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Xiang H, Tang H, He Q, Sun J, Yang Y, Kong L, Wang Y. NDUFA8 is transcriptionally regulated by EP300/H3K27ac and promotes mitochondrial respiration to support proliferation and inhibit apoptosis in cervical cancer. Biochem Biophys Res Commun 2024; 693:149374. [PMID: 38096616 DOI: 10.1016/j.bbrc.2023.149374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024]
Abstract
Cervical cancer, a common malignancy in women, poses a significant health burden worldwide. In this study, we aimed to investigate the expression, function, and potential mechanisms of NADH: ubiquinone oxidoreductase subunit A8 (NDUFA8) in cervical cancer. The Gene Expression Profiling Interactive Analysis (GEPIA) database and immunohistochemical scoring were used to analyze NDUFA8 expression in cervical cancer tissues and normal tissues. Quantitative real-time PCR and Western blot analyses were performed to assess the expression level of NDUFA8 in cervical cancer cell lines. NDUFA8 knockdown or overexpression experiments were conducted to evaluate its impact on cell proliferation and apoptosis. The mitochondrial respiratory status was analyzed by measuring cellular oxygen consumption, adenosine triphosphate (ATP) levels, and the expression levels of Mitochondrial Complex I activity, and Mitochondrial Complex IV-associated proteins Cytochrome C Oxidase Subunit 5B (COX5B) and COX6C. NDUFA8 exhibited high expression levels in cervical cancer tissues, and these levels were correlated with reduced survival rates. A significant upregulation of NDUFA8 expression was observed in cervical cancer cell lines compared to normal cells. Silencing NDUFA8 hindered cell proliferation, promoted apoptosis, and concurrently suppressed cellular mitochondrial respiration, resulting in decreased levels of available ATP. Conversely, NDUFA8 overexpression induced the opposite effects. Herein, we also found that E1A Binding Protein P300 (EP300) overexpression facilitated Histone H3 Lysine 27 (H3K27) acetylation enrichment, enhancing the activity of the NDUFA8 promoter region. NDUFA8, which is highly expressed in cervical cancer, is regulated by transcriptional control via EP300/H3K27 acetylation. By promoting mitochondrial respiration, NDUFA8 contributes to cervical cancer cell proliferation and apoptosis. These findings provide novel insights into NDUFA8 as a therapeutic target in cervical cancer.
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Affiliation(s)
- Huaguo Xiang
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China.
| | - Hongping Tang
- Department of Pathology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, 518028, China
| | - Qingqing He
- Department of Clinical Laboratory, The Second People's Hospital of Shenzhen, Shenzhen, 518025, China
| | - Junfang Sun
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China
| | - Yihui Yang
- Department of Pathology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, 518028, China
| | - Lingyue Kong
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China
| | - Yingzhen Wang
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China
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2
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Yu D, Liang Y, Kim C, Jaganathan A, Ji D, Han X, Yang X, Jia Y, Gu R, Wang C, Zhang Q, Cheung KL, Zhou MM, Zeng L. Structural mechanism of BRD4-NUT and p300 bipartite interaction in propagating aberrant gene transcription in chromatin in NUT carcinoma. Nat Commun 2023; 14:378. [PMID: 36690674 PMCID: PMC9870903 DOI: 10.1038/s41467-023-36063-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023] Open
Abstract
BRD4-NUT, a driver fusion mutant in rare and highly aggressive NUT carcinoma, acts in aberrant transcription of anti-differentiation genes by recruiting histone acetyltransferase (HAT) p300 and promoting p300-driven histone hyperacetylation and nuclear condensation in chromatin. However, the molecular basis of how BRD4-NUT recruits and activates p300 remains elusive. Here, we report that BRD4-NUT contains two transactivation domains (TADs) in NUT that bind to the TAZ2 domain in p300. Our NMR structures reveal that NUT TADs adopt amphipathic helices when bound to the four-helical bundle TAZ2 domain. The NUT protein forms liquid-like droplets in-vitro that are enhanced by TAZ2 binding in 1:2 stoichiometry. The TAD/TAZ2 bipartite binding in BRD4-NUT/p300 triggers allosteric activation of p300 and acetylation-driven liquid-like condensation on chromatin that comprise histone H3 lysine 27 and 18 acetylation and transcription proteins BRD4L/S, CDK9, MED1, and RNA polymerase II. The BRD4-NUT/p300 chromatin condensation is key for activating transcription of pro-proliferation genes such as ALX1, resulting ALX1/Snail signaling and epithelial-to-mesenchymal transition. Our study provides a previously underappreciated structural mechanism illuminating BRD4-NUT's bipartite p300 recruitment and activation in NUT carcinoma that nucleates a feed-forward loop for propagating histone hyperacetylation and chromatin condensation to sustain aberrant anti-differentiation gene transcription and perpetual tumor cell growth.
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Affiliation(s)
- Di Yu
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Yingying Liang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Claudia Kim
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anbalagan Jaganathan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donglei Ji
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Xinye Han
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Xuelan Yang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Yanjie Jia
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ruirui Gu
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
| | - Qiang Zhang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ka Lung Cheung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
- International Center of Future Science, Jilin University, Changchun, 130012, China.
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3
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Hu X, Ono M, Chimge NO, Chosa K, Nguyen C, Melendez E, Lou CH, Lim P, Termini J, Lai KKY, Fueger PT, Teo JL, Higuchi Y, Kahn M. Differential Kat3 Usage Orchestrates the Integration of Cellular Metabolism with Differentiation. Cancers (Basel) 2021; 13:cancers13235884. [PMID: 34884992 PMCID: PMC8656857 DOI: 10.3390/cancers13235884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary The coupling of metabolism with cellular status is critically important and highly evolutionarily conserved. However, how cells coordinate metabolism with transcription as they change their status is not clear. Utilizing multiomic and functional studies, we now demonstrate the dichotomous roles of the Kat3 coactivators CBP and p300 and, in particular, their extreme N-termini, in coordinating cellular metabolism with cell differentiation. Using multiple in vitro and in vivo systems, our study sheds new light on metabolic regulation in homeostasis and disease, including cancer. Abstract The integration of cellular status with metabolism is critically important and the coupling of energy production and cellular function is highly evolutionarily conserved. This has been demonstrated in stem cell biology, organismal, cellular and tissue differentiation and in immune cell biology. However, a molecular mechanism delineating how cells coordinate and couple metabolism with transcription as they navigate quiescence, growth, proliferation, differentiation and migration remains in its infancy. The extreme N-termini of the Kat3 coactivator family members, CBP and p300, by far the least homologous regions with only 66% identity, interact with members of the nuclear receptor family, interferon activated Stat1 and transcriptionally competent β-catenin, a critical component of the Wnt signaling pathway. We now wish to report based on multiomic and functional investigations, utilizing p300 knockdown, N-terminal p300 edited and p300 S89A edited cell lines and p300 S89A knockin mice, that the N-termini of the Kat3 coactivators provide a highly evolutionarily conserved hub to integrate multiple signaling cascades to coordinate cellular metabolism with the regulation of cellular status and function.
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Affiliation(s)
- Xiaohui Hu
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Nyam-Osor Chimge
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Keisuke Chosa
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Cu Nguyen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Elizabeth Melendez
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Chih-Hong Lou
- Gene Editing and Viral Vector Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Punnajit Lim
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - John Termini
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Keane K. Y. Lai
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Patrick T. Fueger
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
- Department of Molecular and Cellular Endocrinology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jia-Ling Teo
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Yusuke Higuchi
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Michael Kahn
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
- Correspondence:
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Kahn M. Taking the road less traveled - the therapeutic potential of CBP/β-catenin antagonists. Expert Opin Ther Targets 2021; 25:701-719. [PMID: 34633266 PMCID: PMC8745629 DOI: 10.1080/14728222.2021.1992386] [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: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Abstract
AREAS COVERED This perspective discusses the challenges of targeting the Wnt signaling cascade, the safety, efficacy, and therapeutic potential of specific CBP/β-catenin antagonists and a rationale for the pleiotropic effects of CBP/β-catenin antagonists beyond Wnt signaling. EXPERT OPINION CBP/β-catenin antagonists can correct lineage infidelity, enhance wound healing, both normal and aberrant (e.g. fibrosis) and force the differentiation and lineage commitment of stem cells and cancer stem cells by regulating enhancer and super-enhancer coactivator occupancy. Small molecule CBP/β-catenin antagonists rebalance the equilibrium between CBP/β-catenin versus p300/β-catenin dependent transcription and may be able to treat or prevent many diseases of aging, via maintenance of our somatic stem cell pool, and regulating mitochondrial function and metabolism involved in differentiation and immune cell function.
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Affiliation(s)
- Michael Kahn
- Department of Molecular Medicine, City of Hope, Beckman Research Institute, 1500 East Duarte Road Flower Building, Duarte, CA, USA
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5
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Zhang Y, Brown K, Yu Y, Ibrahim Z, Zandian M, Xuan H, Ingersoll S, Lee T, Ebmeier CC, Liu J, Panne D, Shi X, Ren X, Kutateladze TG. Nuclear condensates of p300 formed though the structured catalytic core can act as a storage pool of p300 with reduced HAT activity. Nat Commun 2021; 12:4618. [PMID: 34326347 PMCID: PMC8322156 DOI: 10.1038/s41467-021-24950-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/12/2021] [Indexed: 12/03/2022] Open
Abstract
The transcriptional co-activator and acetyltransferase p300 is required for fundamental cellular processes, including differentiation and growth. Here, we report that p300 forms phase separated condensates in the cell nucleus. The phase separation ability of p300 is regulated by autoacetylation and relies on its catalytic core components, including the histone acetyltransferase (HAT) domain, the autoinhibition loop, and bromodomain. p300 condensates sequester chromatin components, such as histone H3 tail and DNA, and are amplified through binding of p300 to the nucleosome. The catalytic HAT activity of p300 is decreased due to occlusion of the active site in the phase separated droplets, a large portion of which co-localizes with chromatin regions enriched in H3K27me3. Our findings suggest a model in which p300 condensates can act as a storage pool of the protein with reduced HAT activity, allowing p300 to be compartmentalized and concentrated at poised or repressed chromatin regions. The histone acetyltransferase p300 mostly localizes to active chromatin; however, some repressed genes marked with H3K27me3 are also bound by p300. Here the authors show p300 is capable of phase separation, which relies on its catalytic core, and that p300 catalytic activity is decreased in phase-separated droplets that co-localize with H3K27me3-marked chromatin.
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Affiliation(s)
- Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kyle Brown
- Department of Chemistry, University of Colorado, Denver, CO, USA
| | - Yucong Yu
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Ziad Ibrahim
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hongwen Xuan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Steven Ingersoll
- Department of Chemistry, University of Colorado, Denver, CO, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | | | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniel Panne
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado, Denver, CO, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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Krošel M, Gabathuler M, Maciukiewicz M, Moser L, Lee GI, Marks M, Tomšič M, Distler O, Ospelt C, Klein K. Individual functions of the histone acetyl transferases CBP and p300 in regulating the inflammatory response of synovial fibroblasts. J Autoimmun 2021; 123:102709. [PMID: 34304080 DOI: 10.1016/j.jaut.2021.102709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/28/2022]
Abstract
Chromatin remodeling, and a persistent histone 3 lysine 27 acetylation (H3K27ac) in particular, are associated with a sustained inflammatory response of synovial fibroblasts (SF) in rheumatoid arthritis (RA). Here we investigated individual functions of the writers of H3K27ac marks, the homologues histone acetyl transferases (HAT) CBP and p300, in controlling the constitutive and inflammatory gene expression in RA SF. We applied a silencing strategy, followed by RNA-sequencing and pathway analysis, complemented with the treatment of SF with inhibitors targeting the HAT (C646) or bromo domains (I-CBP) of CBP and p300. We showed that CBP and p300 undertook overlapping and, in particular at gene levels, distinct regulatory functions in SF. p300 is the major HAT for H3K27ac in SF and regulated more diverse pathways than CBP. Whereas both factors regulated genes associated with extracellular matrix remodeling, adhesion and proliferation, p300 specifically controlled developmental genes associated with limb development. Silencing of CBP specifically down regulated the TNF-induced expression of interferon-signature genes. In contrast, silencing of p300 resulted in anti- and pro-inflammatory effects. Integration of data sets derived from RNA-sequencing and chromatin immunoprecipitation sequencing for H3K27ac revealed that changes in gene expression after CBP or p300 silencing could be only partially explained by changes in levels of H3K27ac. Inhibition of CBP/p300 using HAT and bromo domain inhibitors strongly mirrored effects obtained by silencing of p300, including anti- and pro-inflammatory effects, indicating that such inhibitors are not sufficient to be used as anti-inflammatory drugs.
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Affiliation(s)
- Monika Krošel
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland; Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Marcel Gabathuler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Malgorzata Maciukiewicz
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Larissa Moser
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Gideon Isaac Lee
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | | | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Kerstin Klein
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland; Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland.
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Dúcka M, Kučeríková M, Trčka F, Červinka J, Biglieri E, Šmarda J, Borsig L, Beneš P, Knopfová L. c-Myb interferes with inflammatory IL1α-NF-κB pathway in breast cancer cells. Neoplasia 2021; 23:326-336. [PMID: 33621853 PMCID: PMC7905261 DOI: 10.1016/j.neo.2021.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
The transcription factor c-Myb can be involved in the activation of many genes with protumorigenic function; however, its role in breast cancer (BC) development is still under discussion. c-Myb is considered as a tumor-promoting factor in the early phases of BC, on the other hand, its expression in BC patients relates to a good prognosis. Previously, we have shown that c-Myb controls the capacity of BC cells to form spontaneous lung metastasis. Reduced seeding of BC cells to the lungs is linked to high expression of c-Myb and a decline in expression of a specific set of inflammatory genes. Here, we unraveled a c-Myb-IL1α-NF-κB signaling axis that takes place in tumor cells. We report that an overexpression of c-Myb interfered with the activity of NF-κB in several BC cell lines. We identified IL1α to be essential for this interference since it was abrogated in the IL1α-deficient cells. Overexpression of IL1α, as well as addition of recombinant IL1α protein, activated NF-κB signaling and restored expression of the inflammatory signature genes suppressed by c-Myb. The endogenous levels of c-Myb negatively correlated with IL1α on both transcriptional and protein levels across BC cell lines. We concluded that inhibition of IL1α expression by c-Myb reduces NF-κB activity and disconnects the inflammatory circuit, a potentially targetable mechanism to mimic the antimetastatic effect of c-Myb with therapeutic perspective.
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Affiliation(s)
- Monika Dúcka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Martina Kučeríková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Filip Trčka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Jakub Červinka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Elisabetta Biglieri
- Institute of Physiology, University of Zurich and Comprehensive Cancer Center, Zurich, Switzerland
| | - Jan Šmarda
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lubor Borsig
- Institute of Physiology, University of Zurich and Comprehensive Cancer Center, Zurich, Switzerland
| | - Petr Beneš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Lucia Knopfová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic.
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8
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Blackwood CA, McCoy MT, Ladenheim B, Cadet JL. Oxycodone self-administration activates the mitogen-activated protein kinase/ mitogen- and stress-activated protein kinase (MAPK-MSK) signaling pathway in the rat dorsal striatum. Sci Rep 2021; 11:2567. [PMID: 33510349 PMCID: PMC7843984 DOI: 10.1038/s41598-021-82206-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
To identify signaling pathways activated by oxycodone self-administration (SA), Sprague–Dawley rats self-administered oxycodone for 20 days using short—(ShA, 3 h) and long-access (LgA, 9 h) paradigms. Animals were euthanized 2 h after SA cessation and dorsal striata were used in post-mortem molecular analyses. LgA rats escalated their oxycodone intake and separated into lower (LgA-L) or higher (LgA-H) oxycodone takers. LgA-H rats showed increased striatal protein phosphorylation of ERK1/2 and MSK1/2. Histone H3, phosphorylated at serine 10 and acetylated at lysine 14 (H3S10pK14Ac), a MSK1/2 target, showed increased abundance only in LgA-H rats. RT-qPCR analyses revealed increased AMPA receptor subunits, GluA2 and GluA3 mRNAs, in the LgA-H rats. GluA3, but not GluA2, mRNA expression correlated positively with changes in pMSK1/2 and H3S10pK14Ac. These findings suggest that escalated oxycodone SA results in MSK1/2-dependent histone phosphorylation and increases in striatal gene expression. These observations offer potential avenues for interventions against oxycodone addiction.
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Affiliation(s)
- Christopher A Blackwood
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Michael T McCoy
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Bruce Ladenheim
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, 251 Bayview Boulevard, Baltimore, MD, 21224, USA.
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Inhibition of p300 by Garcinol Protects against Cisplatin-Induced Acute Kidney Injury through Suppression of Oxidative Stress, Inflammation, and Tubular Cell Death in Mice. Antioxidants (Basel) 2020; 9:antiox9121271. [PMID: 33327548 PMCID: PMC7765028 DOI: 10.3390/antiox9121271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/03/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence suggests that epigenetic mechanisms such as histone modification are crucially involved in the pathophysiology of acute kidney injury (AKI). The histone acetyltransferase p300 regulates several biological processes through the acetylation of histones or transcription factors. However, the role of p300 in cisplatin-induced AKI remains poorly understood. Therefore, we investigated the effects of garcinol, a potent p300 inhibitor, on cisplatin-induced AKI and explored the mechanisms. Administration of garcinol significantly reversed the upregulation of p300 and increased acetylation of histone H3, along with amelioration of renal dysfunction and histopathological injury in the kidneys of cisplatin-injected mice. Garcinol also attenuated oxidative stress and reduced expression of pro-oxidant enzymes. In addition, garcinol reduced the elevated production of cytokines and chemokines and suppressed immune cell accumulation together with downregulation of vascular adhesion molecules. These beneficial effects of garcinol were associated with a reduction in acetylation of the p65 subunit of nuclear factor kappa-B. Further, garcinol significantly inhibited apoptosis and caspase-3 activation, with a decrease in p53 acetylation in cisplatin-injected mice. Taken together, we demonstrated that the inhibition of p300 by garcinol ameliorated cisplatin-induced renal injury, presumably through epigenetic mechanisms. These results suggest that garcinol might be a potential preventive agent for cisplatin-induced AKI.
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10
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Khan P, Siddiqui JA, Maurya SK, Lakshmanan I, Jain M, Ganti AK, Salgia R, Batra SK, Nasser MW. Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease. Semin Cancer Biol 2020; 83:57-76. [PMID: 33220460 PMCID: PMC8218609 DOI: 10.1016/j.semcancer.2020.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Small cell lung cancer (SCLC) is a particular subtype of lung cancer with high mortality. Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy have substantially expanded existing knowledge and treatment modalities. However, challenges associated with SCLC remain enigmatic and elusive. Most of the conventional drug discovery approaches targeting altered signaling pathways in SCLC end up in the 'grave-yard of drug discovery', which mandates exploring novel approaches beyond inhibiting cell signaling pathways. Epigenetic modifications have long been documented as the key contributors to the tumorigenesis of almost all types of cancer, including SCLC. The last decade witnessed an exponential increase in our understanding of epigenetic modifications for SCLC. The present review highlights the central role of epigenetic regulations in acquiring neoplastic phenotype, metastasis, aggressiveness, resistance to chemotherapy, and immunotherapeutic approaches of SCLC. Different types of epigenetic modifications (DNA/histone methylation or acetylation) that can serve as predictive biomarkers for prognostication, treatment stratification, neuroendocrine lineage determination, and development of potential SCLC therapies are also discussed. We also review the utility of epigenetic targets/epidrugs in combination with first-line chemotherapy and immunotherapy that are currently under investigation in preclinical and clinical studies. Altogether, the information presents the inclusive landscape of SCLC epigenetics and epidrugs that will help to improve SCLC outcomes.
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Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Apar Kishor Ganti
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA-Nebraska Western Iowa Health Care System, Omaha, NE, 68105, USA; Division of Oncology-Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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11
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Martire S, Nguyen J, Sundaresan A, Banaszynski LA. Differential contribution of p300 and CBP to regulatory element acetylation in mESCs. BMC Mol Cell Biol 2020; 21:55. [PMID: 32690000 PMCID: PMC7370441 DOI: 10.1186/s12860-020-00296-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/25/2020] [Indexed: 01/12/2023] Open
Abstract
Background The transcription coactivators CREB binding protein (CBP) and p300 are highly homologous acetyltransferases that mediate histone 3 lysine 27 acetylation (H3K27ac) at regulatory elements such as enhancers and promoters. Although in most cases, CBP and p300 are considered to be functionally identical, both proteins are indispensable for development and there is evidence of tissue-specific nonredundancy. However, characterization of chromatin and transcription states regulated by each protein is lacking. Results In this study we analyze the individual contribution of p300 and CBP to the H3K27ac landscape, chromatin accessibility, and transcription in mouse embryonic stem cells (mESC). We demonstrate that p300 is the predominant H3K27 acetyltransferase in mESCs and that loss of acetylation in p300KD mESCs is more pronounced at enhancers compared to promoters. While loss of either CBP or p300 has little effect on the open state of chromatin, we observe that distinct gene sets are transcriptionally dysregulated upon depletion of p300 or CBP. Transcriptional dysregulation is generally correlated with dysregulation of promoter acetylation upon depletion of p300 (but not CBP) and appears to be relatively independent of dysregulated enhancer acetylation. Interestingly, both our transcriptional and genomic analyses demonstrate that targets of the p53 pathway are stabilized upon depletion of p300, suggesting an unappreciated view of the relationship between p300 and p53 in mESCs. Conclusions This genomic study sheds light on distinct functions of two important transcriptional regulators in the context of a developmentally relevant cell type. Given the links to both developmental disorders and cancer, we believe that our study may promote new ways of thinking about how these proteins function in settings that lead to disease.
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Affiliation(s)
- Sara Martire
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jennifer Nguyen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Aishwarya Sundaresan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Laura A Banaszynski
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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12
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Dysregulated Transcriptional Control in Prostate Cancer. Int J Mol Sci 2019; 20:ijms20122883. [PMID: 31200487 PMCID: PMC6627928 DOI: 10.3390/ijms20122883] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 12/24/2022] Open
Abstract
Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enhancer identified upstream of the androgen receptor (AR) gene. Super-enhancers are increasingly found to play important roles in aberrant oncogenic transcription. Several players involved in these processes are currently being evaluated as drug targets and may represent new vulnerabilities that can be exploited for prostate cancer treatment. They include factors involved in enhancer and super-enhancer function such as bromodomain proteins and cyclin-dependent kinases. In addition, non-coding RNAs with an important gene regulatory role are being explored. The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment paradigms for the benefit of patients.
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13
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Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC. A practical guide to methods controlling false discoveries in computational biology. Genome Biol 2019; 20:118. [PMID: 31164141 PMCID: PMC6547503 DOI: 10.1186/s13059-019-1716-1] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/10/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have emerged as popular and powerful tools for error rate control. While classic FDR methods use only p values as input, more modern FDR methods have been shown to increase power by incorporating complementary information as informative covariates to prioritize, weight, and group hypotheses. However, there is currently no consensus on how the modern methods compare to one another. We investigate the accuracy, applicability, and ease of use of two classic and six modern FDR-controlling methods by performing a systematic benchmark comparison using simulation studies as well as six case studies in computational biology. RESULTS Methods that incorporate informative covariates are modestly more powerful than classic approaches, and do not underperform classic approaches, even when the covariate is completely uninformative. The majority of methods are successful at controlling the FDR, with the exception of two modern methods under certain settings. Furthermore, we find that the improvement of the modern FDR methods over the classic methods increases with the informativeness of the covariate, total number of hypothesis tests, and proportion of truly non-null hypotheses. CONCLUSIONS Modern FDR methods that use an informative covariate provide advantages over classic FDR-controlling procedures, with the relative gain dependent on the application and informativeness of available covariates. We present our findings as a practical guide and provide recommendations to aid researchers in their choice of methods to correct for false discoveries.
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Affiliation(s)
- Keegan Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215 USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, 02215 USA
| | - Patrick K. Kimes
- Department of Data Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215 USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, 02215 USA
| | - Claire Duvallet
- Department of Biological Engineering, MIT, 77 Massachusetts Avenue, Cambridge, USA
- Center for Microbiome Informatics and Therapeutics, MIT, 77 Massachusetts Avenue, Cambridge, USA
| | - Alejandro Reyes
- Department of Data Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215 USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, 02215 USA
| | | | - Mingxiang Teng
- Department of Biostatistics & Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, 33612 USA
| | - Chinmay Shukla
- Biological and Biomedical Sciences Program, Harvard University, Boston, USA
| | - Eric J. Alm
- Department of Biological Engineering, MIT, 77 Massachusetts Avenue, Cambridge, USA
- Center for Microbiome Informatics and Therapeutics, MIT, 77 Massachusetts Avenue, Cambridge, USA
- Broad Institute, 415 Main Street, Cambridge, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, 21205 USA
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14
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Abstract
Understanding adipogenesis, the process of adipocyte development, may provide new ways to treat obesity and related metabolic diseases. Adipogenesis is controlled by coordinated actions of lineage-determining transcription factors and epigenomic regulators. Peroxisome proliferator-activated receptor gamma (PPARγ) and C/EBPα are master "adipogenic" transcription factors. In recent years, a growing number of studies have reported the identification of novel transcriptional and epigenomic regulators of adipogenesis. However, many of these novel regulators have not been validated in adipocyte development in vivo and their working mechanisms are often far from clear. In this minireview, we discuss recent advances in transcriptional and epigenomic regulation of adipogenesis, with a focus on factors and mechanisms shared by both white adipogenesis and brown adipogenesis. Studies on the transcriptional regulation of adipogenesis highlight the importance of investigating adipocyte differentiation in vivo rather than drawing conclusions based on knockdown experiments in cell culture. Advances in understanding of epigenomic regulation of adipogenesis have revealed critical roles of histone methylation/demethylation, histone acetylation/deacetylation, chromatin remodeling, DNA methylation, and microRNAs in adipocyte differentiation. We also discuss future research directions that may help identify novel factors and mechanisms regulating adipogenesis.
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15
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Ichise T, Yoshida N, Ichise H. CBP/p300 antagonises EGFR‐Ras‐Erk signalling and suppresses increased Ras‐Erk signalling‐induced tumour formation in mice. J Pathol 2019; 249:39-51. [DOI: 10.1002/path.5279] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/25/2019] [Accepted: 04/04/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Taeko Ichise
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science The University of Tokyo Tokyo Japan
- Institute for Animal Research, Faculty of Medicine University of the Ryukyus Okinawa Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Hirotake Ichise
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science The University of Tokyo Tokyo Japan
- Institute for Animal Research, Faculty of Medicine University of the Ryukyus Okinawa Japan
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16
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Zucconi BE, Makofske JL, Meyers DJ, Hwang Y, Wu M, Kuroda MI, Cole PA. Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP. Biochemistry 2019; 58:2133-2143. [PMID: 30924641 DOI: 10.1021/acs.biochem.9b00160] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
p300 and CBP are highly related histone acetyltransferase (HAT) enzymes that regulate gene expression, and their dysregulation has been linked to cancer and other diseases. p300/CBP is composed of a number of domains including a HAT domain, which is inhibited by the small molecule A-485, and an acetyl-lysine binding bromodomain, which was recently found to be selectively antagonized by the small molecule I-CBP112. Here we show that the combination of I-CBP112 and A-485 can synergize to inhibit prostate cancer cell proliferation. We find that the combination confers a dramatic reduction in p300 chromatin occupancy compared to the individual effects of blocking either domain alone. Accompanying this loss of p300 on chromatin, combination treatment leads to the reduction of specific mRNAs including androgen-dependent and pro-oncogenic prostate genes such as KLK3 (PSA) and c-Myc. Consistent with p300 directly affecting gene expression, mRNAs that are significantly reduced by combination treatment also exhibit a strong reduction in p300 chromatin occupancy at their gene promoters. The relatively few mRNAs that are up-regulated upon combination treatment show no correlation with p300 occupancy. These studies provide support for the pharmacologic advantage of concurrent targeting of two domains within one key epigenetic modification enzyme.
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Affiliation(s)
- Beth E Zucconi
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Jessica L Makofske
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Genetics , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - David J Meyers
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Genetics , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Philip A Cole
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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17
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Lipinski M, Del Blanco B, Barco A. CBP/p300 in brain development and plasticity: disentangling the KAT's cradle. Curr Opin Neurobiol 2019; 59:1-8. [PMID: 30856481 DOI: 10.1016/j.conb.2019.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/30/2019] [Indexed: 12/14/2022]
Abstract
The paralogous transcriptional co-activators CBP and p300 (aka KAT3A and KAT3B, respectively) contain a characteristic and promiscuous lysine acetyltransferase (KAT) domain and multiple independent protein-binding domains that enable them to interact with hundreds of proteins, possibly promoting the acetylation of thousands of target lysine residues. Both proteins play critical roles during the development of the nervous system and may also regulate stimuli-driven transcription and plasticity in postmitotic neurons. The multiplicity of functions, substrates, and molecular partners, together with the redundancy and singularity of the two KAT3 paralogs, define a complex cat's cradle of relationships. In this review, we discuss the role of the KAT3 proteins in neurons and integrate recent information regarding their function and mode of action.
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Affiliation(s)
- Michal Lipinski
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain.
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18
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Li S, Xu C, Fu Y, Lei PJ, Yao Y, Yang W, Zhang Y, Washburn MP, Florens L, Jaiswal M, Wu M, Mohan M. DYRK1A interacts with histone acetyl transferase p300 and CBP and localizes to enhancers. Nucleic Acids Res 2018; 46:11202-11213. [PMID: 30137413 PMCID: PMC6265467 DOI: 10.1093/nar/gky754] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022] Open
Abstract
DYRK1A, dual-specificity tyrosine phosphorylation-regulated kinase 1A, which is linked to mental retardation and microcephaly, is a member of the CMGC group of kinases. It has both cytoplasmic and nuclear functions, however, molecular mechanisms of how DYRK1A regulates gene expression is not well understood. Here, we identify two histone acetyltransferases, p300 and CBP, as interaction partners of DYRK1A through a proteomics study. We show that overexpression of DYKR1A causes hyperphosphorylation of p300 and CBP. Using genome-wide location (ChIP-sequencing) analysis of DYRK1A, we show that most of the DYRK1A peaks co-localize with p300 and CBP, at enhancers or near the transcription start sites (TSS). Modulation of DYRK1A, by shRNA mediated reduction or transfection mediated overexpression, leads to alteration of expression of downstream located genes. We show that the knockdown of DYRK1A results in a significant loss of H3K27acetylation at these enhancers, suggesting that DYRK1A modulates the activity of p300/CBP at these enhancers. We propose that DYRK1A functions in enhancer regulation by interacting with p300/CBP and modulating their activity. Overall, DYRK1A function in the regulation of enhancer activity provides a new mechanistic understanding of DYRK1A mediated regulation of gene expression, which may help in better understanding of the roles of DYRK1A in human pathologies.
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Affiliation(s)
- Shanshan Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiaotong University School of Medicine, 280, South Chongqing Road, Shanghai 200025, China
| | - Chu Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiaotong University School of Medicine, 280, South Chongqing Road, Shanghai 200025, China
| | - Yinkun Fu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiaotong University School of Medicine, 280, South Chongqing Road, Shanghai 200025, China
| | - Pin-Ji Lei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanhua Yao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiaotong University School of Medicine, 280, South Chongqing Road, Shanghai 200025, China
| | - Wanli Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiaotong University School of Medicine, 280, South Chongqing Road, Shanghai 200025, China
| | - Ying Zhang
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, MO 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Manish Jaiswal
- TIFR Centre for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Man Mohan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiaotong University School of Medicine, 280, South Chongqing Road, Shanghai 200025, China
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19
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Ortega E, Rengachari S, Ibrahim Z, Hoghoughi N, Gaucher J, Holehouse AS, Khochbin S, Panne D. Transcription factor dimerization activates the p300 acetyltransferase. Nature 2018; 562:538-544. [PMID: 30323286 PMCID: PMC6914384 DOI: 10.1038/s41586-018-0621-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/15/2018] [Indexed: 01/08/2023]
Abstract
The transcriptional coactivator p300 is a histone lysine acetyltransferase that is typically recruited to transcriptional enhancers and regulates gene expression by acetylating chromatin. Here we show that p300 activation directly depends on the activation and oligomerisation status of transcription factor (TF) ligands. Using two model TFs, IRF3 and STAT1, we demonstrate that TF dimerization enables trans-autoacetylation of p300 in a highly conserved and intrinsically disordered autoinhibitory lysine-rich loop (AIL), resulting in HAT activation. We describe a p300 crystal structure in which the AIL invades the active site of a neighbouring HAT domain thus revealing a snap-shot of a trans-autoacetylation reaction intermediate. Substrate access to the active site involves rearrangement of an autoinhibitory RING domain. Our data explain how cellular signalling, TF activation and dimerization controls p300 activation thus explaining why gene transcription is associated with chromatin acetylation.
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Affiliation(s)
- Esther Ortega
- European Molecular Biology Laboratory, Grenoble, France
| | - Srinivasan Rengachari
- European Molecular Biology Laboratory, Grenoble, France.,Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Ziad Ibrahim
- European Molecular Biology Laboratory, Grenoble, France.,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Naghmeh Hoghoughi
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Jonathan Gaucher
- European Molecular Biology Laboratory, Grenoble, France.,Université Grenoble Alpes, INSERM U1042, HP2 Laboratory, Grenoble, France
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Saadi Khochbin
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France. .,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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20
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CBP and P300 regulate distinct gene networks required for human primary myoblast differentiation and muscle integrity. Sci Rep 2018; 8:12629. [PMID: 30135524 PMCID: PMC6105712 DOI: 10.1038/s41598-018-31102-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023] Open
Abstract
The acetyltransferases CBP and P300 have been implicated in myogenesis in mouse immortalized cell lines but these studies focused only on the expression of a handful of myogenic factors. Hence, the respective role of these two related cofactors and their impact at global scale on gene expression rewiring during primary myoblast differentiation remain unknown. Here, we characterised the gene networks regulated by these two epigenetic enzymes during human primary myoblast differentiation (HPM). We found that CBP and p300 play a critical role in the activation of the myogenic program and mostly regulate distinct gene sets to control several aspects of HPM biology, even though they also exhibit some degree of redundancy. Moreover, CBP or P300 knockdown strongly impaired muscle cell adhesion and resulted in the activation of inflammation markers, two hallmarks of dystrophic disease. This was further validated in zebrafish where inhibition of CBP and P300 enzymatic activities led to cell adhesion defects and muscle fiber detachment. Our data highlight an unforeseen link between CBP/P300 activity and the emergence of dystrophic phenotypes. They thereby identify CBP and P300 as mediators of adult muscle integrity and suggest a new lead for intervention in muscular dystrophy.
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21
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Kim DW, Kim KC, Kim KB, Dunn CT, Park KS. Transcriptional deregulation underlying the pathogenesis of small cell lung cancer. Transl Lung Cancer Res 2018. [PMID: 29535909 DOI: 10.21037/tlcr.2017.10.07] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The discovery of recurrent alterations in genes encoding transcription regulators and chromatin modifiers is one of the most important recent developments in the study of the small cell lung cancer (SCLC) genome. With advances in models and analytical methods, the field of SCLC biology has seen remarkable progress in understanding the deregulated transcription networks linked to the tumor development and malignant progression. This review will discuss recent discoveries on the roles of RB and P53 family of tumor suppressors and MYC family of oncogenes in tumor initiation and development. It will also describe the roles of lineage-specific factors in neuroendocrine (NE) cell differentiation and homeostasis and the roles of epigenetic alterations driven by changes in NFIB and chromatin modifiers in malignant progression and chemoresistance. These recent findings have led to a model of transcriptional network in which multiple pathways converge on regulatory regions of crucial genes linked to tumor development. Validation of this model and characterization of target genes will provide critical insights into the biology of SCLC and novel strategies for tumor intervention.
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Affiliation(s)
- Dong-Wook Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Keun-Cheol Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA.,Department of Biological Sciences, Kangwon National University, Chuncheon, Korea
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Colin T Dunn
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
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22
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Bose DA, Berger SL. eRNA binding produces tailored CBP activity profiles to regulate gene expression. RNA Biol 2017; 14:1655-1659. [PMID: 28891741 DOI: 10.1080/15476286.2017.1353862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Enhancers are cis- regulatory genetic elements crucial for controlling temporal and cell-type specific patterns of gene expression. Active enhancers generate bi-directional non-coding RNA transcripts called enhancer RNAs (eRNAs). eRNAs are important for stimulating gene expression, but precise mechanisms for this ability remain unclear. Here we highlight recent findings that demonstrate a direct interaction between RNAs and the transcriptional co-activator Creb-binding protein (CBP). Notably, RNA binding could stimulate the core histone acetyltransferase activity of the enzyme, observable in cells as a link between eRNA production, CBP-dependent histone acetylation and expression of genes regulated by specific enhancers. Although RNA binding was independent of RNA sequence, specificity arises in a locus-specific manner at transcribed sites where CBP was bound to chromatin. The results suggest a functional role for eRNAs as regulatory molecules that are able to stimulate the activity of a key epigenetic regulatory enzyme, thereby promoting gene expression. Furthermore, they suggest an intriguing role for eRNAs: by modulating the activity of chromatin modifying enzymes, they could directly impact transcription by altering the chromatin environment.
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Affiliation(s)
- Daniel A Bose
- a Department of Molecular Biology and Biotechnology , Sheffield Institute for Nucleic Acids, University of Sheffield, Firth Court, Western Bank , Sheffield , UK.,b Departments of Cell and Developmental Biology, Genetics and Biology, Epigenetics Institute , University of Pennsylvania , Philadelphia, Pennsylvania , USA
| | - Shelley L Berger
- c Department of Cell and Developmental Biology, Genetics, Biology , University of Pennsylvania , Philadelphia , Pennsylvania , USA.,d Epigenetics Institute, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania , USA
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23
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Herdman C, Mars JC, Stefanovsky VY, Tremblay MG, Sabourin-Felix M, Lindsay H, Robinson MD, Moss T. A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS Genet 2017; 13:e1006899. [PMID: 28715449 PMCID: PMC5536353 DOI: 10.1371/journal.pgen.1006899] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/31/2017] [Accepted: 06/27/2017] [Indexed: 11/19/2022] Open
Abstract
Transcription of the several hundred of mouse and human Ribosomal RNA (rRNA) genes accounts for the majority of RNA synthesis in the cell nucleus and is the determinant of cytoplasmic ribosome abundance, a key factor in regulating gene expression. The rRNA genes, referred to globally as the rDNA, are clustered as direct repeats at the Nucleolar Organiser Regions, NORs, of several chromosomes, and in many cells the active repeats are transcribed at near saturation levels. The rDNA is also a hotspot of recombination and chromosome breakage, and hence understanding its control has broad importance. Despite the need for a high level of rDNA transcription, typically only a fraction of the rDNA is transcriptionally active, and some NORs are permanently silenced by CpG methylation. Various chromatin-remodelling complexes have been implicated in counteracting silencing to maintain rDNA activity. However, the chromatin structure of the active rDNA fraction is still far from clear. Here we have combined a high-resolution ChIP-Seq protocol with conditional inactivation of key basal factors to better understand what determines active rDNA chromatin. The data resolve questions concerning the interdependence of the basal transcription factors, show that preinitiation complex formation is driven by the architectural factor UBF (UBTF) independently of transcription, and that RPI termination and release corresponds with the site of TTF1 binding. They further reveal the existence of an asymmetric Enhancer Boundary Complex formed by CTCF and Cohesin and flanked upstream by phased nucleosomes and downstream by an arrested RNA Polymerase I complex. We find that the Enhancer Boundary Complex is the only site of active histone modification in the 45kbp rDNA repeat. Strikingly, it not only delimits each functional rRNA gene, but also is stably maintained after gene inactivation and the re-establishment of surrounding repressive chromatin. Our data define a poised state of rDNA chromatin and place the Enhancer Boundary Complex as the likely entry point for chromatin remodelling complexes.
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Affiliation(s)
- Chelsea Herdman
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
| | - Jean-Clement Mars
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
| | - Victor Y. Stefanovsky
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
| | - Michel G. Tremblay
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
| | - Marianne Sabourin-Felix
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
| | - Helen Lindsay
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Mark D. Robinson
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
- * E-mail:
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24
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Modeling gene regulation from paired expression and chromatin accessibility data. Proc Natl Acad Sci U S A 2017; 114:E4914-E4923. [PMID: 28576882 DOI: 10.1073/pnas.1704553114] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rapid increase of genome-wide datasets on gene expression, chromatin states, and transcription factor (TF) binding locations offers an exciting opportunity to interpret the information encoded in genomes and epigenomes. This task can be challenging as it requires joint modeling of context-specific activation of cis-regulatory elements (REs) and the effects on transcription of associated regulatory factors. To meet this challenge, we propose a statistical approach based on paired expression and chromatin accessibility (PECA) data across diverse cellular contexts. In our approach, we model (i) the localization to REs of chromatin regulators (CRs) based on their interaction with sequence-specific TFs, (ii) the activation of REs due to CRs that are localized to them, and (iii) the effect of TFs bound to activated REs on the transcription of target genes (TGs). The transcriptional regulatory network inferred by PECA provides a detailed view of how trans- and cis-regulatory elements work together to affect gene expression in a context-specific manner. We illustrate the feasibility of this approach by analyzing paired expression and accessibility data from the mouse Encyclopedia of DNA Elements (ENCODE) and explore various applications of the resulting model.
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25
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Crebbp loss cooperates with Bcl2 overexpression to promote lymphoma in mice. Blood 2017; 129:2645-2656. [PMID: 28288979 DOI: 10.1182/blood-2016-08-733469] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022] Open
Abstract
CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 overexpression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B cells, we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the proximal regulatory regions of these genes. However, B cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions, enriched for Myc DNA binding motifs, and showed Myc binding. Through the analysis of CREBBP mutations from a large cohort of primary human FL and DLBCL, we show a significant difference in the spectrum of CREBBP mutations in these 2 diseases, with higher frequencies of nonsense/frameshift mutations in DLBCL compared with FL. Together, our data therefore provide important links between Crebbp inactivation and Bcl2 dependence and show a role for Crebbp inactivation in the induction of Myc expression. We suggest this may parallel the role of CREBBP frameshift/nonsense mutations in DLBCL that result in loss of the protein, but may contrast the role of missense mutations in the lysine acetyltransferase domain that are more frequently observed in FL and yield an inactive protein.
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26
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Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL. RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell 2017; 168:135-149.e22. [PMID: 28086087 DOI: 10.1016/j.cell.2016.12.020] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 10/10/2016] [Accepted: 12/14/2016] [Indexed: 12/29/2022]
Abstract
CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300-dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays, we show that an RNA binding region in the HAT domain of CBP-a regulatory motif unique to CBP/p300-allows RNA to stimulate CBP's HAT activity. At enhancers where CBP interacts with eRNAs, stimulation manifests in RNA-dependent changes in the histone acetylation mediated by CBP, such as H3K27ac, and by corresponding changes in gene expression. By interacting directly with CBP, eRNAs contribute to the unique chromatin structure at active enhancers, which, in turn, is required for regulation of target genes.
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Affiliation(s)
- Daniel A Bose
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Danny Reinberg
- Department of Molecular Pharmacology and Biochemistry, New York University School of Medicine, New York, NY 10016, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Roberto Bonasio
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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27
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Izumi K. Disorders of Transcriptional Regulation: An Emerging Category of Multiple Malformation Syndromes. Mol Syndromol 2016; 7:262-273. [PMID: 27867341 DOI: 10.1159/000448747] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/09/2023] Open
Abstract
Some genetic disorders caused by mutations in genes encoding components of the transcriptional machinery as well as proteins involved in epigenetic modification of the genome share many overlapping features, such as facial dysmorphisms, growth problems and developmental delay/intellectual disability. As a basis for some shared phenotypic characteristics in these syndromes, a similar transcriptome disturbance, characterized by global transcriptional dysregulation, is believed to play a major role. In this review article, a general overview of gene transcription is provided, and the current knowledge of the mechanisms underlying some disorders of transcriptional regulation, such as Rubinstein- Taybi, Coffin-Siris, Cornelia de Lange, and CHOPS syndromes, are discussed.
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Affiliation(s)
- Kosuke Izumi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa., USA
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28
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Lun ATL, Smyth GK. From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data. F1000Res 2015; 4:1080. [PMID: 26834993 DOI: 10.12688/f1000research.7016.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 01/17/2023] Open
Abstract
Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites for protein of interest. Most conventional approaches to ChIP-seq data analysis involve the detection of the absolute presence (or absence) of a binding site. However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB). This may yield more relevant results than conventional analyses, as changes in binding can be associated with the biological difference being investigated. The aim of this article is to facilitate the implementation of DB analyses, by comprehensively describing a computational workflow for the detection of DB regions from ChIP-seq data. The workflow is based primarily on R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, from alignment of read sequences to interpretation and visualization of putative DB regions. In particular, detection of DB regions will be conducted using the counts for sliding windows from the csaw package, with statistical modelling performed using methods in the edgeR package. Analyses will be demonstrated on real histone mark and transcription factor data sets. This will provide readers with practical usage examples that can be applied in their own studies.
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Affiliation(s)
- Aaron T L Lun
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
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29
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Lun ATL, Smyth GK. From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data. F1000Res 2015; 4:1080. [PMID: 26834993 PMCID: PMC4706055 DOI: 10.12688/f1000research.7016.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/06/2016] [Indexed: 12/19/2022] Open
Abstract
Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites for protein of interest. Most conventional approaches to ChIP-seq data analysis involve the detection of the absolute presence (or absence) of a binding site. However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB). This may yield more relevant results than conventional analyses, as changes in binding can be associated with the biological difference being investigated. The aim of this article is to facilitate the implementation of DB analyses, by comprehensively describing a computational workflow for the detection of DB regions from ChIP-seq data. The workflow is based primarily on R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, from alignment of read sequences to interpretation and visualization of putative DB regions. In particular, detection of DB regions will be conducted using the counts for sliding windows from the csaw package, with statistical modelling performed using methods in the edgeR package. Analyses will be demonstrated on real histone mark and transcription factor data sets. This will provide readers with practical usage examples that can be applied in their own studies.
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Affiliation(s)
- Aaron T L Lun
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
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30
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Min SW, Chen X, Tracy TE, Li Y, Zhou Y, Wang C, Shirakawa K, Minami SS, Defensor E, Mok SA, Sohn PD, Schilling B, Cong X, Ellerby L, Gibson BW, Johnson J, Krogan N, Shamloo M, Gestwicki J, Masliah E, Verdin E, Gan L. Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits. Nat Med 2015; 21:1154-62. [PMID: 26390242 PMCID: PMC4598295 DOI: 10.1038/nm.3951] [Citation(s) in RCA: 358] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/20/2015] [Indexed: 12/12/2022]
Abstract
Tauopathies, including frontotemporal dementia (FTD) and Alzheimer's disease (AD), are neurodegenerative diseases in which tau fibrils accumulate. Recent evidence supports soluble tau species as the major toxic species. How soluble tau accumulates and causes neurodegeneration remains unclear. Here we identify tau acetylation at Lys174 (K174) as an early change in AD brains and a critical determinant in tau homeostasis and toxicity in mice. The acetyl-mimicking mutant K174Q slows tau turnover and induces cognitive deficits in vivo. Acetyltransferase p300-induced tau acetylation is inhibited by salsalate and salicylate, which enhance tau turnover and reduce tau levels. In the PS19 transgenic mouse model of FTD, administration of salsalate after disease onset inhibited p300 activity, lowered levels of total tau and tau acetylated at K174, rescued tau-induced memory deficits and prevented hippocampal atrophy. The tau-lowering and protective effects of salsalate were diminished in neurons expressing K174Q tau. Targeting tau acetylation could be a new therapeutic strategy against human tauopathies.
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Affiliation(s)
- Sang-Won Min
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Xu Chen
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Tara E Tracy
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Yaqiao Li
- Gladstone Institute of Neurological Disease, San Francisco, California, USA
| | - Yungui Zhou
- Gladstone Institute of Neurological Disease, San Francisco, California, USA
| | - Chao Wang
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Kotaro Shirakawa
- Gladstone Institute of Virology and Immunology, San Francisco, California, USA
| | - S Sakura Minami
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Erwin Defensor
- Stanford Institute for Neuro-Innovation and Translational Neurosciences, Stanford University School of Medicine, Stanford, California, USA
| | - Sue Ann Mok
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, California, USA
| | - Peter Dongmin Sohn
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | | | - Xin Cong
- Buck Institute for Research on Aging, Novato, California, USA
| | - Lisa Ellerby
- Buck Institute for Research on Aging, Novato, California, USA
| | | | - Jeffrey Johnson
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Nevan Krogan
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Mehrdad Shamloo
- Stanford Institute for Neuro-Innovation and Translational Neurosciences, Stanford University School of Medicine, Stanford, California, USA
| | - Jason Gestwicki
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, California, USA
| | - Eliezer Masliah
- Department of Neuroscience, University of California, San Diego, San Diego, California, USA
| | - Eric Verdin
- Gladstone Institute of Virology and Immunology, San Francisco, California, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA.,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, California, USA
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31
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Halsall JA, Turan N, Wiersma M, Turner BM. Cells adapt to the epigenomic disruption caused by histone deacetylase inhibitors through a coordinated, chromatin-mediated transcriptional response. Epigenetics Chromatin 2015; 8:29. [PMID: 26380582 PMCID: PMC4572612 DOI: 10.1186/s13072-015-0021-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The genome-wide hyperacetylation of chromatin caused by histone deacetylase inhibitors (HDACi) is surprisingly well tolerated by most eukaryotic cells. The homeostatic mechanisms that underlie this tolerance are unknown. Here we identify the transcriptional and epigenomic changes that constitute the earliest response of human lymphoblastoid cells to two HDACi, valproic acid and suberoylanilide hydroxamic acid (Vorinostat), both in widespread clinical use. RESULTS Dynamic changes in transcript levels over the first 2 h of exposure to HDACi were assayed on High Density microarrays. There was a consistent response to the two different inhibitors at several concentrations. Strikingly, components of all known lysine acetyltransferase (KAT) complexes were down-regulated, as were genes required for growth and maintenance of the lymphoid phenotype. Up-regulated gene clusters were enriched in regulators of transcription, development and phenotypic change. In untreated cells, HDACi-responsive genes, whether up- or down-regulated, were packaged in highly acetylated chromatin. This was essentially unaffected by HDACi. In contrast, HDACi induced a strong increase in H3K27me3 at transcription start sites, irrespective of their transcriptional response. Inhibition of the H3K27 methylating enzymes, EZH1/2, altered the transcriptional response to HDACi, confirming the functional significance of H3K27 methylation for specific genes. CONCLUSIONS We propose that the observed transcriptional changes constitute an inbuilt adaptive response to HDACi that promotes cell survival by minimising protein hyperacetylation, slowing growth and re-balancing patterns of gene expression. The transcriptional response to HDACi is mediated by a precisely timed increase in H3K27me3 at transcription start sites. In contrast, histone acetylation, at least at the three lysine residues tested, seems to play no direct role. Instead, it may provide a stable chromatin environment that allows transcriptional change to be induced by other factors, possibly acetylated non-histone proteins.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Maaike Wiersma
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Bryan M Turner
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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