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Olea-Flores M, Sharma T, Verdejo-Torres O, DiBartolomeo I, Thompson PR, Padilla-Benavides T, Imbalzano AN. Muscle-specific pyruvate kinase isoforms, PKM1 and PKM2, regulate mammalian SWI/SNF proteins and histone 3 phosphorylation during myoblast differentiation. FASEB J 2024; 38:e23702. [PMID: 38837439 DOI: 10.1096/fj.202400784r] [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: 04/07/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
Pyruvate kinase is a glycolytic enzyme that converts phosphoenolpyruvate and ADP into pyruvate and ATP. There are two genes that encode pyruvate kinase in vertebrates; Pkm and Pkl encode muscle- and liver/erythrocyte-specific forms, respectively. Each gene encodes two isoenzymes due to alternative splicing. Both muscle-specific enzymes, PKM1 and PKM2, function in glycolysis, but PKM2 also has been implicated in gene regulation due to its ability to phosphorylate histone 3 threonine 11 (H3T11) in cancer cells. Here, we examined the roles of PKM1 and PKM2 during myoblast differentiation. RNA-seq analysis revealed that PKM2 promotes the expression of Dpf2/Baf45d and Baf250a/Arid1A. DPF2 and BAF250a are subunits that identify a specific sub-family of the mammalian SWI/SNF (mSWI/SNF) of chromatin remodeling enzymes that is required for the activation of myogenic gene expression during differentiation. PKM2 also mediated the incorporation of DPF2 and BAF250a into the regulatory sequences controlling myogenic gene expression. PKM1 did not affect expression but was required for nuclear localization of DPF2. Additionally, PKM2 was required not only for the incorporation of phosphorylated H3T11 in myogenic promoters but also for the incorporation of phosphorylated H3T6 and H3T45 at myogenic promoters via regulation of AKT and protein kinase C isoforms that phosphorylate those amino acids. Our results identify multiple unique roles for PKM2 and a novel function for PKM1 in gene expression and chromatin regulation during myoblast differentiation.
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Affiliation(s)
- Monserrat Olea-Flores
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Tapan Sharma
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Odette Verdejo-Torres
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Imaru DiBartolomeo
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program in Chemical Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Verdejo-Torres O, Klein DC, Novoa-Aponte L, Carrazco-Carrillo J, Bonilla-Pinto D, Rivera A, Fitisemanu F, Jiménez-González ML, Flinn L, Pezacki AT, Lanzirotti A, Ortiz-Frade LA, Chang CJ, Navea JG, Blaby-Haas C, Hainer SJ, Padilla-Benavides T. Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592485. [PMID: 38746126 PMCID: PMC11092763 DOI: 10.1101/2024.05.03.592485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Copper (Cu) is an essential trace element required for respiration, neurotransmitter synthesis, oxidative stress response, and transcriptional regulation. Imbalance in Cu homeostasis can lead to several pathological conditions, affecting neuronal, cognitive, and muscular development. Mechanistically, Cu and Cu-binding proteins (Cu-BPs) have an important but underappreciated role in transcription regulation in mammalian cells. In this context, our lab investigates the contributions of novel Cu-BPs in skeletal muscle differentiation using murine primary myoblasts. Through an unbiased synchrotron X-ray fluorescence-mass spectrometry (XRF/MS) metalloproteomic approach, we identified the murine cysteine rich intestinal protein 2 (mCrip2) in a sample that showed enriched Cu signal, which was isolated from differentiating primary myoblasts derived from mouse satellite cells. Immunolocalization analyses showed that mCrip2 is abundant in both nuclear and cytosolic fractions. Thus, we hypothesized that mCrip2 might have differential roles depending on its cellular localization in the skeletal muscle lineage. mCrip2 is a LIM-family protein with 4 conserved Zn2+-binding sites. Homology and phylogenetic analyses showed that mammalian Crip2 possesses histidine residues near two of the Zn2+-binding sites (CX2C-HX2C) which are potentially implicated in Cu+-binding and competition with Zn2+. Biochemical characterization of recombinant human hsCRIP2 revealed a high Cu+-binding affinity for two and four Cu+ ions and limited redox potential. Functional characterization using CRISPR/Cas9-mediated deletion of mCrip2 in primary myoblasts did not impact proliferation, but impaired myogenesis by decreasing the expression of differentiation markers, possibly attributed to Cu accumulation. Transcriptome analyses of proliferating and differentiating mCrip2 KO myoblasts showed alterations in mRNA processing, protein translation, ribosome synthesis, and chromatin organization. CUT&RUN analyses showed that mCrip2 associates with a select set of gene promoters, including MyoD1 and metallothioneins, acting as a novel Cu-responsive or Cu-regulating protein. Our work demonstrates novel regulatory functions of mCrip2 that mediate skeletal muscle differentiation, presenting new features of the Cu-network in myoblasts.
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Affiliation(s)
- Odette Verdejo-Torres
- Department of Molecular Biology and Biochemistry, Wesleyan University, CT, 06459. USA
| | - David C. Klein
- Department of Biological Sciences. University of Pittsburgh, Pittsburgh, PA. 15207. USA
| | - Lorena Novoa-Aponte
- Present address: Genetics and Metabolism Section, Liver Diseases Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD. USA
| | | | - Denzel Bonilla-Pinto
- Department of Molecular Biology and Biochemistry, Wesleyan University, CT, 06459. USA
| | - Antonio Rivera
- Department of Molecular Biology and Biochemistry, Wesleyan University, CT, 06459. USA
| | | | | | - Lyra Flinn
- Chemistry Department. Skidmore College, Saratoga Springs New York, 12866. USA
| | - Aidan T. Pezacki
- Department of Chemistry. University of California, Berkeley, California, 94720. USA
| | - Antonio Lanzirotti
- Center for Advanced Radiation Sources, The University of Chicago, Lemont, IL 60439. USA
| | | | - Christopher J. Chang
- Department of Chemistry. University of California, Berkeley, California, 94720. USA
- Department of Molecular and Cell Biology. University of California, Berkeley, California, 94720. USA
| | - Juan G. Navea
- Chemistry Department. Skidmore College, Saratoga Springs New York, 12866. USA
| | - Crysten Blaby-Haas
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA & DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA. USA
| | - Sarah J. Hainer
- Department of Biological Sciences. University of Pittsburgh, Pittsburgh, PA. 15207. USA
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Olea-Flores M, Sharma T, Verdejo-Torres O, DiBartolomeo I, Thompson PR, Padilla-Benavides T, Imbalzano AN. Muscle-Specific Pyruvate Kinase Isoforms, Pkm1 and Pkm2, Regulate Mammalian SWI/SNF Proteins and Histone 3 Phosphorylation During Myoblast Differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588959. [PMID: 38645038 PMCID: PMC11030359 DOI: 10.1101/2024.04.10.588959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pyruvate kinase is a glycolytic enzyme that converts phosphoenolpyruvate and ADP into pyruvate and ATP. There are two genes that encode pyruvate kinase in vertebrates; Pkm and Pkl encode muscle- and liver/erythrocyte-specific forms, respectively. Each gene encodes two isoenzymes due to alternative splicing. Both muscle-specific enzymes, Pkm1 and Pkm2, function in glycolysis, but Pkm2 also has been implicated in gene regulation due to its ability to phosphorylate histone 3 threonine 11 (H3T11) in cancer cells. Here, we examined the roles of Pkm1 and Pkm2 during myoblast differentiation. RNA-seq analysis revealed that Pkm2 promotes the expression of Dpf2/Baf45d and Baf250a/Arid1A. Dpf2 and Baf250a are subunits that identify a specific sub-family of the mammalian SWI/SNF (mSWI/SNF) of chromatin remodeling enzymes that is required for activation of myogenic gene expression during differentiation. Pkm2 also mediated the incorporation of Dpf2 and Baf250a into the regulatory sequences controlling myogenic gene expression. Pkm1 did not affect expression but was required for nuclear localization of Dpf2. Additionally, Pkm2 was required not only for the incorporation of phosphorylated H3T11 in myogenic promoters, but also for the incorporation of phosphorylated H3T6 and H3T45 at myogenic promoters via regulation of AKT and protein kinase C isoforms that phosphorylate those amino acids. Our results identify multiple unique roles for Pkm2 and a novel function for Pkm1 in gene expression and chromatin regulation during myoblast differentiation.
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Affiliation(s)
- Monserrat Olea-Flores
- Department Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Tapan Sharma
- Department Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Odette Verdejo-Torres
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Imaru DiBartolomeo
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Paul R. Thompson
- Department Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Chemical Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Anthony N. Imbalzano
- Department Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Padilla-Benavides T, Olea-Flores M, Sharma T, Syed SA, Witwicka H, Zuñiga-Eulogio MD, Zhang K, Navarro-Tito N, Imbalzano AN. Differential Contributions of mSWI/SNF Chromatin Remodeler Sub-Families to Myoblast Differentiation. Int J Mol Sci 2023; 24:11256. [PMID: 37511016 PMCID: PMC10378909 DOI: 10.3390/ijms241411256] [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: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Mammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions. mSWI/SNF enzymes are classified into three sub-families based on the presence of specific subunit proteins. The sub-families are Brm- or Brg1-associated factor (BAF), ncBAF (non-canonical BAF), and polybromo-associated BAF (PBAF). The biological roles for the different enzyme sub-families are poorly described. We knocked down the expression of genes encoding unique subunit proteins for each sub-family, Baf250A, Brd9, and Baf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that Baf250A and the BAF complex were required to drive lineage-specific gene expression. KD of Brd9 delayed differentiation. However, while the Baf250A-dependent gene expression profile included myogenic genes, the Brd9-dependent gene expression profile did not, suggesting Brd9 and the ncBAF complex indirectly contributed to differentiation. Baf180 was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme sub-families during myoblast differentiation.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Monserrat Olea-Flores
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Tapan Sharma
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Miriam D. Zuñiga-Eulogio
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Kexin Zhang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
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Ahmad N, de la Serna IL, Marathe HG, Fan X, Dube P, Zhang S, Haller ST, Kennedy DJ, Pestov NB, Modyanov NN. Eutherian-Specific Functions of BetaM Acquired through Atp1b4 Gene Co-Option in the Regulation of MyoD Expression. Life (Basel) 2023; 13:414. [PMID: 36836771 PMCID: PMC9962273 DOI: 10.3390/life13020414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Vertebrate ATP1B4 genes represent a rare instance of orthologous gene co-option, resulting in radically different functions of the encoded BetaM proteins. In lower vertebrates, BetaM is a Na, K-ATPase β-subunit that is a component of ion pumps in the plasma membrane. In placental mammals, BetaM lost its ancestral role and, through structural alterations of the N-terminal domain, became a skeletal and cardiac muscle-specific protein of the inner nuclear membrane, highly expressed during late fetal and early postnatal development. We previously determined that BetaM directly interacts with the transcriptional co-regulator SKI-interacting protein (SKIP) and is implicated in the regulation of gene expression. This prompted us to investigate a potential role for BetaM in the regulation of muscle-specific gene expression in neonatal skeletal muscle and cultured C2C12 myoblasts. We found that BetaM can stimulate expression of the muscle regulatory factor (MRF), MyoD, independently of SKIP. BetaM binds to the distal regulatory region (DRR) of MyoD, promotes epigenetic changes associated with activation of transcription, and recruits the SWI/SNF chromatin remodeling subunit, BRG1. These results indicate that eutherian BetaM regulates muscle gene expression by promoting changes in chromatin structure. These evolutionarily acquired new functions of BetaM might be very essential and provide evolutionary advantages to placental mammals.
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Affiliation(s)
- Nisar Ahmad
- Department of Physiology and Pharmacology, Center for Diabetes and Endocrine Research, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Ivana L. de la Serna
- Department of Cell and Cancer Biology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Himangi G. Marathe
- Department of Cell and Cancer Biology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Xiaoming Fan
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Prabhatchandra Dube
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Shungang Zhang
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Steven T. Haller
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - David J. Kennedy
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Nikolay B. Pestov
- Department of Physiology and Pharmacology, Center for Diabetes and Endocrine Research, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Nikolai N. Modyanov
- Department of Physiology and Pharmacology, Center for Diabetes and Endocrine Research, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
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Tabuloc CA, Cai YD, Kwok RS, Chan EC, Hidalgo S, Chiu JC. CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters. PLoS Genet 2023; 19:e1010649. [PMID: 36809369 PMCID: PMC9983840 DOI: 10.1371/journal.pgen.1010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/03/2023] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Circadian clock and chromatin-remodeling complexes are tightly intertwined systems that regulate rhythmic gene expression. The circadian clock promotes rhythmic expression, timely recruitment, and/or activation of chromatin remodelers, while chromatin remodelers regulate accessibility of clock transcription factors to the DNA to influence expression of clock genes. We previously reported that the BRAHMA (BRM) chromatin-remodeling complex promotes the repression of circadian gene expression in Drosophila. In this study, we investigated the mechanisms by which the circadian clock feeds back to modulate daily BRM activity. Using chromatin immunoprecipitation, we observed rhythmic BRM binding to clock gene promoters despite constitutive BRM protein expression, suggesting that factors other than protein abundance are responsible for rhythmic BRM occupancy at clock-controlled loci. Since we previously reported that BRM interacts with two key clock proteins, CLOCK (CLK) and TIMELESS (TIM), we examined their effect on BRM occupancy to the period (per) promoter. We observed reduced BRM binding to the DNA in clk null flies, suggesting that CLK is involved in enhancing BRM occupancy to initiate transcriptional repression at the conclusion of the activation phase. Additionally, we observed reduced BRM binding to the per promoter in flies overexpressing TIM, suggesting that TIM promotes BRM removal from DNA. These conclusions are further supported by elevated BRM binding to the per promoter in flies subjected to constant light and experiments in Drosophila tissue culture in which the levels of CLK and TIM are manipulated. In summary, this study provides new insights into the reciprocal regulation between the circadian clock and the BRM chromatin-remodeling complex.
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Affiliation(s)
- Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Rosanna S. Kwok
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Elizabeth C. Chan
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
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Nguyen VT, Tessema M, Weissman BE. The SWI/SNF Complex: A Frequently Mutated Chromatin Remodeling Complex in Cancer. Cancer Treat Res 2023; 190:211-244. [PMID: 38113003 DOI: 10.1007/978-3-031-45654-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is a global regulator of gene expression known to maintain nucleosome-depleted regions at active enhancers and promoters. The mammalian SWI/SNF protein subunits are encoded by 29 genes and 11-15 subunits including an ATPase domain of either SMARCA4 (BRG1) or SMARCA2 (BRM) are assembled into a complex. Based on the distinct subunits, SWI/SNF are grouped into 3 major types (subfamilies): the canonical BRG1/BRM-associated factor (BAF/cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (GBAF/ncBAF). Pan-cancer genome sequencing studies have shown that nearly 25% of all cancers bear mutations in subunits of the SWI/SNF complex, many of which are loss of function (LOF) mutations, suggesting a tumor suppressor role. Inactivation of SWI/SNF complex subunits causes widespread epigenetic dysfunction, including increased dependence on antagonistic components such as polycomb repressor complexes (PRC1/2) and altered enhancer regulation, likely promoting an oncogenic state leading to cancer. Despite the prevalence of mutations, most SWI/SNF-mutant cancers lack targeted therapeutic strategies. Defining the dependencies created by LOF mutations in SWI/SNF subunits will identify better targets for these cancers.
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Affiliation(s)
- Vinh The Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Mathewos Tessema
- Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Bernard Ellis Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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Firnau MB, Brieger A. CK2 and the Hallmarks of Cancer. Biomedicines 2022; 10:biomedicines10081987. [PMID: 36009534 PMCID: PMC9405757 DOI: 10.3390/biomedicines10081987] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer is a leading cause of death worldwide. Casein kinase 2 (CK2) is commonly dysregulated in cancer, impacting diverse molecular pathways. CK2 is a highly conserved serine/threonine kinase, constitutively active and ubiquitously expressed in eukaryotes. With over 500 known substrates and being estimated to be responsible for up to 10% of the human phosphoproteome, it is of significant importance. A broad spectrum of diverse types of cancer cells has been already shown to rely on disturbed CK2 levels for their survival. The hallmarks of cancer provide a rationale for understanding cancer’s common traits. They constitute the maintenance of proliferative signaling, evasion of growth suppressors, resisting cell death, enabling of replicative immortality, induction of angiogenesis, the activation of invasion and metastasis, as well as avoidance of immune destruction and dysregulation of cellular energetics. In this work, we have compiled evidence from the literature suggesting that CK2 modulates all hallmarks of cancer, thereby promoting oncogenesis and operating as a cancer driver by creating a cellular environment favorable to neoplasia.
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Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast cell cycle progression and expression of the Pax7 regulator. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194801. [PMID: 35217218 PMCID: PMC8948540 DOI: 10.1016/j.bbagrm.2022.194801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/29/2022] [Accepted: 02/14/2022] [Indexed: 11/21/2022]
Abstract
The mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) families of ATP-dependent chromatin remodeling enzymes are established co-regulators of gene expression. mSWI/SNF complexes can be assembled into three major subfamilies: BAF (BRG1 or BRM-Associated Factor), PBAF (Polybromo containing BAF), or ncBAF (non-canonical BAF) that are distinguished by the presence of mutually exclusive subunits. The mechanisms by which each subfamily contributes to the establishment or function of specific cell lineages are poorly understood. Here, we determined the contributions of the BAF, ncBAF, and PBAF complexes to myoblast proliferation via knock down (KD) of distinguishing subunits from each complex. KD of subunits unique to the BAF or the ncBAF complexes reduced myoblast proliferation rate, while KD of PBAF-specific subunits did not affect proliferation. RNA-seq from proliferating KD myoblasts targeting Baf250A (BAF complex), Brd9 (ncBAF complex), or Baf180 (PBAF complex) showed mis-regulation of a limited number of genes. KD of Baf250A specifically reduced the expression of Pax7, which is required for myoblast proliferation, concomitant with decreased binding of Baf250A to and impaired chromatin remodeling at the Pax7 gene promoter. Although Brd9 also bound to the Pax7 promoter, suggesting occupancy by the ncBAF complex, no changes were detected in Pax7 gene expression, Pax7 protein expression or chromatin remodeling at the Pax7 promoter upon Brd9 KD. The data indicate that the BAF subfamily of the mSWI/SNF enzymes is specifically required for myoblast proliferation via regulation of Pax7 expression.
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10
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Yang Y, Wang H, Zhao H, Miao X, Guo Y, Zhuo L, Xu Y. A GSK3-SRF Axis Mediates Angiotensin II Induced Endothelin Transcription in Vascular Endothelial Cells. Front Cell Dev Biol 2021; 9:698254. [PMID: 34381779 PMCID: PMC8350349 DOI: 10.3389/fcell.2021.698254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Endothelin, encoded by ET1, is a vasoactive substance primarily synthesized in vascular endothelial cells (VECs). Elevation of endothelin levels, due to transcriptional hyperactivation, has been observed in a host of cardiovascular diseases. We have previously shown that serum response factor (SRF) is a regulator of ET1 transcription in VECs. Here we report that angiotensin II (Ang II) induced ET1 transcription paralleled activation of glycogen synthase kinase 3 (GSK3) in cultured VECs. GSK3 knockdown or pharmaceutical inhibition attenuated Ang II induced endothelin expression. Of interest, the effect of GSK3 on endothelin transcription relied on the conserved SRF motif within the ET1 promoter. Further analysis revealed that GSK3 interacted with and phosphorylated SRF at serine 224. Phosphorylation of SRF by GSK3 did not influence its recruitment to the ET1 promoter. Instead, GSK3-mediated SRF phosphorylation potentiated its interaction with MRTF-A, a key co-factor for SRF, which helped recruit the chromatin remodeling protein BRG1 to the ET1 promoter resulting in augmented histone H3 acetylation/H3K4 trimethylation. Consistently, over-expression of a constitutively active GSK enhanced Ang II-induced ET1 transcription and knockdown of either MRTF-A or BRG1 abrogated the enhancement of ET1 transcription. In conclusion, our data highlight a previously unrecognized mechanism that contributes to the transcriptional regulation of endothelin. Targeting this GSK3-SRF axis may yield novel approaches in the intervention of cardiovascular diseases.
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Affiliation(s)
- Yuyu Yang
- Jiangsu Key Laboratory for Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Huidi Wang
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Hongwei Zhao
- Jiangsu Key Laboratory for Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiulian Miao
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China.,College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Yan Guo
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China.,College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Lili Zhuo
- Department of Geriatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Xu
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China.,Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
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11
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Sharma T, Robinson DCL, Witwicka H, Dilworth FJ, Imbalzano AN. The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation. Nucleic Acids Res 2021; 49:8060-8077. [PMID: 34289068 PMCID: PMC8373147 DOI: 10.1093/nar/gkab617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/17/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.
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Affiliation(s)
- Tapan Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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12
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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13
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Kimura A, Arakawa N, Kagawa H, Kimura Y, Hirano H. Phosphorylation of Ser1452 on BRG1 inhibits the function of the SWI/SNF complex in chromatin activation. J Proteomics 2021; 247:104319. [PMID: 34237461 DOI: 10.1016/j.jprot.2021.104319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
BRG1, one of core subunits of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancers. Previously, we reported significant downregulation of the phosphorylation level of BRG1 on Ser1452 (<10%) in cell lines derived from ovarian clear cell carcinoma with frequent recurrence and acquired drug resistance. In this study, we tried to elucidate the roles of BRG1 phosphorylation, using cell lines expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable (brg1-S1452A) BRG1. Quantitative proteomic analyses revealed upregulation of proteins and phosphoproteins related to linker histone H1s, histone methylation, and protein ubiquitylation in brg1-S1452D cells, which may coordinately promote the chromatin inactivation and ubiquitin-dependent degradation of target proteins. Consistent with these results, brg1-S1452D cells exhibited an increase in condensed chromatin and polyubiquitylated proteins. In brg1-S1452D cells, we also detected downregulation of various cancer-related proteins (e.g., EGFR and MET) as well as decreased migration, proliferation, and sensitivity to taxanes and oxaliplatin. Together, our results reveal that BRG1 phosphorylation drives tumor malignancy by inhibiting the functions of SWI/SNF complex in chromatin activation, thereby promoting expression of various cancer-related proteins. SIGNIFICANCE: For the first time we demonstrated that the mutation on Ser1452 phosphorylation site of BRG1, a component of SWI/SNF chromatin remodeling complex, changed protein and phosphoprotein levels of linker histone H1s, binding competitor of histone H1s, and histone methylase/demethylase involved in the heterochromatic histone modifications to promote the chromatin inactivation. In phosphorylation-mimic mutant, significant decrease of various cancer-related proteins as well as migration, proliferation, and sensitivity to specific antitumor agents were detected. Our results reveal that BRG1 phosphorylation drives tumor malignancy by inhibiting the functions of SWI/SNF complex in chromatin activation, thereby promoting expression of various cancer-related proteins.
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Affiliation(s)
- Ayuko Kimura
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Science, Gunma Paz University, Tonyamachi 1-7-1, Takasaki City, Gunma 370-0006, Japan.
| | - Noriaki Arakawa
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Tonomachi 3-25-26, Kawasaki-ku, Kawasaki City, Kanagawa 210-9501, Japan
| | - Hiroyuki Kagawa
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Science, Gunma Paz University, Tonyamachi 1-7-1, Takasaki City, Gunma 370-0006, Japan
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14
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Massenet J, Gardner E, Chazaud B, Dilworth FJ. Epigenetic regulation of satellite cell fate during skeletal muscle regeneration. Skelet Muscle 2021; 11:4. [PMID: 33431060 PMCID: PMC7798257 DOI: 10.1186/s13395-020-00259-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
In response to muscle injury, muscle stem cells integrate environmental cues in the damaged tissue to mediate regeneration. These environmental cues are tightly regulated to ensure expansion of muscle stem cell population to repair the damaged myofibers while allowing repopulation of the stem cell niche. These changes in muscle stem cell fate result from changes in gene expression that occur in response to cell signaling from the muscle environment. Integration of signals from the muscle environment leads to changes in gene expression through epigenetic mechanisms. Such mechanisms, including post-translational modification of chromatin and nucleosome repositioning, act to make specific gene loci more, or less, accessible to the transcriptional machinery. In youth, the muscle environment is ideally structured to allow for coordinated signaling that mediates efficient regeneration. Both age and disease alter the muscle environment such that the signaling pathways that shape the healthy muscle stem cell epigenome are altered. Altered epigenome reduces the efficiency of cell fate transitions required for muscle repair and contributes to muscle pathology. However, the reversible nature of epigenetic changes holds out potential for restoring cell fate potential to improve muscle repair in myopathies. In this review, we will describe the current knowledge of the mechanisms allowing muscle stem cell fate transitions during regeneration and how it is altered in muscle disease. In addition, we provide some examples of how epigenetics could be harnessed therapeutically to improve regeneration in various muscle pathologies.
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Affiliation(s)
- Jimmy Massenet
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.,Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS 5310, INSERM U1217, 8 Rockefeller Ave, 69008, Lyon, France
| | - Edward Gardner
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS 5310, INSERM U1217, 8 Rockefeller Ave, 69008, Lyon, France
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada. .,LIFE Research Institute, University of Ottawa, Ottawa, ON, K1H 8L6, Canada.
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15
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The Role of BRG1 in Antioxidant and Redox Signaling. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6095673. [PMID: 33014273 PMCID: PMC7512085 DOI: 10.1155/2020/6095673] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/13/2020] [Accepted: 09/01/2020] [Indexed: 12/15/2022]
Abstract
Redox homeostasis is regulated by critical molecules that modulate antioxidant and redox signaling (ARS) within the cell. Imbalances among these molecules can lead to oxidative stress and damage to cell functions, causing a variety of diseases. Brahma-related gene 1 (BRG1), also known as SMARCA4, is the central ATPase catalytic subunit of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a core role in DNA replication, repair, recombination, and transcriptional regulation. Numerous recent studies show that BRG1 is involved in the regulation of various cellular processes associated with ARS. BRG1, as a major factor in chromatin remodeling, is essential for the repair of oxidative stress-induced DNA damage and the activation of antioxidant genes under oxidative stress. Consequently, a comprehensive understanding of the roles of BRG1 in redox homeostasis is crucial to understand the normal functioning as well as pathological mechanisms. In this review, we summarized and discussed the role of BRG1 in the regulation of ARS.
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16
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Buljan M, Ciuffa R, van Drogen A, Vichalkovski A, Mehnert M, Rosenberger G, Lee S, Varjosalo M, Pernas LE, Spegg V, Snijder B, Aebersold R, Gstaiger M. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. Mol Cell 2020; 79:504-520.e9. [PMID: 32707033 PMCID: PMC7427327 DOI: 10.1016/j.molcel.2020.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/14/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022]
Abstract
Protein kinases are essential for signal transduction and control of most cellular processes, including metabolism, membrane transport, motility, and cell cycle. Despite the critical role of kinases in cells and their strong association with diseases, good coverage of their interactions is available for only a fraction of the 535 human kinases. Here, we present a comprehensive mass-spectrometry-based analysis of a human kinase interaction network covering more than 300 kinases. The interaction dataset is a high-quality resource with more than 5,000 previously unreported interactions. We extensively characterized the obtained network and were able to identify previously described, as well as predict new, kinase functional associations, including those of the less well-studied kinases PIM3 and protein O-mannose kinase (POMK). Importantly, the presented interaction map is a valuable resource for assisting biomedical studies. We uncover dozens of kinase-disease associations spanning from genetic disorders to complex diseases, including cancer.
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Affiliation(s)
- Marija Buljan
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland
| | - Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - George Rosenberger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Columbia University Department of Systems Biology, New York, NY 10032, USA
| | - Sohyon Lee
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lucia Espona Pernas
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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17
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Regulation of the Mammalian SWI/SNF Family of Chromatin Remodeling Enzymes by Phosphorylation during Myogenesis. BIOLOGY 2020; 9:biology9070152. [PMID: 32635263 PMCID: PMC7407365 DOI: 10.3390/biology9070152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
Abstract
Myogenesis is the biological process by which skeletal muscle tissue forms. Regulation of myogenesis involves a variety of conventional, epigenetic, and epigenomic mechanisms that control chromatin remodeling, DNA methylation, histone modification, and activation of transcription factors. Chromatin remodeling enzymes utilize ATP hydrolysis to alter nucleosome structure and/or positioning. The mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) family of chromatin remodeling enzymes is essential for myogenesis. Here we review diverse and novel mechanisms of regulation of mSWI/SNF enzymes by kinases and phosphatases. The integration of classic signaling pathways with chromatin remodeling enzyme function impacts myoblast viability and proliferation as well as differentiation. Regulated processes include the assembly of the mSWI/SNF enzyme complex, choice of subunits to be incorporated into the complex, and sub-nuclear localization of enzyme subunits. Together these processes influence the chromatin remodeling and gene expression events that control myoblast function and the induction of tissue-specific genes during differentiation.
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18
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Hashemolhosseini S. The role of protein kinase CK2 in skeletal muscle: Myogenesis, neuromuscular junctions, and rhabdomyosarcoma. Neurosci Lett 2020; 729:135001. [DOI: 10.1016/j.neulet.2020.135001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 01/08/2023]
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19
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Padilla-Benavides T, Haokip DT, Yoon Y, Reyes-Gutierrez P, Rivera-Pérez JA, Imbalzano AN. CK2-Dependent Phosphorylation of the Brg1 Chromatin Remodeling Enzyme Occurs during Mitosis. Int J Mol Sci 2020; 21:ijms21030923. [PMID: 32019271 PMCID: PMC7036769 DOI: 10.3390/ijms21030923] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 11/16/2022] Open
Abstract
Brg1 (Brahma-related gene 1) is one of two mutually exclusive ATPases that can act as the catalytic subunit of mammalian SWI/SNF (mSWI/SfigureNF) chromatin remodeling enzymes that facilitate utilization of the DNA in eukaryotic cells. Brg1 is a phospho-protein, and its activity is regulated by specific kinases and phosphatases. Previously, we showed that Brg1 interacts with and is phosphorylated by casein kinase 2 (CK2) in a manner that regulates myoblast proliferation. Here, we use biochemical and cell and molecular biology approaches to demonstrate that the Brg1-CK2 interaction occurred during mitosis in embryonic mouse somites and in primary myoblasts derived from satellite cells isolated from mouse skeletal muscle tissue. The interaction of CK2 with Brg1 and the incorporation of a number of other subunits into the mSWI/SNF enzyme complex were independent of CK2 enzymatic activity. CK2-mediated hyperphosphorylation of Brg1 was observed in mitotic cells derived from multiple cell types and organisms, suggesting functional conservation across tissues and species. The mitotically hyperphosphorylated form of Brg1 was localized with soluble chromatin, demonstrating that CK2-mediated phosphorylation of Brg1 is associated with specific partitioning of Brg1 within subcellular compartments. Thus, CK2 acts as a mitotic kinase that regulates Brg1 phosphorylation and subcellular localization.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; (T.P.-B.); (D.T.H.); (P.R.-G.)
| | - Dominic T. Haokip
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; (T.P.-B.); (D.T.H.); (P.R.-G.)
| | - Yeonsoo Yoon
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical School, Worcester, MA 01655, USA; (Y.Y.); (J.A.R.-P.)
| | - Pablo Reyes-Gutierrez
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; (T.P.-B.); (D.T.H.); (P.R.-G.)
| | - Jaime A. Rivera-Pérez
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical School, Worcester, MA 01655, USA; (Y.Y.); (J.A.R.-P.)
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; (T.P.-B.); (D.T.H.); (P.R.-G.)
- Correspondence: ; Tel.: +1-508-856-1029
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20
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Tavera-Montañez C, Hainer SJ, Cangussu D, Gordon SJV, Xiao Y, Reyes-Gutierrez P, Imbalzano AN, Navea JG, Fazzio TG, Padilla-Benavides T. The classic metal-sensing transcription factor MTF1 promotes myogenesis in response to copper. FASEB J 2019; 33:14556-14574. [PMID: 31690123 PMCID: PMC6894080 DOI: 10.1096/fj.201901606r] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022]
Abstract
Metal-regulatory transcription factor 1 (MTF1) is a conserved metal-binding transcription factor in eukaryotes that binds to conserved DNA sequence motifs, termed metal response elements. MTF1 responds to both metal excess and deprivation, protects cells from oxidative and hypoxic stresses, and is required for embryonic development in vertebrates. To examine the role for MTF1 in cell differentiation, we use multiple experimental strategies [including gene knockdown (KD) mediated by small hairpin RNA and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9), immunofluorescence, chromatin immunopreciptation sequencing, subcellular fractionation, and atomic absorbance spectroscopy] and report a previously unappreciated role for MTF1 and copper (Cu) in cell differentiation. Upon initiation of myogenesis from primary myoblasts, both MTF1 expression and nuclear localization increased. Mtf1 KD impaired differentiation, whereas addition of nontoxic concentrations of Cu+-enhanced MTF1 expression and promoted myogenesis. Furthermore, we observed that Cu+ binds stoichiometrically to a C terminus tetra-cysteine of MTF1. MTF1 bound to chromatin at the promoter regions of myogenic genes, and Cu addition stimulated this binding. Of note, MTF1 formed a complex with myogenic differentiation (MYOD)1, the master transcriptional regulator of the myogenic lineage, at myogenic promoters. These findings uncover unexpected mechanisms by which Cu and MTF1 regulate gene expression during myoblast differentiation.-Tavera-Montañez, C., Hainer, S. J., Cangussu, D., Gordon, S. J. V., Xiao, Y., Reyes-Gutierrez, P., Imbalzano, A. N., Navea, J. G., Fazzio, T. G., Padilla-Benavides, T. The classic metal-sensing transcription factor MTF1 promotes myogenesis in response to copper.
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Affiliation(s)
- Cristina Tavera-Montañez
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Sarah J. Hainer
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA; and
| | - Daniella Cangussu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Shellaina J. V. Gordon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yao Xiao
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, USA
| | - Pablo Reyes-Gutierrez
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Juan G. Navea
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, USA
| | - Thomas G. Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA; and
| | - Teresita Padilla-Benavides
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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21
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Salizzato V, Zanin S, Borgo C, Lidron E, Salvi M, Rizzuto R, Pallafacchina G, Donella-Deana A. Protein kinase CK2 subunits exert specific and coordinated functions in skeletal muscle differentiation and fusogenic activity. FASEB J 2019; 33:10648-10667. [PMID: 31268746 PMCID: PMC6766657 DOI: 10.1096/fj.201801833rr] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 06/04/2019] [Indexed: 01/01/2023]
Abstract
Casein kinase 2 (CK2) is a tetrameric protein kinase composed of 2 catalytic (α and α') and 2 regulatory β subunits. Our study provides the first molecular and cellular characterization of the different CK2 subunits, highlighting their individual roles in skeletal muscle specification and differentiation. Analysis of C2C12 cell knockout for each CK2 subunit reveals that: 1) CK2β is mandatory for the expression of the muscle master regulator myogenic differentiation 1 in proliferating myoblasts, thus controlling both myogenic commitment and subsequent muscle-specific gene expression and myotube formation; 2) CK2α is involved in the activation of the muscle-specific gene program; and 3) CK2α' activity regulates myoblast fusion by mediating plasma membrane translocation of fusogenic proteins essential for membrane coalescence, like myomixer. Accordingly, CK2α' overexpression in C2C12 cells and in mouse regenerating muscle is sufficient to increase myofiber size and myonuclei content via enhanced satellite cell fusion. Consistent with these results, pharmacological inhibition of CK2 activity substantially blocks the expression of myogenic markers and muscle cell fusion both in vitro in C2C12 and primary myoblasts and in vivo in mouse regenerating muscle and zebrafish development. Overall, our work describes the specific and coordinated functions of CK2 subunits in orchestrating muscle differentiation and fusogenic activity, highlighting CK2 relevance in the physiopathology of skeletal muscle tissue.-Salizzato, V., Zanin, S., Borgo, C., Lidron, E., Salvi, M., Rizzuto, R., Pallafacchina, G., Donella-Deana, A. Protein kinase CK2 subunits exert specific and coordinated functions in skeletal muscle differentiation and fusogenic activity.
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Affiliation(s)
- Valentina Salizzato
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Italian National Research Council (CNR) Neuroscience Institute, Padua, Italy
| | - Sofia Zanin
- Department of Medicine, University of Padua, Padua, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Elisa Lidron
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Giorgia Pallafacchina
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Italian National Research Council (CNR) Neuroscience Institute, Padua, Italy
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22
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Ho PJ, Lloyd SM, Bao X. Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Development 2019; 146:146/19/dev178780. [PMID: 31570369 DOI: 10.1242/dev.178780] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The BAF (SWI/SNF) chromatin remodeling complex plays a crucial role in modulating spatiotemporal gene expression during mammalian development. Although its remodeling activity was characterized in vitro decades ago, the complex actions of BAF in vivo have only recently begun to be unraveled. In living cells, BAF only binds to and remodels a subset of genomic locations. This selectivity of BAF genomic targeting is crucial for cell-type specification and for mediating precise responses to environmental signals. Here, we provide an overview of the distinct molecular mechanisms modulating BAF chromatin binding, including its combinatory assemblies, DNA/histone modification-binding modules and post-translational modifications, as well as its interactions with proteins, RNA and lipids. This Review aims to serve as a primer for future studies to decode the actions of BAF in developmental processes.
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Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA .,Department of Dermatology, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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23
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Calcineurin Broadly Regulates the Initiation of Skeletal Muscle-Specific Gene Expression by Binding Target Promoters and Facilitating the Interaction of the SWI/SNF Chromatin Remodeling Enzyme. Mol Cell Biol 2019; 39:MCB.00063-19. [PMID: 31308130 PMCID: PMC6751634 DOI: 10.1128/mcb.00063-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/08/2019] [Indexed: 12/22/2022] Open
Abstract
Calcineurin (Cn) is a calcium-activated serine/threonine protein phosphatase that is broadly implicated in diverse cellular processes, including the regulation of gene expression. During skeletal muscle differentiation, Cn activates the nuclear factor of activated T-cell (NFAT) transcription factor but also promotes differentiation by counteracting the negative influences of protein kinase C beta (PKCβ) via dephosphorylation and activation of Brg1, an enzymatic subunit of the mammalian SWI/SNF ATP-dependent chromatin remodeling enzyme. Here we identified four major temporal patterns of Cn-dependent gene expression in differentiating myoblasts and determined that Cn is broadly required for the activation of the myogenic gene expression program. Mechanistically, Cn promotes gene expression through direct binding to myogenic promoter sequences and facilitating the binding of Brg1, other SWI/SNF subunit proteins, and MyoD, a critical lineage determinant for skeletal muscle differentiation. We conclude that the Cn phosphatase directly impacts the expression of myogenic genes by promoting ATP-dependent chromatin remodeling and formation of transcription-competent promoters.
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24
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Sartorelli V, Puri PL. Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master. Mol Cell 2018; 71:375-388. [PMID: 29887393 DOI: 10.1016/j.molcel.2018.04.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/05/2018] [Accepted: 04/27/2018] [Indexed: 01/14/2023]
Abstract
Since its discovery as a skeletal muscle-specific transcription factor able to reprogram somatic cells into differentiated myofibers, MyoD has provided an instructive model to understand how transcription factors regulate gene expression. Reciprocally, studies of other transcriptional regulators have provided testable hypotheses to further understand how MyoD activates transcription. Using MyoD as a reference, in this review, we discuss the similarities and differences in the regulatory mechanisms employed by tissue-specific transcription factors to access DNA and regulate gene expression by cooperatively shaping the chromatin landscape within the context of cellular differentiation.
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Affiliation(s)
- Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA 92037, USA; Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, Rome, Italy.
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25
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Temporal regulation of chromatin during myoblast differentiation. Semin Cell Dev Biol 2017; 72:77-86. [PMID: 29079444 DOI: 10.1016/j.semcdb.2017.10.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/06/2017] [Accepted: 10/22/2017] [Indexed: 11/23/2022]
Abstract
The commitment to and execution of differentiation programmes involves a significant change in gene expression in the precursor cell to facilitate development of the mature cell type. In addition to being regulated by lineage-determining and auxiliary transcription factors that drive these changes, the structural status of the chromatin has a considerable impact on the transcriptional competence of differentiation-specific genes, which is clearly demonstrated by the large number of cofactors and the extraordinary complex mechanisms by which these genes become activated. The terminal differentiation of myoblasts to myotubes and mature skeletal muscle is an excellent system to illustrate these points. The MyoD family of closely related, lineage-determining transcription factors directs, largely through targeting to chromatin, a cascade of cooperating transcription factors and enzymes that incorporate or remove variant histones, post-translationally modify histones, and alter nucleosome structure and positioning via energy released by ATP hydrolysis. The coordinated action of these transcription factors and enzymes prevents expression of differentiation-specific genes in myoblasts and facilitates the transition of these genes from transcriptionally repressed to activated during the differentiation process. Regulation is achieved in both a temporal as well as spatial manner, as at least some of these factors and enzymes affect local chromatin structure at myogenic gene regulatory sequences as well as higher-order genome organization. Here we discuss the transition of genes that promote myoblast differentiation from the silenced to the activated state with an emphasis on the changes that occur to individual histones and the chromatin structure present at these loci.
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