis, while Brm and Osa are required for survival of MBγ axons during ageing. We used the courtship conditioning assay to test the effect of MB-specific SWI/SNF knockdown on short- and long-term memory. Several subunits, including Brm, Bap60, Snr1 and E(y)3, were required in the MB for both short- and long-term memory. In contrast, Osa knockdown only reduced long-term memory. Our results suggest that individual components of the SWI/SNF complex have different roles in the regulation of structural plasticity, survival and functionality of post-mitotic MB neurons. This study highlights the many possible processes that might be disrupted in SWI/SNF-related ID disorders. Our broad phenotypic characterization provides a starting point for understanding SWI/SNF-mediated gene regulatory mechanisms that are important for development and function of post-mitotic neurons. Summary: The SWI/SNF chromatin remodelling complex is the most over-represented protein complex in the intellectual disability. Different components of this complex have distinct roles in development and function of memory-forming neurons in the Drosophila mushroom body.
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Affiliation(s)
- Melissa C Chubak
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada
| | - Kevin C J Nixon
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Max H Stone
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
| | - Nicholas Raun
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
| | - Shelby L Rice
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada
| | - Mohammed Sarikahya
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Spencer G Jones
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Taylor A Lyons
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Taryn E Jakub
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Roslyn L M Mainland
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Maria J Knip
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Tara N Edwards
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Jamie M Kramer
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada .,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
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27
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Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWM. MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res 2019; 79:2404-2414. [PMID: 30755442 DOI: 10.1158/0008-5472.can-18-3066] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/28/2018] [Accepted: 02/07/2019] [Indexed: 12/21/2022]
Abstract
Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. In this study, we screened several MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers. We discovered MDM2 and MDM4, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin (MDM2-specific) and ATSP-7041 (MDM2/4-dual), we show that MRT cells were more sensitive than other p53 wild-type cancer cell lines to inhibition of MDM2 alone as well as dual inhibition of MDM2/4. These compounds caused significant upregulation of the p53 pathway in MRT cells, and sensitivity was ablated by CRISPR-Cas9-mediated inactivation of TP53. We show that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRTs, sensitized cells to MDM2 and MDM2/4 inhibition by enhancing p53-mediated apoptosis. Both MDM2 and MDM2/4 inhibition slowed MRT xenograft growth in vivo, with a 5-day idasanutlin pulse causing marked regression of all xenografts, including durable complete responses in 50% of mice. Together, these studies identify a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene TP53 and provide preclinical evidence to support the targeting of MDM2 and MDM4 in this often-fatal pediatric cancer. SIGNIFICANCE: This study identifies two targets, MDM2 and MDM4, as vulnerabilities in a deadly pediatric cancer and provides preclinical evidence that compounds inhibiting these proteins have therapeutic potential.
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Affiliation(s)
- Thomas P Howard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Taylor E Arnoff
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Melinda R Song
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Xiaofeng Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Andrew L Hong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Su Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | | | - Minh-Tam Pham
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ann M Morgan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Elaine M Oberlick
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew G Rees
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Katherine H Walsh
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - April Cook
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Oncology, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
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28
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Stiller JW, Yang C, Collén J, Kowalczyk N, Thompson BE. Evolution and expression of core SWI/SNF genes in red algae. JOURNAL OF PHYCOLOGY 2018; 54:879-887. [PMID: 30288746 DOI: 10.1111/jpy.12795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue-specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin-remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.
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Affiliation(s)
- John W Stiller
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Chunlin Yang
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Nathalie Kowalczyk
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Beth E Thompson
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
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29
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Yu X, Meng X, Liu Y, Li N, Zhang A, Wang TJ, Jiang L, Pang J, Zhao X, Qi X, Zhang M, Wang S, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize. PLANT MOLECULAR BIOLOGY 2018; 97:451-465. [PMID: 29956114 DOI: 10.1007/s11103-018-0751-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/18/2018] [Indexed: 05/16/2023]
Abstract
The maize chromatin remodeler ZmCHB101 plays an essential role in the osmotic stress response. ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Drought and osmotic stresses are recurring conditions that severely constrain crop production. Evidence accumulated in the model plant Arabidopsis thaliana suggests that core components of SWI/SNF chromatin remodeling complexes play essential roles in abiotic stress responses. However, how maize SWI/SNF chromatin remodeling complexes function in osmotic and drought stress responses remains unknown. Here we show that ZmCHB101, a homolog of A. thaliana SWI3D in maize, plays essential roles in osmotic and dehydration stress responses. ZmCHB101-RNA interference (RNAi) transgenic plants displayed osmotic, salt and drought stress-sensitive phenotypes. Genome-wide RNA-sequencing analysis revealed that ZmCHB101 impacts the transcriptional expression landscape of osmotic stress-responsive genes. Intriguingly, ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Furthermore, we identified that ZmCHB101 associates with RNA polymerase II (RNAPII) in vivo and is a prerequisite for the proper occupancy of RNAPII on the proximal regions of transcription start sites of stress-response genes. Taken together, our findings suggest that ZmCHB101 affects gene expression by remodeling chromatin states and controls RNAPII occupancies in maize under osmotic stress.
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Affiliation(s)
- Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
- Department of Bioengineering, Jilin Agricultural Science and Technology College, Jilin, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Jinsong Pang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Xinxin Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Meishan Zhang
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
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Wang RR, Pan R, Zhang W, Fu J, Lin JD, Meng ZX. The SWI/SNF chromatin-remodeling factors BAF60a, b, and c in nutrient signaling and metabolic control. Protein Cell 2018; 9:207-215. [PMID: 28688083 PMCID: PMC5818368 DOI: 10.1007/s13238-017-0442-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/21/2017] [Indexed: 01/29/2023] Open
Abstract
Metabolic syndrome has become a global epidemic that adversely affects human health. Both genetic and environmental factors contribute to the pathogenesis of metabolic disorders; however, the mechanisms that integrate these cues to regulate metabolic physiology and the development of metabolic disorders remain incompletely defined. Emerging evidence suggests that SWI/SNF chromatin-remodeling complexes are critical for directing metabolic reprogramming and adaptation in response to nutritional and other physiological signals. The ATP-dependent SWI/SNF chromatin-remodeling complexes comprise up to 11 subunits, among which the BAF60 subunit serves as a key link between the core complexes and specific transcriptional factors. The BAF60 subunit has three members, BAF60a, b, and c. The distinct tissue distribution patterns and regulatory mechanisms of BAF60 proteins confer each isoform with specialized functions in different metabolic cell types. In this review, we summarize the emerging roles and mechanisms of BAF60 proteins in the regulation of nutrient sensing and energy metabolism under physiological and disease conditions.
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Affiliation(s)
- Ruo-Ran Wang
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Ran Pan
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Wenjing Zhang
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Junfen Fu
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA
| | - Zhuo-Xian Meng
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China.
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA.
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Meng ZX, Tao W, Sun J, Wang Q, Mi L, Lin JD. Uncoupling Exercise Bioenergetics From Systemic Metabolic Homeostasis by Conditional Inactivation of Baf60 in Skeletal Muscle. Diabetes 2018; 67:85-97. [PMID: 29092888 PMCID: PMC5741141 DOI: 10.2337/db17-0367] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/24/2017] [Indexed: 12/19/2022]
Abstract
Impaired skeletal muscle energy metabolism is linked to the pathogenesis of insulin resistance and glucose intolerance in type 2 diabetes. The contractile and metabolic properties of myofibers exhibit a high degree of heterogeneity and plasticity. The regulatory circuitry underpinning skeletal muscle energy metabolism is critically linked to exercise endurance and systemic homeostasis. Recent work has identified the Baf60 subunits of the SWI/SNF chromatin-remodeling complex as powerful regulators of the metabolic gene programs. However, their role in integrating myofiber energy metabolism with exercise endurance and metabolic physiology remains largely unknown. In this study, we conditionally inactivated Baf60a, Baf60c, or both in mature skeletal myocytes to delineate their contribution to muscle bioenergetics and metabolic physiology. Our work revealed functional redundancy between Baf60a and Baf60c in maintaining oxidative and glycolytic metabolism in skeletal myofibers and exercise endurance. Unexpectedly, mice lacking these two factors in skeletal muscle were protected from diet-induced and age-associated metabolic disorders. Transcriptional profiling analysis identified the muscle thermogenic gene program and myokine secretion as key pathways that integrate myofiber metabolism with systemic energy balance. As such, Baf60 deficiency in skeletal muscle illustrates a surprising disconnect between exercise endurance and systemic metabolic homeostasis.
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Affiliation(s)
- Zhuo-Xian Meng
- Life Sciences Institute, University of Michigan, and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, and Chronic Disease Research Institute of School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weiwei Tao
- Life Sciences Institute, University of Michigan, and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Jingxia Sun
- Life Sciences Institute, University of Michigan, and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, and Chronic Disease Research Institute of School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiuyu Wang
- Life Sciences Institute, University of Michigan, and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Lin Mi
- Life Sciences Institute, University of Michigan, and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Jiandie D Lin
- Life Sciences Institute, University of Michigan, and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
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Jégu T, Veluchamy A, Ramirez-Prado JS, Rizzi-Paillet C, Perez M, Lhomme A, Latrasse D, Coleno E, Vicaire S, Legras S, Jost B, Rougée M, Barneche F, Bergounioux C, Crespi M, Mahfouz MM, Hirt H, Raynaud C, Benhamed M. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biol 2017; 18:114. [PMID: 28619072 PMCID: PMC5471679 DOI: 10.1186/s13059-017-1246-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. RESULTS In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. BAF60 binds nucleosome-free regions of multiple G box-containing genes, opposing in cis the promoting effect of the photomorphogenic and thermomorphogenic regulator Phytochrome Interacting Factor 4 (PIF4) on hypocotyl elongation. Furthermore, BAF60 expression level is regulated in response to light and daily rhythms. CONCLUSIONS These results unveil a short path between a chromatin remodeler and a signaling component to fine-tune plant morphogenesis in response to environmental conditions.
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Affiliation(s)
- Teddy Jégu
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Present address: Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Present address: Department of Genetics, Harvard Medical School, Boston, MA, 02114, USA
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charley Rizzi-Paillet
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Magalie Perez
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Anaïs Lhomme
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - David Latrasse
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Emeline Coleno
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Serge Vicaire
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Stéphanie Legras
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Bernard Jost
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Martin Rougée
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Fredy Barneche
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Catherine Bergounioux
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Martin Crespi
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Heribert Hirt
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Cécile Raynaud
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France.
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Menoni H, Di Mascio P, Cadet J, Dimitrov S, Angelov D. Chromatin associated mechanisms in base excision repair - nucleosome remodeling and DNA transcription, two key players. Free Radic Biol Med 2017; 107:159-169. [PMID: 28011149 DOI: 10.1016/j.freeradbiomed.2016.12.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022]
Abstract
Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to overcome the general repression associated with the nucleosomal organization. It is broadly accepted that energy-dependent nucleosome remodeling factors disrupt histones-DNA interactions at the expense of ATP hydrolysis to favor transcription as well as DNA repair. Importantly, unlike transcription, BER is not part of a regulated developmental process but represents a maintenance system that should be efficient anytime and anywhere in the genome. In this review we will discuss how BER can deal with chromatin organization to maintain genetic information. Emphasis will be placed on the following challenging question: how BER is initiated within chromatin?
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Affiliation(s)
- Hervé Menoni
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL UMR 5239 and Institut NeuroMyoGène - INMG CNRS/UCBL UMR 5310, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France.
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000 São Paulo, SP, Brazil
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stefan Dimitrov
- Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL UMR 5239 and Institut NeuroMyoGène - INMG CNRS/UCBL UMR 5310, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon, France.
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Brg1-mediated Nrf2/HO-1 pathway activation alleviates hepatic ischemia-reperfusion injury. Cell Death Dis 2017; 8:e2841. [PMID: 28569786 PMCID: PMC5520895 DOI: 10.1038/cddis.2017.236] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 04/20/2017] [Accepted: 04/26/2017] [Indexed: 12/11/2022]
Abstract
Cytoprotective gene heme oxygenase 1 (HO-1) could be induced by nuclear factor E2-related factor 2 (Nrf2) nuclear translocation. The purpose of this study was to determine the role of Brahma-related gene 1 (Brg1), a catalytic subunit of SWI2/SNF2-like chromatin remodeling complexes, in Nrf2/HO-1 pathway activation during hepatic ischemia–reperfusion (HIR). Our results showed that hepatic Brg1 was inhibited during early HIR while Brg1 overexpression reduced oxidative injury in CMV-Brg1 mice subjected to HIR. Moreover, promoter-driven luciferase assay showed that overexpression of Brg1 by adenovirus transfection in AML12 cells selectively enhanced HO-1 gene expression after hypoxia/reoxygenation (H/R) treatment but did not affect the other Nrf2 target gene NQO1. Furthermore, inhibition of HO-1 by the selective HO-1 inhibitor zinc protoporphyria could partly reverse the hepatic protective effects of Brg1 overexpression while HO-1-Adv attenuated AML12 cells H/R damage. Further, chromatin immunoprecipitation analysis revealed that Brg1 overexpression, which could significantly increase the recruitment of Brg1 protein to HO-1 but not NQO1 promoter, was recruited by Nrf2 to the HO-1 regulatory regions in AML12 hepatocytes subjected to H/R. In conclusion, our results demonstrated that restoration of Brg1 during reperfusion could enhance Nrf2-mediated inducible expression of HO-1 during HIR to effectively increase antioxidant ability to combat against hepatocytes damage.
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The SWI/SNF Chromatin Regulator BRG1 Modulates the Transcriptional Regulatory Activity of the Epstein-Barr Virus DNA Polymerase Processivity Factor BMRF1. J Virol 2017; 91:JVI.02114-16. [PMID: 28228591 DOI: 10.1128/jvi.02114-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/14/2017] [Indexed: 12/14/2022] Open
Abstract
During the lytic phase of Epstein-Barr virus (EBV), binding of the transactivator Zta to the origin of lytic replication (oriLyt) and the BHLF1 transcript, forming a stable RNA-DNA hybrid, is required to initiate viral DNA replication. EBV-encoded viral DNA replication proteins form complexes to amplify viral DNA. BMRF1, the viral DNA polymerase accessory factor, is essential for lytic DNA replication and also known as a transcriptional regulator of the expression of BHLF1 and BALF2 (single-stranded DNA [ssDNA]-binding protein). In order to determine systematically how BMRF1 regulates viral transcription, a BMRF1 knockout bacmid was generated to analyze viral gene expression using a viral DNA microarray. We found that a subset of Rta-responsive late genes, including BcLF1, BLLF1, BLLF2, and BDLF3, were downregulated in cells harboring a BMRF1 knockout EBV bacmid (p2089ΔBMRF1). In reporter assays, BMRF1 appears to transactivate a subset of viral late promoters through distinct pathways. BMRF1 activates the BDLF3 promoter in an SP1-dependent manner. Notably, BMRF1 associates with the transcriptional regulator BRG1 in EBV-reactivated cells. BMRF1-mediated transactivation activities on the BcLF1 and BLLF1 promoters were attenuated by knockdown of BRG1. In BRG1-depleted EBV-reactivated cells, BcLF1 and BLLF1 transcripts were reduced in number, resulting in reduced virion secretion. BMRF1 and BRG1 bound to the adjacent upstream regions of the BcLF1 and BLLF1 promoters, and depletion of BRG1 attenuated the recruitment of BMRF1 onto both promoters, suggesting that BRG1 is involved in BMRF1-mediated regulation of these two genes. Overall, we reveal a novel pathway by which BMRF1 can regulate viral promoters through interaction with BRG1.IMPORTANCE The cascade of viral gene expression during Epstein-Barr virus (EBV) replication is exquisitely regulated by the coordination of the viral DNA replication machinery and cellular factors. Upon lytic replication, the EBV immediate early proteins Zta and Rta turn on the expression of early proteins that assemble into viral DNA replication complexes. The DNA polymerase accessory factor, BMRF1, also is known to transactivate early gene expression through its interaction with SP1 or Zta on specific promoters. Through a global analysis, we demonstrate that BMRF1 also turns on a subset of Rta-regulated, late structural gene promoters. Searching for BMRF1-interacting cellular partners revealed that the SWI/SNF chromatin modifier BRG1 contributes to BMRF1-mediated transactivation of a subset of late promoters through protein-protein interaction and viral chromatin binding. Our findings indicate that BMRF1 regulates the expression of more viral genes than thought previously through distinct viral DNA replication-independent mechanisms.
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Festuccia N, Gonzalez I, Navarro P. The Epigenetic Paradox of Pluripotent ES Cells. J Mol Biol 2016; 429:1476-1503. [PMID: 27988225 DOI: 10.1016/j.jmb.2016.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
The propagation and maintenance of gene expression programs are at the foundation of the preservation of cell identity. A large and complex set of epigenetic mechanisms enables the long-term stability and inheritance of transcription states. A key property of authentic epigenetic regulation is being independent from the instructive signals used for its establishment. This makes epigenetic regulation, particularly epigenetic silencing, extremely robust and powerful to lock regulatory states and stabilise cell identity. In line with this, the establishment of epigenetic silencing during development restricts cell potency and maintains the cell fate choices made by transcription factors (TFs). However, how more immature cells that have not yet established their definitive fate maintain their transitory identity without compromising their responsiveness to signalling cues remains unclear. A paradigmatic example is provided by pluripotent embryonic stem (ES) cells derived from a transient population of cells of the blastocyst. Here, we argue that ES cells represent an interesting "epigenetic paradox": even though they are captured in a self-renewing state characterised by extremely efficient maintenance of their identity, which is a typical manifestation of robust epigenetic regulation, they seem not to heavily rely on classical epigenetic mechanisms. Indeed, self-renewal strictly depends on the TFs that previously instructed their undifferentiated identity and relies on a particular signalling-dependent chromatin state where repressive chromatin marks play minor roles. Although this "epigenetic paradox" may underlie their exquisite responsiveness to developmental cues, it suggests that alternative mechanisms to faithfully propagate gene regulatory states might be prevalent in ES cells.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France.
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Yu X, Jiang L, Wu R, Meng X, Zhang A, Li N, Xia Q, Qi X, Pang J, Xu ZY, Liu B. The Core Subunit of A Chromatin-Remodeling Complex, ZmCHB101, Plays Essential Roles in Maize Growth and Development. Sci Rep 2016; 6:38504. [PMID: 27917953 PMCID: PMC5137073 DOI: 10.1038/srep38504] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/09/2016] [Indexed: 11/18/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages. Independent ZmCHB101 RNA interference plant lines displayed abaxially curling leaf phenotype due to increase of bulliform cell numbers, and showed impaired development of tassel and cob. RNA-seq-based transcriptome profiling revealed that ZmCHB101 dictated transcriptional reprogramming of a significant set of genes involved in plant development, photosynthesis, metabolic regulation, stress response and gene expressional regulation. Intriguingly, we found that ZmCHB101 was required for maintaining normal nucleosome density and 45 S rDNA compaction. Our findings suggest that the SWI3 protein, ZmCHB101, plays pivotal roles in maize normal growth and development via regulation of chromatin structure.
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Affiliation(s)
- Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China.,School of Bioengineering, Jilin College of Agricultural Science &Technology, Jilin 132301, P. R. China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Rui Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Qiong Xia
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, P. R. China
| | - Jinsong Pang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, P. R. China
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Abstract
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
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40
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Zhang P, Li L, Bao Z, Huang F. Role of BAF60a/BAF60c in chromatin remodeling and hepatic lipid metabolism. Nutr Metab (Lond) 2016; 13:30. [PMID: 27127533 PMCID: PMC4848843 DOI: 10.1186/s12986-016-0090-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/19/2016] [Indexed: 02/07/2023] Open
Abstract
The switching defective/sucrose non-fermenting (SWI/SNF) complexes play an important role in hepatic lipid metabolism regulating both transcriptional activation and repression. BAF60a is a core subunit of the SWI/SNF chromatin-remodeling complexes that activates the transcription of fatty acid oxidation genes during fasting/glucagon. BAF60c, another subunit of SWI/SNF complexes, is recruited to form the lipoBAF complex that activates lipogenic genes, promoting lipogenesis and increasing the triglyceride level in response to feeding/insulin. Interestingly, hepatocytes located in the periportal and perivenous zones of the liver display a remarkable heterogeneity in the activity of various enzymes, metabolic functions and gene expression. Especially, fatty-acid oxidation was shown to be mostly periportal, whereas lipogenesis was mostly perivenous. Therefore, the present review highlights the role of of SWI/SNF regulating lipid metabolism under nutritional and hormonal control, which may be associated with hepatocyte heterogeneity.
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Affiliation(s)
- Ping Zhang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lulu Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhengxi Bao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Feiruo Huang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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41
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Sinha S, Verma S, Chaturvedi MM. Differential Expression of SWI/SNF Chromatin Remodeler Subunits Brahma and Brahma-Related Gene During Drug-Induced Liver Injury and Regeneration in Mouse Model. DNA Cell Biol 2016; 35:373-84. [PMID: 27097303 DOI: 10.1089/dna.2015.3155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The chromatin remodeling activity of mammalian SWI/SNF complex is carried out by either Brahma (BRM) or Brahma-related gene (BRG-1). The BRG-1 regulates genes involved in cell proliferation, whereas BRM is associated with cell differentiation, and arrest of cell growth. Global modifications of histones and expression of genes of chromatin-remodeling subunits have not been studied in in vivo model systems. In the present study, we investigate epigenetic modifications of histones and the expression of genes in thioacetamide (TAA)-induced liver injury and regeneration in a mouse model. In the present study, we report that hepatocyte proliferation and H3S10 phosphorylation occur during 60 to 72 h post TAA treatment in mice. Furthermore, there was change in the H3K9 acetylation and H3K9 trimethylation pattern with respect to liver injury and regeneration phase. Looking into the expression pattern of Brg-1 and Brm, it is evident that they contribute substantially to the process of liver regeneration. The SWI/SNF remodeler might contain BRG-1 as its ATPase subunit during injury phase. Whereas, BRM-associated SWI/SNF remodeler might probably be predominant during decline of injury phase and initiation of regeneration phase. Furthermore, during the regeneration phase, BRG-1-containing remodeler again predominates. Considering all these observations, the present study depicts an interplay between chromatin interacting machineries in different phases of thioacetamide-induced liver injury and regeneration.
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Affiliation(s)
- Sonal Sinha
- 1 Laboratory for Chromatin Biology, Department of Zoology, University of Delhi , New Delhi, India
| | - Sudhir Verma
- 1 Laboratory for Chromatin Biology, Department of Zoology, University of Delhi , New Delhi, India
| | - Madan M Chaturvedi
- 1 Laboratory for Chromatin Biology, Department of Zoology, University of Delhi , New Delhi, India .,2 Cluster Innovation Center, Delhi University , Delhi, India
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42
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Chia NY, Tan P. Molecular classification of gastric cancer. Ann Oncol 2016; 27:763-9. [PMID: 26861606 DOI: 10.1093/annonc/mdw040] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/19/2016] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC), a heterogeneous disease characterized by epidemiologic and histopathologic differences across countries, is a leading cause of cancer-related death. Treatment of GC patients is currently suboptimal due to patients being commonly treated in a uniform fashion irrespective of disease subtype. With the advent of next-generation sequencing and other genomic technologies, GCs are now being investigated in great detail at the molecular level. High-throughput technologies now allow a comprehensive study of genomic and epigenomic alterations associated with GC. Gene mutations, chromosomal aberrations, differential gene expression and epigenetic alterations are some of the genetic/epigenetic influences on GC pathogenesis. In addition, integrative analyses of molecular profiling data have led to the identification of key dysregulated pathways and importantly, the establishment of GC molecular classifiers. Recently, The Cancer Genome Atlas (TCGA) network proposed a four subtype classification scheme for GC based on the underlying tumor molecular biology of each subtype. This landmark study, together with other studies, has expanded our understanding on the characteristics of GC at the molecular level. Such knowledge may improve the medical management of GC in the future.
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Affiliation(s)
- N-Y Chia
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School
| | - P Tan
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School Genome Institute of Singapore, Agency for Science, Technology, and Research Cancer Science Institute of Singapore, National University of Singapore Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
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43
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Folta A, Bargsten JW, Bisseling T, Nap JP, Mlynarova L. Compact tomato seedlings and plants upon overexpression of a tomato chromatin remodelling ATPase gene. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:581-591. [PMID: 25974127 DOI: 10.1111/pbi.12400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/13/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
Control of plant growth is an important aspect of crop productivity and yield in agriculture. Overexpression of the AtCHR12/23 genes in Arabidopsis thaliana reduced growth habit without other morphological changes. These two genes encode Snf2 chromatin remodelling ATPases. Here, we translate this approach to the horticultural crop tomato (Solanum lycopersicum). We identified and cloned the single tomato ortholog of the two Arabidopsis Snf2 genes, designated SlCHR1. Transgenic tomato plants (cv. Micro-Tom) that constitutively overexpress the coding sequence of SlCHR1 show reduced growth in all developmental stages of tomato. This confirms that SlCHR1 combines the functions of both Arabidopsis genes in tomato. Compared to the wild type, the transgenic seedlings of tomato have significantly shorter roots, hypocotyls and reduced cotyledon size. Transgenic plants have a much more compact growth habit with markedly reduced plant height, severely compacted reproductive structures with smaller flowers and smaller fruits. The results indicate that either GMO-based or non-GMO-based approaches to modulate the expression of chromatin remodelling ATPase genes could develop into methods to control plant growth, for example to replace the use of chemical growth retardants. This approach is likely to be applicable and attractive for any crop for which growth habit reduction has added value.
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Affiliation(s)
- Adam Folta
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Joachim W Bargsten
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan-Peter Nap
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences Groningen, Groningen, The Netherlands
| | - Ludmila Mlynarova
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
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44
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Meng ZX, Wang L, Chang L, Sun J, Bao J, Li Y, Chen YE, Lin JD. A Diet-Sensitive BAF60a-Mediated Pathway Links Hepatic Bile Acid Metabolism to Cholesterol Absorption and Atherosclerosis. Cell Rep 2015; 13:1658-69. [PMID: 26586440 DOI: 10.1016/j.celrep.2015.10.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 09/14/2015] [Accepted: 10/10/2015] [Indexed: 12/27/2022] Open
Abstract
Dietary nutrients interact with gene networks to orchestrate adaptive responses during metabolic stress. Here, we identify Baf60a as a diet-sensitive subunit of the SWI/SNF chromatin-remodeling complexes in the mouse liver that links the consumption of fat- and cholesterol-rich diet to elevated plasma cholesterol levels. Baf60a expression was elevated in the liver following feeding with a western diet. Hepatocyte-specific inactivation of Baf60a reduced bile acid production and cholesterol absorption, and attenuated diet-induced hypercholesterolemia and atherosclerosis in mice. Baf60a stimulates expression of genes involved in bile acid synthesis, modification, and transport through a CAR/Baf60a feedforward regulatory loop. Baf60a is required for the recruitment of the SWI/SNF chromatin-remodeling complexes to facilitate an activating epigenetic switch on target genes. These studies elucidate a regulatory pathway that mediates the hyperlipidemic and atherogenic effects of western diet consumption.
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Affiliation(s)
- Zhuo-Xian Meng
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Lin Wang
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lin Chang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jingxia Sun
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiangyin Bao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Yaqiang Li
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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45
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Wang X, Xu X, Lu X, Zhang Y, Pan W. Transcriptome Bioinformatical Analysis of Vertebrate Stages of Schistosoma japonicum Reveals Alternative Splicing Events. PLoS One 2015; 10:e0138470. [PMID: 26407301 PMCID: PMC4583307 DOI: 10.1371/journal.pone.0138470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/31/2015] [Indexed: 01/22/2023] Open
Abstract
Alternative splicing is a molecular process that contributes greatly to the diversification of proteome and to gene functions. Understanding the mechanisms of stage-specific alternative splicing can provide a better understanding of the development of eukaryotes and the functions of different genes. Schistosoma japonicum is an infectious blood-dwelling trematode with a complex lifecycle that causes the tropical disease schistosomiasis. In this study, we analyzed the transcriptome of Schistosoma japonicum to discover alternative splicing events in this parasite, by applying RNA-seq to cDNA library of adults and schistosomula. Results were validated by RT-PCR and sequencing. We found 11,623 alternative splicing events among 7,099 protein encoding genes and average proportion of alternative splicing events per gene was 42.14%. We showed that exon skip is the most common type of alternative splicing events as found in high eukaryotes, whereas intron retention is the least common alternative splicing type. According to intron boundary analysis, the parasite possesses same intron boundaries as other organisms, namely the classic "GT-AG" rule. And in alternative spliced introns or exons, this rule is less strict. And we have attempted to detect alternative splicing events in genes encoding proteins with signal peptides and transmembrane helices, suggesting that alternative splicing could change subcellular locations of specific gene products. Our results indicate that alternative splicing is prevalent in this parasitic worm, and that the worm is close to its hosts. The revealed secretome involved in alternative splicing implies new perspective into understanding interaction between the parasite and its host.
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Affiliation(s)
- Xinye Wang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xindong Xu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xingyu Lu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanbin Zhang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Weiqing Pan
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
- * E-mail:
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46
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Ozawa Y, Nakamura Y, Fujishima F, Felizola SJA, Takeda K, Okamoto H, Ito K, Ishida H, Konno T, Kamei T, Ohuchi N, Sasano H. Decreased expression of ARID1A contributes to infiltrative growth of esophageal squamous cell carcinoma. TOHOKU J EXP MED 2015; 235:185-91. [PMID: 25757668 DOI: 10.1620/tjem.235.185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The clinical outcome for esophageal squamous cell carcinoma (ESCC) patients is often poor because of the invasive nature of this tumor type. AT-rich interactive domain 1A (ARID1A) functions as a tumor suppressor, and its gene mutation has been reported in various human malignancies. ARID1A is a non-catalytic subunit of the SWItch/Sucrose Non Fermentable (SWI/SNF) chromatin-remodeling complex that regulates gene transcription. Decreased expression of ARID1A protein has been reported to decrease the expression of E-cadherin, an adhesion protein. However, the correlation between ARID1A and E-cadherin expression status in ESCC remains largely unknown. To address this issue, we examined the expression of ARID1A and E-cadherin in tumor specimens excised from 83 ESCC patients using immunohistochemical analysis. The intensity of the ARID1A immunoreactivity was significantly lower in tumors with a growth pattern characterized by ill-defined borders than that in tumors with an expansive growth pattern having a well-demarcated border or tumors with an intermediate growth pattern. Thus, decreased ARID1A immunoreactivity correlated with infiltrative growth of ESCC. In contrast, E-cadherin status did not correlate with the infiltrative growth pattern of ESCC. Moreover, ARID1A expression status did not significantly correlate with any of other clinicopathological factors, E-cadherin expression levels, or the clinical outcome of the patients. On the other hand, the patients with tumors expressing low levels of E-cadherin exhibited significantly lower survival rates than those with high expression. In conclusion, reduced ARID1A expression in tumor tissues contributes to infiltrative growth of ESCC, irrespective of E-cadherin expression levels.
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Affiliation(s)
- Yohei Ozawa
- Division of Advanced Surgical Science and Technology, Tohoku University Graduate School of Medicine; Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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47
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Brg-1 targeting of novel miR550a-5p/RNF43/Wnt signaling axis regulates colorectal cancer metastasis. Oncogene 2015; 35:651-61. [PMID: 25961913 DOI: 10.1038/onc.2015.124] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/07/2015] [Accepted: 03/12/2015] [Indexed: 12/25/2022]
Abstract
Metastasis is one of the main causes of death in patients with colorectal cancer (CRC). Brg-1 is a central component of the SWItch/Sucrose NonFermentable chromatin-remodeling complex, which features a bromodomain and helicase/ATPase activity. The gene encoding Brg-1 is frequently mutated or silenced in human cancers. Several reports have proposed Brg-1 as a tumor suppressor; however, little is known about its role in oncogenesis and metastasis. Here we demonstrated that decreased Brg-1 regulates a novel miR-550a-5p/RNF43/Wnt/β-catenin signaling pathway, to promote CRC metastasis in vitro and in vivo. In particular, we used high-throughput RNA-sequencing analysis to show that Brg-1 negatively regulates miR-550a-5p in CRC cells. We further found that Brg-1 inhibits the transcriptional activity of miR-550a-5p promoter, and that decreased Brg-1 expression increased miR-550a-5p expression. We also identified ring finger 43 (RNF43), an inhibitor of Wnt/β-catenin signaling, as a target of miR-550a-5p. Knockdown of Brg-1 by small interfering RNA led to decreased RNF43 expression, increased Wnt signaling and increased CRC cell migration and invasion. This novel pathway defines a new function for Brg-1 and provides potential targets for the treatment of Brg-1 mutant and loss-of-function tumors.
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48
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McKenna B, Guo M, Reynolds A, Hara M, Stein R. Dynamic recruitment of functionally distinct Swi/Snf chromatin remodeling complexes modulates Pdx1 activity in islet β cells. Cell Rep 2015; 10:2032-42. [PMID: 25801033 DOI: 10.1016/j.celrep.2015.02.054] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/21/2015] [Accepted: 02/23/2015] [Indexed: 02/03/2023] Open
Abstract
Pdx1 is a transcription factor of fundamental importance to pancreas formation and adult islet β cell function. However, little is known about the positive- and negative-acting coregulators recruited to mediate transcriptional control. Here, we isolated numerous Pdx1-interacting factors possessing a wide range of cellular functions linked with this protein, including, but not limited to, coregulators associated with transcriptional activation and repression, DNA damage response, and DNA replication. Because chromatin remodeling activities are essential to developmental lineage decisions and adult cell function, our analysis focused on investigating the influence of the Swi/Snf chromatin remodeler on Pdx1 action. The two mutually exclusive and indispensable Swi/Snf core ATPase subunits, Brg1 and Brm, distinctly affected target gene expression in β cells. Furthermore, physiological and pathophysiological conditions dynamically regulated Pdx1 binding to these Swi/Snf complexes in vivo. We discuss how context-dependent recruitment of coregulatory complexes by Pdx1 could impact pancreas cell development and adult islet β cell activity.
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Affiliation(s)
- Brian McKenna
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Min Guo
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Albert Reynolds
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Manami Hara
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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49
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Dutta A, Gogol M, Kim JH, Smolle M, Venkatesh S, Gilmore J, Florens L, Washburn MP, Workman JL. Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions. Genes Dev 2014; 28:2314-30. [PMID: 25319830 PMCID: PMC4201291 DOI: 10.1101/gad.243584.114] [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] [Indexed: 12/26/2022]
Abstract
The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. Dutta et al. find that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. The intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. The presence of histone acetylation and activator-dependent recruitment and retention of Swi/Snf is important for its efficient function. It is not understood, however, why such mechanisms are required to enhance Swi/Snf activity on nucleosomes. Snf2, the catalytic subunit of the Swi/Snf remodeling complex, has been shown to be a target of the Gcn5 acetyltransferase. Our study found that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. Also, the intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Interestingly, the presence of transcription activators mitigates the effects of the reduced affinity of acetylated Snf2 for acetylated nucleosomes. Supporting our in vitro results, we found that activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. Our studies demonstrate that competing effects of (1) Swi/Snf retention by activators or high levels of histone acetylation and (2) Snf2 acetylation-mediated release regulate dynamics of Swi/Snf occupancy at target genes.
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Affiliation(s)
- Arnob Dutta
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeong-Hoon Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, Korea
| | - Michaela Smolle
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | - Joshua Gilmore
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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50
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Zhu Y, Li D, Wang Y, Pei C, Liu S, Zhang L, Yuan Z, Zhang P. Brahma regulates the Hippo pathway activity through forming complex with Yki-Sd and regulating the transcription of Crumbs. Cell Signal 2014; 27:606-13. [PMID: 25496831 DOI: 10.1016/j.cellsig.2014.12.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/16/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The Hippo signaling pathway restricts organ size by inactivating the Yorkie (Yki)/Yes-associated protein (YAP) family proteins. The oncogenic Yki/YAP transcriptional coactivator family promotes tissue growth by activating target gene transcription, but the regulation of Yki/YAP activation remains elusive. In mammalian cells, we identified Brg1, a major subunit of chromatin-remodeling SWI/SNF family proteins, which interacts with YAP. This finding led us to investigate the in vivo functional interaction of Yki and Brahma (Brm), the Drosophila homolog of Brg1. We found that Brm functions at the downstream of Hippo pathway and interacts with Yki and Scalloped (Sd) to promotes Yki-dependent transcription and tissue growth. Furthermore, we demonstrated that Brm is required for the Crumbs (Crb) dysregulation-induced Yki activation. Interestingly, we also found that crb is a downstream target of Yki-Brm complex. Brm physically binds to the promoter of crb and regulates its transcription through Yki. Together, we showed that Brm functions as a critical regulator of Hippo signaling during tissue growth and plays an important role in the feedback loop between Crb and Yki.
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Affiliation(s)
- Ye Zhu
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Li
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Yadong Wang
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunli Pei
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Liu
- Department of Respiratory Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zengqiang Yuan
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Peng Zhang
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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