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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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Pane R, Laib L, Formoso K, Détrait M, Sainte-Marie Y, Bourgailh F, Ruffenach N, Faugeras H, Simon I, Lhuillier E, Lezoualc'h F, Conte C. Macromolecular Complex Including MLL3, Carabin and Calcineurin Regulates Cardiac Remodeling. Circ Res 2024; 134:100-113. [PMID: 38084599 DOI: 10.1161/circresaha.123.323458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Cardiac hypertrophy is an intermediate stage in the development of heart failure. The structural and functional processes occurring in cardiac hypertrophy include extensive gene reprogramming, which is dependent on epigenetic regulation and chromatin remodeling. However, the chromatin remodelers and their regulatory functions involved in the pathogenesis of cardiac hypertrophy are not well characterized. METHODS Protein interaction was determined by immunoprecipitation assay in primary cardiomyocytes and mouse cardiac samples subjected or not to transverse aortic constriction for 1 week. Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) experiments were performed on the chromatin of adult mouse cardiomyocytes. RESULTS We report that the calcium-activated protein phosphatase CaN (calcineurin), its endogenous inhibitory protein carabin, the STK24 (STE20-like protein kinase 3), and the histone monomethyltransferase, MLL3 (mixed lineage leukemia 3) form altogether a macromolecular complex at the chromatin of cardiomyocytes. Under basal conditions, carabin prevents CaN activation while the serine/threonine kinase STK24 maintains MLL3 inactive via phosphorylation. After 1 week of transverse aortic constriction, both carabin and STK24 are released from the CaN-MLL3 complex leading to the activation of CaN, dephosphorylation of MLL3, and in turn, histone H3 lysine 4 monomethylation. Selective cardiac MLL3 knockdown mitigates hypertrophy, and chromatin immunoprecipitation and DNA sequencing analysis demonstrates that MLL3 is de novo recruited at the transcriptional start site of genes implicated in cardiomyopathy in stress conditions. We also show that CaN and MLL3 colocalize at chromatin and that CaN activates MLL3 histone methyl transferase activity at distal intergenic regions under hypertrophic conditions. CONCLUSIONS Our study reveals an unsuspected epigenetic mechanism of CaN that directly regulates MLL3 histone methyl transferase activity to promote cardiac remodeling.
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Affiliation(s)
- Roberto Pane
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Loubna Laib
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Karina Formoso
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Maximin Détrait
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Yannis Sainte-Marie
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Florence Bourgailh
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Nolan Ruffenach
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Hanamée Faugeras
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Ilias Simon
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Emeline Lhuillier
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
- GeT-Sante, Plateforme Genome et Transcriptome, GenoToul, Toulouse, France (E.L.)
| | - Frank Lezoualc'h
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Caroline Conte
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
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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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Sharma T, Olea-Flores M, Imbalzano AN. Regulation of the Wnt signaling pathway during myogenesis by the mammalian SWI/SNF ATPase BRG1. Front Cell Dev Biol 2023; 11:1160227. [PMID: 37484913 PMCID: PMC10360407 DOI: 10.3389/fcell.2023.1160227] [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: 02/06/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Skeletal muscle differentiation is a tightly regulated process, and the importance of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling family for regulation of genes involved in skeletal myogenesis is well-established. Our prior work showed that bromodomains of mSWI/SNF ATPases BRG1 and BRM contribute to myogenesis by facilitating the binding of mSWI/SNF enzymes to regulatory regions of myogenic and other target genes. Here, we report that pathway analyses of differentially expressed genes from that study identified an additional role for mSWI/SNF enzymes via the regulation of the Wnt signaling pathway. The Wnt pathway has been previously shown to be important for skeletal muscle development. To investigate the importance of mSWI/SNF enzymes for the regulation of the Wnt pathway, individual and dual knockdowns were performed for BRG1 and BRM followed by RNA-sequencing. The results show that BRG1, but not BRM, is a regulator of Wnt pathway components and downstream genes. Reactivation of Wnt pathway by stabilization of β-catenin could rescue the defect in myogenic gene expression and differentiation due to BRG1 knockdown or bromodomain inhibition using a specific small molecule inhibitor, PFI-3. These results demonstrate that BRG1 is required upstream of β-catenin function. Chromatin immunoprecipitation of BRG1, BRM and β-catenin at promoters of Wnt pathway component genes showed binding of BRG1 and β-catenin, which provides further mechanistic insight to the transcriptional regulation of these genes.
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Affiliation(s)
| | | | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, United States
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Syed SA, Shqillo K, Nand A, Zhan Y, Dekker J, Imbalzano AN. Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544859. [PMID: 37398486 PMCID: PMC10312757 DOI: 10.1101/2023.06.13.544859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.
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Affiliation(s)
- Sabriya A Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Kristina Shqillo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ankita Nand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ye Zhan
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Job Dekker
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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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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Lv F, Shao T, Xue Y, Miao X, Guo Y, Wang Y, Xu Y. Dual Regulation of Tank Binding Kinase 1 by BRG1 in Hepatocytes Contributes to Reactive Oxygen Species Production. Front Cell Dev Biol 2021; 9:745985. [PMID: 34660604 PMCID: PMC8517266 DOI: 10.3389/fcell.2021.745985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/15/2021] [Indexed: 01/14/2023] Open
Abstract
Excessive accumulation of reactive oxygen species (ROS) is considered a major culprit for the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We have previously shown that deletion of Brahma related gene 1 (BRG1) mitigated NAFLD in mice in part by attenuating ROS production in hepatocyte. Here we report that BRG1 deletion led to simultaneous down-regulation in expression and phosphorylation of tank binding kinase 1 (TBK1) in vivo and in vitro. On the one hand, BRG1 interacted with AP-1 to bind to the TBK1 promoter and directly activated TBK1 transcription in hepatocytes. On the other hand, BRG1 interacted with Sp1 to activate the transcription of c-SRC, a tyrosine kinase essential for TBK1 phosphorylation. Over-expression of c-SRC and TBK1 corrected the deficiency in ROS production in BRG1-null hepatocytes whereas depletion of TBK1 or c-SRC attenuated ROS production. In conclusion, our data suggest that dual regulation of TBK1 activity, at the transcription level and the post-transcriptional level, by BRG1 may constitute an important mechanism underlying excessive ROS production in hepatocytes.
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Affiliation(s)
- Fangqiao Lv
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Tinghui Shao
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yujia Xue
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiulian Miao
- College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yan Guo
- College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yutong Wang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, 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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Jia Z, Yue F, Chen X, Narayanan N, Qiu J, Syed SA, Imbalzano AN, Deng M, Yu P, Hu C, Kuang S. Protein Arginine Methyltransferase PRMT5 Regulates Fatty Acid Metabolism and Lipid Droplet Biogenesis in White Adipose Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002602. [PMID: 33304767 PMCID: PMC7709973 DOI: 10.1002/advs.202002602] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 02/06/2023]
Abstract
The protein arginine methyltransferase 5 (PRMT5) is an emerging regulator of cancer and stem cells including adipogenic progenitors. Here, a new physiological role of PRMT5 in adipocytes and systemic metabolism is reported. Conditional knockout mice were generated to ablate the Prmt5 gene specifically in adipocytes (Prmt5AKO). The Prmt5AKO mice exhibit sex- and depot-dependent progressive lipodystrophy that is more pronounced in females and in visceral (than subcutaneous) white fat. The lipodystrophy and associated energy imbalance, hyperlipidemia, hepatic steatosis, glucose intolerance, and insulin resistance are exacerbated by high-fat-diet. Mechanistically, Prmt5 methylates and releases the transcription elongation factor SPT5 from Berardinelli-Seip congenital lipodystrophy 2 (Bscl2, encoding Seipin) promoter, and Prmt5AKO disrupts Seipin-mediated lipid droplet biogenesis. Prmt5 also methylates Sterol Regulatory Element-Binding Transcription Factor 1a (SREBP1a) and promotes lipogenic gene expression, and Prmt5AKO suppresses SREBP1a-dependent fatty acid metabolic pathways in adipocytes. Thus, PRMT5 plays a critical role in regulating lipid metabolism and lipid droplet biogenesis in adipocytes.
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Affiliation(s)
- Zhihao Jia
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Feng Yue
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Xiyue Chen
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Naagarajan Narayanan
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIN47907USA
- Bindley Bioscience CenterPurdue UniversityWest LafayetteIN47907USA
| | - Jiamin Qiu
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMA01605USA
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMA01605USA
| | - Meng Deng
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIN47907USA
- Bindley Bioscience CenterPurdue UniversityWest LafayetteIN47907USA
| | - Peng Yu
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
- Medical Big Data CenterSichuan UniversityChengdu610041China
| | - Changdeng Hu
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue University Center for Cancer ResearchWest LafayetteIndiana47907USA
| | - Shihuan Kuang
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
- Purdue University Center for Cancer ResearchWest LafayetteIndiana47907USA
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13
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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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14
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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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15
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Mechanisms regulating myoblast fusion: A multilevel interplay. Semin Cell Dev Biol 2020; 104:81-92. [PMID: 32063453 DOI: 10.1016/j.semcdb.2020.02.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 02/07/2023]
Abstract
Myoblast fusion into myotubes is one of the crucial steps of skeletal muscle development (myogenesis). The fusion is preceded by specification of a myogenic lineage (mesodermal progenitors) differentiating into myoblasts and is followed by myofiber-type specification and neuromuscular junction formation. Similarly to other processes of myogenesis, the fusion requires a very precise spatial and temporal regulation occuring both during embryonic development as well as regeneration and repair of the muscle. A plethora of genes and their products is involved in regulation of myoblast fusion and a precise multilevel interplay between them is crucial for myogenic cells to fuse. In this review, we describe both cellular events taking place during myoblast fusion (migration, adhesion, elongation, cell-cell recognition, alignment, and fusion of myoblast membranes enabling formation of myotubes) as well as recent findings on mechanisms regulating this process. Also, we present muscle disorders in humans that have been associated with defects in genes involved in regulation of myoblast fusion.
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16
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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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