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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Kalani L, Jorge-Torres OC, Esteller M, Ausio J, Abian O, Velazquez-Campoy A. Extending MeCP2 interactome: canonical nucleosomal histones interact with MeCP2. Nucleic Acids Res 2024; 52:3636-3653. [PMID: 38321951 DOI: 10.1093/nar/gkae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
MeCP2 is a general regulator of transcription involved in the repression/activation of genes depending on the local epigenetic context. It acts as a chromatin regulator and binds with exquisite specificity to gene promoters. The set of epigenetic marks recognized by MeCP2 has been already established (mainly, cytosine modifications in CpG and CpA), as well as many of the constituents of its interactome. We unveil a new set of interactions for MeCP2 with the four canonical nucleosomal histones. MeCP2 interacts with high affinity with H2A, H2B, H3 and H4. In addition, Rett syndrome associated mutations in MeCP2 and histone epigenetic marks modulate these interactions. Given the abundance and the structural/functional relevance of histones and their involvement in epigenetic regulation, this new set of interactions and its modulating elements provide a new addition to the 'alphabet' for this epigenetic reader.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | | | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Olga C Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907 l'Hospitalet de Llobregat, Barcelona, Spain
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
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Kalani L, Kim BH, Vincent JB, Ausió J. MeCP2 ubiquitination and sumoylation, in search of a function†. Hum Mol Genet 2023; 33:1-11. [PMID: 37694858 DOI: 10.1093/hmg/ddad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023] Open
Abstract
MeCP2 (Methyl CpG binding protein 2) is an intrinsically disordered protein that binds to methylated genome regions. The protein is a critical transcriptional regulator of the brain, and its mutations account for 95% of Rett syndrome (RTT) cases. Early studies of this neurodevelopmental disorder revealed a close connection with dysregulations of the ubiquitin system (UbS), notably as related to UBE3A, a ubiquitin ligase involved in the proteasome-mediated degradation of proteins. MeCP2 undergoes numerous post-translational modifications (PTMs), including ubiquitination and sumoylation, which, in addition to the potential functional outcomes of their monomeric forms in gene regulation and synaptic plasticity, in their polymeric organization, these modifications play a critical role in proteasomal degradation. UbS-mediated proteasomal degradation is crucial in maintaining MeCP2 homeostasis for proper function and is involved in decreasing MeCP2 in some RTT-causing mutations. However, regardless of all these connections to UbS, the molecular details involved in the signaling of MeCP2 for its targeting by the ubiquitin-proteasome system (UPS) and the functional roles of monomeric MeCP2 ubiquitination and sumoylation remain largely unexplored and are the focus of this review.
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Affiliation(s)
- Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, 27 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Influence of the disordered domain structure of MeCP2 on its structural stability and dsDNA interaction. Int J Biol Macromol 2021; 175:58-66. [PMID: 33548325 DOI: 10.1016/j.ijbiomac.2021.01.206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a transcriptional regulator and a chromatin-associated structural protein. MeCP2 deregulation results in two neurodevelopmental disorders: MeCP2 dysfunction is associated with Rett syndrome, while excess of activity is associated with MeCP2 duplication syndrome. MeCP2 is an intrinsically disordered protein (IDP) constituted by six structural domains with variable, small percentage of well-defined secondary structure. Two domains, methyl-CpG binding domain (MBD) and transcription repressor domain (TRD), are the elements responsible for dsDNA binding ability and recruitment of the gene transcription/silencing machinery, respectively. Previously we studied the influence of the completely disordered, MBD-flanking domains (N-terminal domain, NTD, and intervening domain, ID) on the structural and functional features of the MBD (Claveria-Gimeno, R. et al. Sci Rep. 2017, 7, 41,635). Here we report the biophysical study of the influence of the remaining domains (transcriptional repressor domain, TRD, and C-terminal domains, CTDα and CTDβ) on the structural stability of MBD and the dsDNA binding capabilities of MBD and ID. The influence of distant disordered domains on MBD properties makes it necessary to consider the NTD-MBD-ID variant as the minimal protein construct for studying dsDNA/chromatin binding properties, while the full-length protein should be considered for transcriptional regulation studies.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Olga C Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907, l'Hospitalet de Llobregat, Barcelona, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Fundación ARAID, Gobierno de Aragón, 50018 Zaragoza, Spain.
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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Molecular Context-Dependent Effects Induced by Rett Syndrome-Associated Mutations in MeCP2. Biomolecules 2020; 10:biom10111533. [PMID: 33182787 PMCID: PMC7696773 DOI: 10.3390/biom10111533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 01/21/2023] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a transcriptional regulator and a chromatin-binding protein involved in neuronal development and maturation. Loss-of-function mutations in MeCP2 result in Rett syndrome (RTT), a neurodevelopmental disorder that is the main cause of mental retardation in females. MeCP2 is an intrinsically disordered protein (IDP) constituted by six domains. Two domains are the main responsible elements for DNA binding (methyl-CpG binding domain, MBD) and recruitment of gene transcription/silencing machinery (transcription repressor domain, TRD). These two domains concentrate most of the RTT-associated mutations. R106W and R133C are associated with severe and mild RTT phenotype, respectively. We have performed a comprehensive characterization of the structural and functional impact of these substitutions at molecular level. Because we have previously shown that the MBD-flanking disordered domains (N-terminal domain, NTD, and intervening domain, ID) exert a considerable influence on the structural and functional features of the MBD (Claveria-Gimeno, R. et al. Sci Rep. 2017, 7, 41635), here we report the biophysical study of the influence of the protein scaffold on the structural and functional effect induced by these two RTT-associated mutations. These results represent an example of how a given mutation may show different effects (sometimes opposing effects) depending on the molecular context.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (R.C.-G.); (S.V.)
| | - Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (R.C.-G.); (S.V.)
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (R.C.-G.); (S.V.)
| | - Olga C. Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; (O.C.J.-T.); (M.E.)
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; (O.C.J.-T.); (M.E.)
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), l’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (R.C.-G.); (S.V.)
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Correspondence: (O.A.); (A.V.-C.); Tel.: +34-876-555-417 (O.A.); +34-976-762-996 (A.V.-C.)
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (R.C.-G.); (S.V.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundación ARAID, Gobierno de Aragón, 50009 Zaragoza, Spain
- Correspondence: (O.A.); (A.V.-C.); Tel.: +34-876-555-417 (O.A.); +34-976-762-996 (A.V.-C.)
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Good KV, Martínez de Paz A, Tyagi M, Cheema MS, Thambirajah AA, Gretzinger TL, Stefanelli G, Chow RL, Krupke O, Hendzel M, Missiaen K, Underhill A, Landsberger N, Ausió J. Trichostatin A decreases the levels of MeCP2 expression and phosphorylation and increases its chromatin binding affinity. Epigenetics 2017; 12:934-944. [PMID: 29099289 DOI: 10.1080/15592294.2017.1380760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
MeCP2 binds to methylated DNA in a chromatin context and has an important role in cancer and brain development and function. Histone deacetylase (HDAC) inhibitors are currently being used to palliate many cancer and neurological disorders. Yet, the molecular mechanisms involved are not well known for the most part and, in particular, the relationship between histone acetylation and MeCP2 is not well understood. In this paper, we study the effect of the HDAC inhibitor trichostatin A (TSA) on MeCP2, a protein whose dysregulation plays an important role in these diseases. We find that treatment of cells with TSA decreases the phosphorylation state of this protein and appears to result in a higher MeCP2 chromatin binding affinity. Yet, the binding dynamics with which the protein binds to DNA appear not to be significantly affected despite the chromatin reorganization resulting from the high levels of acetylation. HDAC inhibition also results in an overall decrease in MeCP2 levels of different cell lines. Moreover, we show that miR132 increases upon TSA treatment, and is one of the players involved in the observed downregulation of MeCP2.
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Affiliation(s)
- Katrina V Good
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Alexia Martínez de Paz
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Monica Tyagi
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Manjinder S Cheema
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Anita A Thambirajah
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada.,b Douglas Hospital Research Center , Department of Psychiatry , McGill University , Montréal , Québec H3G 1Y6 , Canada
| | - Taylor L Gretzinger
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Gilda Stefanelli
- c Department of Medical Biotechnology and Translational Medicine , University of Milan , Milan , Italy
| | - Robert L Chow
- d Department of Biology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Oliver Krupke
- d Department of Biology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
| | - Michael Hendzel
- e Department of Cell Biology , Faculty of Medicine and Dentistry , University of Alberta , Edmonton , Alberta , Canada.,f Department of Oncology and Department of Cell Biology , Faculty of Medicine and Dentistry , University of Alberta , Edmonton , Alberta , Canada
| | - Kristal Missiaen
- f Department of Oncology and Department of Cell Biology , Faculty of Medicine and Dentistry , University of Alberta , Edmonton , Alberta , Canada
| | - Alan Underhill
- f Department of Oncology and Department of Cell Biology , Faculty of Medicine and Dentistry , University of Alberta , Edmonton , Alberta , Canada
| | - Nicoletta Landsberger
- c Department of Medical Biotechnology and Translational Medicine , University of Milan , Milan , Italy
| | - Juan Ausió
- a Department of Biochemistry and Microbiology , University of Victoria , Victoria , BC , V8W 3P6 , Canada
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