1
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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2
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Zhang X, Cattoglio C, Zoltek M, Vetralla C, Mozumdar D, Schepartz A. Dose-Dependent Nuclear Delivery and Transcriptional Repression with a Cell-Penetrant MeCP2. ACS CENTRAL SCIENCE 2023; 9:277-288. [PMID: 36844491 PMCID: PMC9951310 DOI: 10.1021/acscentsci.2c01226] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Indexed: 06/13/2023]
Abstract
The vast majority of biologic-based therapeutics operate within serum, on the cell surface, or within endocytic vesicles, in large part because proteins and nucleic acids fail to efficiently cross cell or endosomal membranes. The impact of biologic-based therapeutics would expand exponentially if proteins and nucleic acids could reliably evade endosomal degradation, escape endosomal vesicles, and remain functional. Using the cell-permeant mini-protein ZF5.3, here we report the efficient nuclear delivery of functional Methyl-CpG-binding-protein 2 (MeCP2), a transcriptional regulator whose mutation causes Rett syndrome (RTT). We report that ZF-tMeCP2, a conjugate of ZF5.3 and MeCP2(Δaa13-71, 313-484), binds DNA in a methylation-dependent manner in vitro, and reaches the nucleus of model cell lines intact to achieve an average concentration of 700 nM. When delivered to live cells, ZF-tMeCP2 engages the NCoR/SMRT corepressor complex, selectively represses transcription from methylated promoters, and colocalizes with heterochromatin in mouse primary cortical neurons. We also report that efficient nuclear delivery of ZF-tMeCP2 relies on an endosomal escape portal provided by HOPS-dependent endosomal fusion. The Tat conjugate of MeCP2 (Tat-tMeCP2), evaluated for comparison, is degraded within the nucleus, is not selective for methylated promoters, and trafficks in a HOPS-independent manner. These results support the feasibility of a HOPS-dependent portal for delivering functional macromolecules to the cell interior using the cell-penetrant mini-protein ZF5.3. Such a strategy could broaden the impact of multiple families of biologic-based therapeutics.
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Affiliation(s)
- Xizi Zhang
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Claudia Cattoglio
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
| | - Madeline Zoltek
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
| | - Carlo Vetralla
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
| | - Deepto Mozumdar
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alanna Schepartz
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
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3
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Shevkoplyas D, Vuu YM, Davie JR, Rastegar M. The Chromatin Structure at the MECP2 Gene and In Silico Prediction of Potential Coding and Non-Coding MECP2 Splice Variants. Int J Mol Sci 2022; 23:ijms232415643. [PMID: 36555295 PMCID: PMC9779294 DOI: 10.3390/ijms232415643] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) is an epigenetic reader that binds to methylated CpG dinucleotides and regulates gene transcription. Mecp2/MECP2 gene has 4 exons, encoding for protein isoforms MeCP2E1 and MeCP2E2. MeCP2 plays key roles in neurodevelopment, therefore, its gain- and loss-of-function mutations lead to neurodevelopmental disorders including Rett Syndrome. Here, we describe the structure, functional domains, and evidence support for potential additional alternatively spliced MECP2 transcripts and protein isoforms. We conclude that NCBI MeCP2 isoforms 3 and 4 contain certain MeCP2 functional domains. Our in silico analysis led to identification of histone modification and accessibility profiles at the MECP2 gene and its cis-regulatory elements. We conclude that the human MECP2 gene associated histone post-translational modifications exhibit high similarity between males and females. Between brain regions, histone modifications were found to be less conserved and enriched within larger genomic segments named as "S1-S11". We also identified highly conserved DNA accessibility regions in different tissues and brain regions, named as "A1-A9" and "B1-B9". DNA methylation profile was similar between mid-frontal gyrus of donors 35 days-25 years of age. Based on ATAC-seq data, the identified hypomethylated regions "H1-H8" intersected with most regions of the accessible chromatin (A regions).
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4
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Schmidt A, Frei J, Poetsch A, Chittka A, Zhang H, Aßmann C, Lehmkuhl A, Bauer UM, Nuber UA, Cardoso MC. MeCP2 heterochromatin organization is modulated by arginine methylation and serine phosphorylation. Front Cell Dev Biol 2022; 10:941493. [PMID: 36172281 PMCID: PMC9510713 DOI: 10.3389/fcell.2022.941493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Rett syndrome is a human intellectual disability disorder that is associated with mutations in the X-linked MECP2 gene. The epigenetic reader MeCP2 binds to methylated cytosines on the DNA and regulates chromatin organization. We have shown previously that MECP2 Rett syndrome missense mutations are impaired in chromatin binding and heterochromatin reorganization. Here, we performed a proteomics analysis of post-translational modifications of MeCP2 isolated from adult mouse brain. We show that MeCP2 carries various post-translational modifications, among them phosphorylation on S80 and S421, which lead to minor changes in either heterochromatin binding kinetics or clustering. We found that MeCP2 is (di)methylated on several arginines and that this modification alters heterochromatin organization. Interestingly, we identified the Rett syndrome mutation site R106 as a dimethylation site. In addition, co-expression of protein arginine methyltransferases (PRMT)1 and PRMT6 lead to a decrease of heterochromatin clustering. Altogether, we identified and validated novel modifications of MeCP2 in the brain and show that these can modulate its ability to bind as well as reorganize heterochromatin, which may play a role in the pathology of Rett syndrome.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jana Frei
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang, China
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Alexandra Chittka
- Division of Medicine, The Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Chris Aßmann
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
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5
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MeCP2 and transcriptional control of eukaryotic gene expression. Eur J Cell Biol 2022; 101:151237. [DOI: 10.1016/j.ejcb.2022.151237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
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6
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Zhang H, Romero H, Schmidt A, Gagova K, Qin W, Bertulat B, Lehmkuhl A, Milden M, Eck M, Meckel T, Leonhardt H, Cardoso MC. MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation. Nucleus 2022; 13:1-34. [PMID: 35156529 PMCID: PMC8855868 DOI: 10.1080/19491034.2021.2024691] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Hui Zhang
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Hector Romero
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Annika Schmidt
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Katalina Gagova
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Bianca Bertulat
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Manuela Milden
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Malte Eck
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Tobias Meckel
- Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
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7
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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8
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Chávez-García C, Hénin J, Karttunen M. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. J Chem Inf Model 2022; 62:958-970. [PMID: 35130441 DOI: 10.1021/acs.jcim.1c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The malfunction of the methyl-CpG binding protein 2 (MeCP2) is associated with the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the databases, and only the structure of its MBD domain has been solved. We used this structure to build a full-length model of MeCP2 by completing the rest of the protein via ab initio modeling. Using a combination of all-atom and coarse-grained simulations, we characterized its structure and dynamics as well as the conformational space sampled by the ID and transcriptional repression domain (TRD) domains in the absence of the rest of the protein. The present work is the first computational study of the full-length protein. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. Our all-atom model is in good agreement with the available experimental data, predicting amino acid W104 to be buried, amino acids R111 and R133 to be solvent-accessible, and having a 4.1% α-helix content, compared to the 4% found experimentally. Finally, we compared the model predicted by AlphaFold to our Modeller model. The model was not stable in water and underwent further folding. Together, these simulations provide a detailed (if perhaps incomplete) conformational ensemble of the full-length MeCP2, which is compatible with experimental data and can be the basis of further studies, e.g., on mutants of the protein or its interactions with its biological partners.
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Affiliation(s)
- Cecilia Chávez-García
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique UPR 9080, CNRS and Université de Paris, Paris 75005, France
| | - Mikko Karttunen
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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9
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Shukla S, Agarwal P, Kumar A. Disordered regions tune order in chromatin organization and function. Biophys Chem 2022; 281:106716. [PMID: 34844028 DOI: 10.1016/j.bpc.2021.106716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered regions (both collectively designated as IDP(R)s) defy the well-established structure-function paradigm due to their ability to perform multiple biological functions even in the absence of a well-defined 3D structure. IDP(R)s have a unique ability to exist as a functional heterogeneous ensemble, where they adopt multiple thermodynamically stable conformations with low energy barriers between states. The resultant structural plasticity or conformational adaptability provides them with a high functional diversity and ease of regulation. Hence, IDP(R)s are highly efficient biological machinery to mediate intricate cellular functions such as signaling, gene expression, and assembly of complex structures. One such structure is the nucleoprotein complex known as Chromatin. Interestingly, the proteins involved in shaping up the structure and function of chromatin are abundant in disordered regions, which serve more than just as mere flexible linkers. The disordered regions are involved in crucial processes such as gene expression regulation, chromatin architecture maintenance, and liquid-liquid phase separation initiation. This review is an attempt to explore the advantages and the functional and regulatory roles of intrinsic disorder in several Chromatin Associated Proteins from a mechanistic standpoint.
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Affiliation(s)
- Shivangi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Prakhar Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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10
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Collins BE, Neul JL. Rett Syndrome and MECP2 Duplication Syndrome: Disorders of MeCP2 Dosage. Neuropsychiatr Dis Treat 2022; 18:2813-2835. [PMID: 36471747 PMCID: PMC9719276 DOI: 10.2147/ndt.s371483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder caused predominantly by loss-of-function mutations in the gene Methyl-CpG-binding protein 2 (MECP2), which encodes the MeCP2 protein. RTT is a MECP2-related disorder, along with MECP2 duplication syndrome (MDS), caused by gain-of-function duplications of MECP2. Nearly two decades of research have advanced our knowledge of MeCP2 function in health and disease. The following review will discuss MeCP2 protein function and its dysregulation in the MECP2-related disorders RTT and MDS. This will include a discussion of the genetic underpinnings of these disorders, specifically how sporadic X-chromosome mutations arise and manifest in specific populations. We will then review current diagnostic guidelines and clinical manifestations of RTT and MDS. Next, we will delve into MeCP2 biology, describing the dual landscapes of methylated DNA and its reader MeCP2 across the neuronal genome as well as the function of MeCP2 as a transcriptional modulator. Following this, we will outline common MECP2 mutations and genotype-phenotype correlations in both diseases, with particular focus on mutations associated with relatively mild disease in RTT. We will also summarize decades of disease modeling and resulting molecular, synaptic, and behavioral phenotypes associated with RTT and MDS. Finally, we list several therapeutics in the development pipeline for RTT and MDS and available evidence of their safety and efficacy.
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Affiliation(s)
- Bridget E Collins
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey L Neul
- Vanderbilt Kennedy Center, Departments of Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center and Vanderbilt University, Nashville, TN, USA
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11
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Jiang Y, Fu X, Zhang Y, Wang SF, Zhu H, Wang WK, Zhang L, Wu P, Wong CCL, Li J, Ma J, Guan JS, Huang Y, Hui J. Rett syndrome linked to defects in forming the MeCP2/Rbfox/LASR complex in mouse models. Nat Commun 2021; 12:5767. [PMID: 34599184 PMCID: PMC8486766 DOI: 10.1038/s41467-021-26084-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/13/2021] [Indexed: 01/01/2023] Open
Abstract
Rett syndrome (RTT) is a severe neurological disorder and a leading cause of intellectual disability in young females. RTT is mainly caused by mutations found in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Despite extensive studies, the molecular mechanism underlying RTT pathogenesis is still poorly understood. Here, we report MeCP2 as a key subunit of a higher-order multiunit protein complex Rbfox/LASR. Defective MeCP2 in RTT mouse models disrupts the assembly of the MeCP2/Rbfox/LASR complex, leading to reduced binding of Rbfox proteins to target pre-mRNAs and aberrant splicing of Nrxns and Nlgn1 critical for synaptic plasticity. We further show that MeCP2 disease mutants display defective condensate properties and fail to promote phase-separated condensates with Rbfox proteins in vitro and in cultured cells. These data link an impaired function of MeCP2 with disease mutation in splicing control to its defective properties in mediating the higher-order assembly of the MeCP2/Rbfox/LASR complex. MeCP2 mutations can cause Rett syndrome, a severe childhood neurological disorder. Here the authors show that MeCP2 mediates the higher-order assembly of a large splicing complex Rbfox/LASR, which is disrupted in the mouse models of Rett syndrome.
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Affiliation(s)
- Yan Jiang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 201602, Shanghai, China
| | - Yuhan Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, 200092, Shanghai, China
| | - Shen-Fei Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Hong Zhu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Wei-Kang Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Lin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Catherine C L Wong
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China.,Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, School of Basic Medical Sciences, Peking University, 100191, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, 200092, Shanghai, China.
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.
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12
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Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2. Biomolecules 2021; 11:biom11081216. [PMID: 34439881 PMCID: PMC8391517 DOI: 10.3390/biom11081216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/04/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
Intrinsic disorder plays an important functional role in proteins. Disordered regions are linked to posttranslational modifications, conformational switching, extra/intracellular trafficking, and allosteric control, among other phenomena. Disorder provides proteins with enhanced plasticity, resulting in a dynamic protein conformational/functional landscape, with well-structured and disordered regions displaying reciprocal, interdependent features. Although lacking well-defined conformation, disordered regions may affect the intrinsic stability and functional properties of ordered regions. MeCP2, methyl-CpG binding protein 2, is a multifunctional transcriptional regulator associated with neuronal development and maturation. MeCP2 multidomain structure makes it a prototype for multidomain, multifunctional, intrinsically disordered proteins (IDP). The methyl-binding domain (MBD) is one of the key domains in MeCP2, responsible for DNA recognition. It has been reported previously that the two disordered domains flanking MBD, the N-terminal domain (NTD) and the intervening domain (ID), increase the intrinsic stability of MBD against thermal denaturation. In order to prove unequivocally this stabilization effect, ruling out any artifactual result from monitoring the unfolding MBD with a local fluorescence probe (the single tryptophan in MBD) or from driving the protein unfolding by temperature, we have studied the MBD stability by differential scanning calorimetry (reporting on the global unfolding process) and chemical denaturation (altering intramolecular interactions by a different mechanism compared to thermal denaturation).
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13
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Ibrahim A, Papin C, Mohideen-Abdul K, Le Gras S, Stoll I, Bronner C, Dimitrov S, Klaholz BP, Hamiche A. MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion. Science 2021; 372:372/6549/eabd5581. [PMID: 34324427 DOI: 10.1126/science.abd5581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.
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Affiliation(s)
- Abdulkhaleg Ibrahim
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Biotechnology Research Center (BTRC), 30303 Tripoli, Libya
| | - Christophe Papin
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Kareem Mohideen-Abdul
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France
| | - Stéphanie Le Gras
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Isabelle Stoll
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Christian Bronner
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France. .,Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Bruno P Klaholz
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France. .,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Center of Excellence in Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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14
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Transcriptomic and Epigenomic Landscape in Rett Syndrome. Biomolecules 2021; 11:biom11070967. [PMID: 34209228 PMCID: PMC8301932 DOI: 10.3390/biom11070967] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Rett syndrome (RTT) is an extremely invalidating, cureless, developmental disorder, and it is considered one of the leading causes of intellectual disability in female individuals. The vast majority of RTT cases are caused by de novo mutations in the X-linked Methyl-CpG binding protein 2 (MECP2) gene, which encodes a multifunctional reader of methylated DNA. MeCP2 is a master epigenetic modulator of gene expression, with a role in the organization of global chromatin architecture. Based on its interaction with multiple molecular partners and the diverse epigenetic scenario, MeCP2 triggers several downstream mechanisms, also influencing the epigenetic context, and thus leading to transcriptional activation or repression. In this frame, it is conceivable that defects in such a multifaceted factor as MeCP2 lead to large-scale alterations of the epigenome, ranging from an unbalanced deposition of epigenetic modifications to a transcriptional alteration of both protein-coding and non-coding genes, with critical consequences on multiple downstream biological processes. In this review, we provide an overview of the current knowledge concerning the transcriptomic and epigenomic alterations found in RTT patients and animal models.
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15
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Wang S, Gan M, Chen C, Zhang Y, Kong J, Zhang H, Lai M. Methyl CpG binding protein 2 promotes colorectal cancer metastasis by regulating N 6 -methyladenosine methylation through methyltransferase-like 14. Cancer Sci 2021; 112:3243-3254. [PMID: 34097350 PMCID: PMC8353896 DOI: 10.1111/cas.15011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022] Open
Abstract
RNA N6‐methyladenosine (m6A) is an emerging regulatory mechanism for tumor progression in several types of cancer. However, the underlying regulation mechanisms of m6A methylation in colorectal cancer (CRC) remain unknown. Although the oncogenic function of methyl CpG binding protein 2 (MeCP2) has been reported, it is still unclear whether MeCP2 could alter RNA m6A methylation state. Here, we systematically identified MeCP2 as a prometastasis gene to regulate m6A methylation in CRC. Interestingly, MeCP2 could bind to methyltransferase‐like 14 (METTL14) to coregulate tumor suppressor Kruppel‐like factor 4 (KLF4) expression through changing m6A methylation modification. Furthermore, insulin‐like growth factor 2 mRNA‐binding protein 2 recognized the unique modified m6A methylation sites to enhance KLF4 mRNA stability. Taken together, these findings highlight the novel function of MeCP2 for regulating m6A methylation and reveal the underlying molecular mechanism for the interaction between MeCP2 and METTL14, which offers a better understanding of CRC progression and metastasis.
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Affiliation(s)
- Shuo Wang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Meifu Gan
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
| | - Chaoyi Chen
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Zhang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Jianlu Kong
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Honghe Zhang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, China Pharmaceutical University, Nanjing, China
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16
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Sharifi O, Yasui DH. The Molecular Functions of MeCP2 in Rett Syndrome Pathology. Front Genet 2021; 12:624290. [PMID: 33968128 PMCID: PMC8102816 DOI: 10.3389/fgene.2021.624290] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
MeCP2 protein, encoded by the MECP2 gene, binds to DNA and affects transcription. Outside of this activity the true range of MeCP2 function is still not entirely clear. As MECP2 gene mutations cause the neurodevelopmental disorder Rett syndrome in 1 in 10,000 female births, much of what is known about the biologic function of MeCP2 comes from studying human cell culture models and rodent models with Mecp2 gene mutations. In this review, the full scope of MeCP2 research available in the NIH Pubmed (https://pubmed.ncbi.nlm.nih.gov/) data base to date is considered. While not all original research can be mentioned due to space limitations, the main aspects of MeCP2 and Rett syndrome research are discussed while highlighting the work of individual researchers and research groups. First, the primary functions of MeCP2 relevant to Rett syndrome are summarized and explored. Second, the conflicting evidence and controversies surrounding emerging aspects of MeCP2 biology are examined. Next, the most obvious gaps in MeCP2 research studies are noted. Finally, the most recent discoveries in MeCP2 and Rett syndrome research are explored with a focus on the potential and pitfalls of novel treatments and therapies.
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Affiliation(s)
- Osman Sharifi
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, United States
| | - Dag H Yasui
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, United States
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17
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D'Mello SR. MECP2 and the Biology of MECP2 Duplication Syndrome. J Neurochem 2021; 159:29-60. [PMID: 33638179 DOI: 10.1111/jnc.15331] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 11/27/2022]
Abstract
MECP2 duplication syndrome (MDS), a rare X-linked genomic disorder affecting predominantly males, is caused by duplication of the chromosomal region containing the methyl CpG binding protein-2 (MECP2) gene, which encodes methyl-CpG-binding protein 2 (MECP2), a multi-functional protein required for proper brain development and maintenance of brain function during adulthood. Disease symptoms include severe motor and cognitive impairment, delayed or absent speech development, autistic features, seizures, ataxia, recurrent respiratory infections and shortened lifespan. The cellular and molecular mechanisms by which a relatively modest increase in MECP2 protein causes such severe disease symptoms are poorly understood and consequently there are no treatments available for this fatal disorder. This review summarizes what is known to date about the structure and complex regulation of MECP2 and its many functions in the developing and adult brain. Additionally, recent experimental findings on the cellular and molecular underpinnings of MDS based on cell culture and mouse models of the disorder are reviewed. The emerging picture from these studies is that MDS is a neurodegenerative disorder in which neurons die in specific parts of the central nervous system, including the cortex, hippocampus, cerebellum and spinal cord. Neuronal death likely results from astrocytic dysfunction, including a breakdown of glutamate homeostatic mechanisms. The role of elevations in the expression of glial acidic fibrillary protein (GFAP) in astrocytes and the microtubule-associated protein, Tau, in neurons to the pathogenesis of MDS is discussed. Lastly, potential therapeutic strategies to potentially treat MDS are discussed.
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18
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Ehrhart F, Jacobsen A, Rigau M, Bosio M, Kaliyaperumal R, Laros JFJ, Willighagen EL, Valencia A, Roos M, Capella-Gutierrez S, Curfs LMG, Evelo CT. A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration. Sci Data 2021; 8:10. [PMID: 33452270 PMCID: PMC7810705 DOI: 10.1038/s41597-020-00794-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/30/2020] [Indexed: 11/09/2022] Open
Abstract
Rett syndrome (RTT) is a rare neurological disorder mostly caused by a genetic variation in MECP2. Making new MECP2 variants and the related phenotypes available provides data for better understanding of disease mechanisms and faster identification of variants for diagnosis. This is, however, currently hampered by the lack of interoperability between genotype-phenotype databases. Here, we demonstrate on the example of MECP2 in RTT that by making the genotype-phenotype data more Findable, Accessible, Interoperable, and Reusable (FAIR), we can facilitate prioritization and analysis of variants. In total, 10,968 MECP2 variants were successfully integrated. Among these variants 863 unique confirmed RTT causing and 209 unique confirmed benign variants were found. This dataset was used for comparison of pathogenicity predicting tools, protein consequences, and identification of ambiguous variants. Prediction tools generally recognised the RTT causing and benign variants, however, there was a broad range of overlap Nineteen variants were identified that were annotated as both disease-causing and benign, suggesting that there are additional factors in these cases contributing to disease development. Measurement(s) | Rett syndrome • phenotype • MECP2 Gene | Technology Type(s) | digital curation • network analysis | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13359476
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Affiliation(s)
- Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, MHeNS School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands. .,GKC - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Annika Jacobsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maria Rigau
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
| | - Mattia Bosio
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
| | - Rajaram Kaliyaperumal
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, MHeNS School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Leopold M G Curfs
- GKC - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, MHeNS School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.,GKC - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands
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19
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Role of DNA Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome Pathobiology and Mechanism of Disease. Biomolecules 2021; 11:biom11010075. [PMID: 33429932 PMCID: PMC7827577 DOI: 10.3390/biom11010075] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/16/2022] Open
Abstract
Rett Syndrome (RTT) is a severe, rare, and progressive developmental disorder with patients displaying neurological regression and autism spectrum features. The affected individuals are primarily young females, and more than 95% of patients carry de novo mutation(s) in the Methyl-CpG-Binding Protein 2 (MECP2) gene. While the majority of RTT patients have MECP2 mutations (classical RTT), a small fraction of the patients (atypical RTT) may carry genetic mutations in other genes such as the cyclin-dependent kinase-like 5 (CDKL5) and FOXG1. Due to the neurological basis of RTT symptoms, MeCP2 function was originally studied in nerve cells (neurons). However, later research highlighted its importance in other cell types of the brain including glia. In this regard, scientists benefitted from modeling the disease using many different cellular systems and transgenic mice with loss- or gain-of-function mutations. Additionally, limited research in human postmortem brain tissues provided invaluable findings in RTT pathobiology and disease mechanism. MeCP2 expression in the brain is tightly regulated, and its altered expression leads to abnormal brain function, implicating MeCP2 in some cases of autism spectrum disorders. In certain disease conditions, MeCP2 homeostasis control is impaired, the regulation of which in rodents involves a regulatory microRNA (miR132) and brain-derived neurotrophic factor (BDNF). Here, we will provide an overview of recent advances in understanding the underlying mechanism of disease in RTT and the associated genetic mutations in the MECP2 gene along with the pathobiology of the disease, the role of the two most studied protein variants (MeCP2E1 and MeCP2E2 isoforms), and the regulatory mechanisms that control MeCP2 homeostasis network in the brain, including BDNF and miR132.
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20
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MeCP2 and Chromatin Compartmentalization. Cells 2020; 9:cells9040878. [PMID: 32260176 PMCID: PMC7226738 DOI: 10.3390/cells9040878] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked to Rett syndrome in humans. Here, we focus on its isoforms and functional domains, interactions, modifications and mutations found in Rett patients. Finally, we address how these properties regulate and mediate the ability of MeCP2 to orchestrate chromatin compartmentalization and higher order genome architecture.
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21
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Lavery LA, Zoghbi HY. The distinct methylation landscape of maturing neurons and its role in Rett syndrome pathogenesis. Curr Opin Neurobiol 2019; 59:180-188. [PMID: 31542590 PMCID: PMC6892602 DOI: 10.1016/j.conb.2019.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Rett syndrome (RTT) is one of the most common causes of intellectual and developmental disabilities in girls, and is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2). Here we will review our current understanding of RTT, the landscape of pathogenic mutations and function of MeCP2, and culminate with recent advances elucidating the distinct DNA methylation landscape in the brain that may explain why disease symptoms are delayed and selective to the nervous system.
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Affiliation(s)
- Laura A Lavery
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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22
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Sysoeva OV, Smirnov K, Stroganova TA. Sensory evoked potentials in patients with Rett syndrome through the lens of animal studies: Systematic review. Clin Neurophysiol 2019; 131:213-224. [PMID: 31812082 DOI: 10.1016/j.clinph.2019.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Systematically review the abnormalities in event related potential (ERP) recorded in Rett Syndrome (RTT) patients and animals in search of translational biomarkers of deficits related to the particular neurophysiological processes of known genetic origin (MECP2 mutations). METHODS Pubmed, ISI Web of Knowledge and BIORXIV were searched for the relevant articles according to PRISMA standards. RESULTS ERP components are generally delayed across all sensory modalities both in RTT patients and its animal model, while findings on ERPs amplitude strongly depend on stimulus properties and presentation rate. Studies on RTT animal models uncovered the abnormalities in the excitatory and inhibitory transmission as critical mechanisms underlying the ERPs changes, but showed that even similar ERP alterations in auditory and visual domains have a diverse neural basis. A range of novel approaches has been developed in animal studies bringing along the meaningful neurophysiological interpretation of ERP measures in RTT patients. CONCLUSIONS While there is a clear evidence for sensory ERPs abnormalities in RTT, to further advance the field there is a need in a large-scale ERP studies with the functionally-relevant experimental paradigms. SIGNIFICANCE The review provides insights into domain-specific neural basis of the ERP abnormalities and promotes clinical application of the ERP measures as the non-invasive functional biomarkers of RTT pathophysiology.
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Affiliation(s)
- Olga V Sysoeva
- The Cognitive Neurophysiology Laboratory, Department of Pediatrics, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, USA; The Cognitive Neurophysiology Laboratory, Ernest J. Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; The Laboratory of Human Higher Nervous Activity, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia.
| | - Kirill Smirnov
- Department of Neuroontogenesis, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Science, Moscow, Russia.
| | - Tatiana A Stroganova
- Center for Neurocognitive Research (MEG-Center), Moscow State University of Psychology and Education (MSUPE), Moscow, Russia; Autism Research Laboratory, Moscow State University of Psychology and Education (MSUPE), Moscow, Russia.
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23
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Yang H, Li K, Han S, Zhou A, Zhou ZJ. Leveraging the genetic basis of Rett syndrome to ascertain pathophysiology. Neurobiol Learn Mem 2019; 165:106961. [PMID: 30447288 PMCID: PMC6635128 DOI: 10.1016/j.nlm.2018.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 09/18/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Mutations in the methyl-CpG binding protein 2 (MECP2) gene cause Rett syndrome (RTT), a progressive X-linked neurological disorder characterized by loss of developmental milestones, intellectual disability and breathing abnormality. Despite being a monogenic disorder, the pathogenic mechanisms by which mutations in MeCP2 impair neuronal function and underlie the RTT symptoms have been challenging to elucidate. The seemingly simple genetic root and the availability of genetic data from RTT patients have led to the generation and characterization of a series of mouse models recapitulating RTT-associated genetic mutations. This review focuses on the studies of RTT mouse models and describe newly obtained pathogenic insights from these studies. We also highlight the potential of studying pathophysiology using genetics-based modeling approaches in rodents and suggest a future direction to tackle the pathophysiology of intellectual disability with known or complex genetic causes.
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Affiliation(s)
- Hua Yang
- Qingdao Jiaozhou Central Hospital, Jiaozhou City, Shandong Province 266300, China
| | - Kequan Li
- Qingdao Jiaozhou Central Hospital, Jiaozhou City, Shandong Province 266300, China
| | - Song Han
- Jiaozhou People's Hospital, Jiaozhou City, Shandong Province 266300, China
| | - Ailing Zhou
- Jiaozhou People's Hospital, Jiaozhou City, Shandong Province 266300, China
| | - Zhaolan Joe Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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24
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Schmelter C, Funke S, Treml J, Beschnitt A, Perumal N, Manicam C, Pfeiffer N, Grus FH. Comparison of Two Solid-Phase Extraction (SPE) Methods for the Identification and Quantification of Porcine Retinal Protein Markers by LC-MS/MS. Int J Mol Sci 2018; 19:E3847. [PMID: 30513899 PMCID: PMC6321002 DOI: 10.3390/ijms19123847] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/18/2018] [Accepted: 11/27/2018] [Indexed: 01/08/2023] Open
Abstract
Proper sample preparation protocols represent a critical step for liquid chromatography-mass spectrometry (LC-MS)-based proteomic study designs and influence the speed, performance and automation of high-throughput data acquisition. The main objective of this study was to compare two commercial solid-phase extraction (SPE)-based sample preparation protocols (comprising SOLAµTM HRP SPE spin plates from Thermo Fisher Scientific and ZIPTIP® C18 pipette tips from Merck Millipore) for analytical performance, reproducibility, and analysis speed. The house swine represents a promising animal model for studying human eye diseases including glaucoma and provides excellent requirements for the qualitative and quantitative MS-based comparison in terms of ocular proteomics. In total six technical replicates of two protein fractions [extracted with 0.1% dodecyl-ß-maltoside (DDM) or 1% trifluoroacetic acid (TFA)] of porcine retinal tissues were subjected to in-gel trypsin digestion and purified with both SPE-based workflows (N = 3) prior to LC-MS analysis. On average, 550 ± 70 proteins (1512 ± 199 peptides) and 305 ± 48 proteins (806 ± 144 peptides) were identified from DDM and TFA protein fractions, respectively, after ZIPTIP® C18 purification, and SOLAµTM workflow resulted in the detection of 513 ± 55 proteins (1347 ± 180 peptides) and 300 ± 33 proteins (722 ± 87 peptides), respectively (FDR < 1%). Venn diagram analysis revealed an average overlap of 65 ± 2% (DDM fraction) and 69 ± 4% (TFA fraction) in protein identifications between both SPE-based methods. Quantitative analysis of 25 glaucoma-related protein markers also showed no significant differences (P > 0.05) regarding protein recovery between both SPE methods. However, only glaucoma-associated marker MECP2 showed a significant (P = 0.02) higher abundance in ZIPTIP®-purified replicates in comparison to SOLAµTM-treated study samples. Nevertheless, this result was not confirmed in the verification experiment using in-gel trypsin digestion of recombinant MECP2 (P = 0.24). In conclusion, both SPE-based purification methods worked equally well in terms of analytical performance and reproducibility, whereas the analysis speed and the semi-automation of the SOLAµTM spin plates workflow is much more convenient in comparison to the ZIPTIP® C18 method.
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Affiliation(s)
- Carsten Schmelter
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Sebastian Funke
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Jana Treml
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Anja Beschnitt
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Natarajan Perumal
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Caroline Manicam
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Norbert Pfeiffer
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
| | - Franz H Grus
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
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D'Annessa I, Gandaglia A, Brivio E, Stefanelli G, Frasca A, Landsberger N, Di Marino D. Tyr120Asp mutation alters domain flexibility and dynamics of MeCP2 DNA binding domain leading to impaired DNA interaction: Atomistic characterization of a Rett syndrome causing mutation. Biochim Biophys Acta Gen Subj 2018; 1862:1180-1189. [PMID: 29428602 DOI: 10.1016/j.bbagen.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 11/28/2022]
Abstract
Mutations in the X-linked MECP2 gene represent the main origin of Rett syndrome, causing a profound intellectual disability in females. MeCP2 is an epigenetic transcriptional regulator containing two main functional domains: a methyl-CpG binding domain (MBD) and a transcription repression domain (TRD). Over 600 pathogenic mutations were reported to affect the whole protein; almost half of missense mutations affect the MBD. Understanding the impact of these mutations on the MBD structure and interaction with DNA will foster the comprehension of their pathogenicity and possibly genotype/phenotype correlation studies. Herein, we use molecular dynamics simulations to obtain a detailed view of the dynamics of WT and mutated MBD in the presence and absence of DNA. The pathogenic mutation Y120D is used as paradigm for our studies. Further, since the Y120 residue was previously found to be a phosphorylation site, we characterize the dynamic profile of the MBD also in the presence of Y120 phosphorylation (pY120). We found that addition of a phosphate group to Y120 or mutation in aspartic acid affect domain mobility that samples an alternative conformational space with respect to the WT, leading to impaired ability to interact with DNA. Experimental assays showing a significant reduction in the binding affinity between the mutated MBD and the DNA confirmed our predictions.
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Affiliation(s)
- Ilda D'Annessa
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | - Anna Gandaglia
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Elena Brivio
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Gilda Stefanelli
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Angelisa Frasca
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Nicoletta Landsberger
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy.
| | - Daniele Di Marino
- Department of Informatics, Institute of Computational Science, Università della Svizzera Italiana, Lugano, Switzerland.
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Kyle SM, Vashi N, Justice MJ. Rett syndrome: a neurological disorder with metabolic components. Open Biol 2018; 8:170216. [PMID: 29445033 PMCID: PMC5830535 DOI: 10.1098/rsob.170216] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/18/2018] [Indexed: 02/06/2023] Open
Abstract
Rett syndrome (RTT) is a neurological disorder caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2), a ubiquitously expressed transcriptional regulator. Despite remarkable scientific progress since its discovery, the mechanism by which MECP2 mutations cause RTT symptoms is largely unknown. Consequently, treatment options for patients are currently limited and centred on symptom relief. Thought to be an entirely neurological disorder, RTT research has focused on the role of MECP2 in the central nervous system. However, the variety of phenotypes identified in Mecp2 mutant mouse models and RTT patients implicate important roles for MeCP2 in peripheral systems. Here, we review the history of RTT, highlighting breakthroughs in the field that have led us to present day. We explore the current evidence supporting metabolic dysfunction as a component of RTT, presenting recent studies that have revealed perturbed lipid metabolism in the brain and peripheral tissues of mouse models and patients. Such findings may have an impact on the quality of life of RTT patients as both dietary and drug intervention can alter lipid metabolism. Ultimately, we conclude that a thorough knowledge of MeCP2's varied functional targets in the brain and body will be required to treat this complex syndrome.
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Affiliation(s)
- Stephanie M Kyle
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada M5G 0A4
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neeti Vashi
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada M5G 0A4
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A1
| | - Monica J Justice
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada M5G 0A4
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A1
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Abstract
This paper provides a brief introductory review of the most recent advances in our knowledge about the structural and functional aspects of two transcriptional regulators: MeCP2, a protein whose mutated forms are involved in Rett syndrome; and CTCF, a constitutive transcriptional insulator. This is followed by a description of the PTMs affecting these two proteins and an analysis of their known interacting partners. A special emphasis is placed on the recent studies connecting these two proteins, focusing on the still poorly understood potential structural and functional interactions between the two of them on the chromatin substrate. An overview is provided for some of the currently known genes that are dually regulated by these two proteins. Finally, a model is put forward to account for their possible involvement in their regulation of gene expression.
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Affiliation(s)
- Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,b Center for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Philippe T Georgel
- c Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,d Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
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28
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Zhao LY, Tong DD, Xue M, Ma HL, Liu SY, Yang J, Liu YX, Guo B, Ni L, Liu LY, Qin YN, Wang LM, Zhao XG, Huang C. MeCP2, a target of miR-638, facilitates gastric cancer cell proliferation through activation of the MEK1/2-ERK1/2 signaling pathway by upregulating GIT1. Oncogenesis 2017; 6:e368. [PMID: 28759023 PMCID: PMC5541712 DOI: 10.1038/oncsis.2017.60] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 05/02/2017] [Accepted: 06/07/2017] [Indexed: 02/08/2023] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is involved in the carcinogenesis and progression of multiple types of cancer. However, its precise role in gastric cancer (GC) and the relevant molecular mechanism remain unknown. In the present study, we found that miR-638 levels were lower in GC tissues and GC cell lines than in adjacent normal tissues and normal gastric epithelial cell lines, respectively. Low miR-638 levels were associated with poor tumor differentiation, tumor size and lymph node metastasis. MeCP2 expression levels were higher in GC tissues than in adjacent normal tissues. It was found that miR-638 inhibited GC cell proliferation, colony formation, G1–S transition and tumor growth, and induced cell apoptosis by directly targeting MeCP2. MeCP2 promoted GC cell proliferation, colony formation and G1–S cell-cycle transition, and suppressed apoptosis. Molecular mechanistic investigations were performed using an integrated approach with a combination of microarray analysis, chromatin immunoprecipitation sequencing and a reporter gene assay. The results showed that MeCP2 bound to the methylated CpG islands of G-protein-coupled receptor kinase-interacting protein 1 (GIT1) promoter and upregulated its expression, thereby activating the MEK1/2–ERK1/2 signaling pathway and promoting GC cell proliferation. Taken together, our study demonstrates that MeCP2, a target of miR-638, facilitates GC cell proliferation and induces cell-cycle progression through activation of the MEK1/2–ERK1/2 signaling pathway by upregulating GIT1. The findings suggest that MeCP2 plays a significant role in GC progression, and may serve as a potential target for GC therapy.
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Affiliation(s)
- L Y Zhao
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - D D Tong
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - M Xue
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - H L Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - S Y Liu
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - J Yang
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Y X Liu
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - B Guo
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - L Ni
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - L Y Liu
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Y N Qin
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - L M Wang
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - X G Zhao
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - C Huang
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Medical College of Yan'an University, Yan'an, Shaanxi, China
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Pandey S, Pruitt K. Functional assessment of MeCP2 in Rett syndrome and cancers of breast, colon, and prostate. Biochem Cell Biol 2017; 95:368-378. [DOI: 10.1139/bcb-2016-0154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Ever since the first report that mutations in methyl-CpG-binding protein 2 (MeCP2) causes Rett syndrome (RTT), a severe neurological disorder in females world-wide, there has been a keen interest to gain a comprehensive understanding of this protein. While the classical model associated with MeCP2 function suggests its role in gene suppression via recruitment of co-repressor complexes and histone deacetylases to methylated CpG-sites, recent discoveries have brought to light its role in transcription activation, modulation of RNA splicing, and chromatin compaction. Various post-translational modifications (PTMs) of MeCP2 further increase its functional versatility. Involvement of MeCP2 in pathologies other than RTT, such as tumorigenesis however, remains poorly explored and understood. This review provides a survey of the literature implicating MeCP2 in breast, colon and prostate cancer.
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Affiliation(s)
- Somnath Pandey
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
| | - Kevin Pruitt
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
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30
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MeCP2 Promotes Gastric Cancer Progression Through Regulating FOXF1/Wnt5a/β-Catenin and MYOD1/Caspase-3 Signaling Pathways. EBioMedicine 2017; 16:87-100. [PMID: 28131747 PMCID: PMC5474507 DOI: 10.1016/j.ebiom.2017.01.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 01/25/2023] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) has recently been characterized as an oncogene frequently amplified in several types of cancer. However, its precise role in gastric cancer (GC) and the molecular mechanism of MeCP2 regulation are still largely unknown. Here we report that MeCP2 is highly expressed in primary GC tissues and the expression level is correlated with the clinicopathologic features of GC. In our experiments, knockdown of MeCP2 inhibited tumor growth. Molecular mechanism of MeCP2 regulation was investigated using an integrated approach with combination of microarray analysis and chromatin immunoprecipitation sequencing (ChIP-Seq). The results suggest that MeCP2 binds to the methylated CpG islands of FOXF1 and MYOD1 promoters and inhibits their expression at the transcription level. Furthermore, we show that MeCP2 promotes GC cell proliferation via FOXF1-mediated Wnt5a/β-Catenin signaling pathway and suppresses apoptosis through MYOD1-mediated Caspase-3 signaling pathway. Due to its high expression level in GC and its critical function in driving GC progression, MeCP2 represents a promising therapeutic target for GC treatment. MeCP2 inhibits FOXF1 and MYOD1 transcription by binding to their promoter regions. MeCP2 promotes GC cell proliferation via FOXF1-mediated Wnt/β-Catenin signaling pathway. MeCP2 suppresses GC cell apoptosis through MYOD1-mediated Caspase-3 signaling pathway.
Gastric cancer is the fourth most common malignant cancer and the third most frequent cause of cancer-related deaths worldwide. The molecular mechanism underlying gastric carcinogenesis and progression is still unknown. Methyl-CpG binding protein 2 (MeCP2) has recently been characterized as an oncogene frequently amplified in several types of cancer. However, its precise role and the molecular mechanism of MeCP2 regulation in gastric cancer are largely unknown. Our results show that MeCP2 promotes gastric cancer cell proliferation via FOXF1-mediated Wnt5a/β-Catenin signaling pathway and suppresses cell apoptosis through MYOD1-mediated Caspase-3 signaling pathway. MeCP2 represents a promising therapeutic target for gastric cancer treatment.
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31
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MeCP2, A Modulator of Neuronal Chromatin Organization Involved in Rett Syndrome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:3-21. [PMID: 28523538 DOI: 10.1007/978-3-319-53889-1_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
From an epigenetic perspective, the genomic chromatin organization of neurons exhibits unique features when compared to somatic cells. Methyl CpG binding protein 2 (MeCP2), through its ability to bind to methylated DNA, seems to be a major player in regulating such unusual organization. An important contribution to this uniqueness stems from the intrinsically disordered nature of this highly abundant chromosomal protein in neurons. Upon its binding to methylated/hydroxymethylated DNA, MeCP2 is able to recruit a plethora of interacting protein and RNA partners. The final outcome is a highly specialized chromatin organization wherein linker histones (histones of the H1 family) and MeCP2 share an organizational role that dynamically changes during neuronal development and that it is still poorly understood. MeCP2 mutations alter its chromatin-binding dynamics and/or impair the ability of the protein to interact with some of its partners, resulting in Rett syndrome (RTT). Therefore, deciphering the molecular details involved in the MeCP2 neuronal chromatin arrangement is critical for our understanding of the proper and altered functionality of these cells.
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32
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Ehrhart F, Coort SLM, Cirillo E, Smeets E, Evelo CT, Curfs LMG. Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes. Orphanet J Rare Dis 2016; 11:158. [PMID: 27884167 PMCID: PMC5123333 DOI: 10.1186/s13023-016-0545-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
Rett syndrome (RTT) is a rare disease but still one of the most abundant causes for intellectual disability in females. Typical symptoms are onset at month 6-18 after normal pre- and postnatal development, loss of acquired skills and severe intellectual disability. The type and severity of symptoms are individually highly different. A single mutation in one gene, coding for methyl-CpG-binding protein 2 (MECP2), is responsible for the disease. The most important action of MECP2 is regulating epigenetic imprinting and chromatin condensation, but MECP2 influences many different biological pathways on multiple levels although the molecular pathways from gene to phenotype are currently not fully understood. In this review the known changes in metabolite levels, gene expression and biological pathways in RTT are summarized, discussed how they are leading to some characteristic RTT phenotypes and therefore the gaps of knowledge are identified. Namely, which phenotypes have currently no mechanistic explanation leading back to MECP2 related pathways? As a result of this review the visualization of the biologic pathways showing MECP2 up- and downstream regulation was developed and published on WikiPathways which will serve as template for future omics data driven research. This pathway driven approach may serve as a use case for other rare diseases, too.
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Affiliation(s)
- Friederike Ehrhart
- Governor Kremers Centre - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands. .,Department of Bioinformatics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.
| | - Susan L M Coort
- Department of Bioinformatics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Elisa Cirillo
- Department of Bioinformatics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Eric Smeets
- Governor Kremers Centre - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Chris T Evelo
- Governor Kremers Centre - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Bioinformatics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Leopold M G Curfs
- Governor Kremers Centre - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands
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Claveria-Gimeno R, Abian O, Velazquez-Campoy A, Ausió J. MeCP2… Nature’s Wonder Protein or Medicine’s Most Feared One? CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0107-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Khrapunov S, Tao Y, Cheng H, Padlan C, Harris R, Galanopoulou AS, Greally JM, Girvin ME, Brenowitz M. MeCP2 Binding Cooperativity Inhibits DNA Modification-Specific Recognition. Biochemistry 2016; 55:4275-85. [PMID: 27420643 DOI: 10.1021/acs.biochem.6b00451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a multifunctional protein that guides neuronal development through its binding to DNA, recognition of sites of methyl-CpG (mCpG) DNA modification, and interaction with other regulatory proteins. Our study explores the relationship between mCpG and hydroxymethyl-CpG (hmCpG) recognition mediated by its mCpG binding domain (MBD) and binding cooperativity mediated by its C-terminal polypeptide. Previous study of the isolated MBD of MeCP2 documented an unusual mechanism by which ion uptake is required for discrimination of mCpG and hmCpG from CpG. MeCP2 binding cooperativity suppresses discrimination of modified DNA and is highly sensitive to both the total ion concentration and the type of counterions. Higher than physiological total ion concentrations completely suppress MeCP2 binding cooperativity, indicating a dominant electrostatic component to the interaction. Substitution of SO4(2-) for Cl(-) at physiological total ion concentrations also suppresses MeCP2 binding cooperativity, This effect is of particular note as the intracellular Cl(-) concentration changes during neuronal development. A related effect is that the protein-stabilizing solutes, TMAO and glutamate, reduce MeCP2 (but not isolated MBD) binding affinity by 2 orders of magnitude without affecting the apparent binding cooperativity. These observations suggest that polypeptide flexibility facilitates DNA binding by MeCP2. Consistent with this view, nuclear magnetic resonance (NMR) analyses show that ions have discrete effects on the structure of MeCP2, both MBD and the C-terminal domains. Notably, anion substitution results in changes in the NMR chemical shifts of residues, including some whose mutation causes the autism spectrum disorder Rett syndrome. Binding cooperativity makes MeCP2 an effective competitor with histone H1 for accessible DNA sites. The relationship between MeCP2 binding specificity and cooperativity is discussed in the context of chromatin binding, neuronal function, and neuronal development.
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Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Yisong Tao
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Huiyong Cheng
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Camille Padlan
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Richard Harris
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Aristea S Galanopoulou
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - John M Greally
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Mark E Girvin
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Michael Brenowitz
- Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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35
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Pedretti A, Granito C, Mazzolari A, Vistoli G. Structural Effects of Some Relevant Missense Mutations on the MECP2-DNA Binding: A MD Study Analyzed by Rescore+, a Versatile Rescoring Tool of the VEGA ZZ Program. Mol Inform 2016; 35:424-33. [PMID: 27546046 DOI: 10.1002/minf.201501030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/03/2016] [Indexed: 01/22/2023]
Abstract
DNA methylation plays key roles in mammalian cells and is modulated by a set of proteins which recognize symmetrically methylated nucleotides. Among them, the protein MECP2 shows multifunctional roles repressing and/or activating genes by binding to both methylated and unmethylated regions of the genome. The interest for this protein markedly increased from the observation that its mutations are the primary cause of Rett syndrome, a neurodevelopmental disorder which causes mental retardation in young females. Thus, the present study is aimed to investigate the effects of some of these known pathogenic missense mutations (i.e. R106Q, R106W, R111G, R133C and R133H) on the MECP2 folding and DNA binding by molecular dynamics simulations. The effects of the simulated mutations are also parameterized by using a here proposed new tool, named Rescore+, implemented in the VEGA ZZ suite of programs, which calculates a set of scoring functions on all frames of a trajectory or on all complexes contained in a database thus allowing an easy rescoring of results coming from MD or docking simulations. The obtained results revealed that the reported loss of the MECP2 function induced by the simulated mutations can be ascribed to both stabilizing and destabilizing effect on DNA binding. The study confirms that MD simulations are particularly useful to rationalize and predict the mutation effects offering insightful information for diagnostics and drug design.
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Affiliation(s)
- Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy
| | - Cinzia Granito
- Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy
| | - Angelica Mazzolari
- Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133, Milano, Italy.
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36
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Brain phosphorylation of MeCP2 at serine 164 is developmentally regulated and globally alters its chromatin association. Sci Rep 2016; 6:28295. [PMID: 27323888 PMCID: PMC4915018 DOI: 10.1038/srep28295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/01/2016] [Indexed: 12/31/2022] Open
Abstract
MeCP2 is a transcriptional regulator whose functional alterations are responsible for several autism spectrum and mental disorders. Post-translational modifications (PTMs), and particularly differential phosphorylation, modulate MeCP2 function in response to diverse stimuli. Understanding the detailed role of MeCP2 phosphorylation is thus instrumental to ascertain how MeCP2 integrates the environmental signals and directs its adaptive transcriptional responses. The evolutionarily conserved serine 164 (S164) was found phosphorylated in rodent brain but its functional role has remained uncharacterized. We show here that phosphorylation of S164 in brain is dynamically regulated during neuronal maturation. S164 phosphorylation highly impairs MeCP2 binding to DNA in vitro and largely affects its nucleosome binding and chromatin affinity in vivo. Strikingly, the chromatin-binding properties of the global MeCP2 appear also extensively altered during the course of brain maturation. Functional assays reveal that proper temporal regulation of S164 phosphorylation controls the ability of MeCP2 to regulate neuronal morphology. Altogether, our results support the hypothesis of a complex PTM-mediated functional regulation of MeCP2 potentially involving a still poorly characterized epigenetic code. Furthermore, they demonstrate the relevance of the Intervening Domain of MeCP2 for binding to DNA.
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37
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Ludwig AK, Zhang P, Cardoso MC. Modifiers and Readers of DNA Modifications and Their Impact on Genome Structure, Expression, and Stability in Disease. Front Genet 2016; 7:115. [PMID: 27446199 PMCID: PMC4914596 DOI: 10.3389/fgene.2016.00115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/06/2016] [Indexed: 12/16/2022] Open
Abstract
Cytosine base modifications in mammals underwent a recent expansion with the addition of several naturally occurring further modifications of methylcytosine in the last years. This expansion was accompanied by the identification of the respective enzymes and proteins reading and translating the different modifications into chromatin higher order organization as well as genome activity and stability, leading to the hypothesis of a cytosine code. Here, we summarize the current state-of-the-art on DNA modifications, the enzyme families setting the cytosine modifications and the protein families reading and translating the different modifications with emphasis on the mouse protein homologs. Throughout this review, we focus on functional and mechanistic studies performed on mammalian cells, corresponding mouse models and associated human diseases.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
| | - M C Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
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38
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Della Ragione F, Vacca M, Fioriniello S, Pepe G, D'Esposito M. MECP2, a multi-talented modulator of chromatin architecture. Brief Funct Genomics 2016; 15:420-431. [PMID: 27296483 DOI: 10.1093/bfgp/elw023] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been a long trip from 1992, the year of the discovery of MECP2, to the present day. What is surprising is that some of the pivotal roles of MeCP2 were already postulated at that time, such as repression of inappropriate expression from repetitive elements and the regulation of pericentric heterochromatin condensation. However, MeCP2 performs many more functions. MeCP2 is a reader of epigenetic information contained in methylated (and hydroxymethylated) DNA, moving from the 'classical' CpG doublet to the more complex view addressed by the non-CpG methylation, which is a feature of the postnatal brain. MECP2 is a transcriptional repressor, although when it forms complexes with the appropriate molecules, it can become a transcriptional activator. For all of these aspects, Rett syndrome, which is caused by MECP2 mutations, is considered a paradigmatic example of a 'chromatin disorder'. Even if the hunt for bona-fide MECP2 target genes is far from concluded today, the role of MeCP2 in the maintenance of chromatin architecture appears to be clearly established. Taking a cue from the non-scientific literature, we can firmly attest that MeCP2 is a player with 'a great future behind it'*.*V. Gassmann 'Un grande avvenire dietro le spalle'. TEA Eds.
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39
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Kyle SM, Saha PK, Brown HM, Chan LC, Justice MJ. MeCP2 co-ordinates liver lipid metabolism with the NCoR1/HDAC3 corepressor complex. Hum Mol Genet 2016; 25:3029-3041. [PMID: 27288453 PMCID: PMC5181597 DOI: 10.1093/hmg/ddw156] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/02/2016] [Accepted: 05/18/2016] [Indexed: 01/11/2023] Open
Abstract
Rett syndrome (RTT; OMIM 312750), a progressive neurological disorder, is caused by mutations in methyl-CpG-binding protein 2 (MECP2; OMIM 300005), a ubiquitously expressed factor. A genetic suppressor screen designed to identify therapeutic targets surprisingly revealed that downregulation of the cholesterol biosynthesis pathway improves neurological phenotypes in Mecp2 mutant mice. Here, we show that MeCP2 plays a direct role in regulating lipid metabolism. Mecp2 deletion in mice results in a host of severe metabolic defects caused by lipid accumulation, including insulin resistance, fatty liver, perturbed energy utilization, and adipose inflammation by macrophage infiltration. We show that MeCP2 regulates lipid homeostasis by anchoring the repressor complex containing NCoR1 and HDAC3 to its lipogenesis targets in hepatocytes. Consistently, we find that liver targeted deletion of Mecp2 causes fatty liver disease and dyslipidemia similar to HDAC3 liver-specific deletion. These findings position MeCP2 as a novel component in metabolic homeostasis. Rett syndrome patients also show signs of peripheral dyslipidemia; thus, together these data suggest that RTT should be classified as a neurological disorder with systemic metabolic components. We previously showed that treatment of Mecp2 mice with statin drugs alleviated motor symptoms and improved health and longevity. Lipid metabolism is a highly treatable target; therefore, our results shed light on new metabolic pathways for treatment of Rett syndrome.
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Affiliation(s)
- Stephanie M Kyle
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada.,Department of Molecular and Human Genetics
| | - Pradip K Saha
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Lawrence C Chan
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica J Justice
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada .,Department of Molecular and Human Genetics.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
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Ausió J. MeCP2 and the enigmatic organization of brain chromatin. Implications for depression and cocaine addiction. Clin Epigenetics 2016; 8:58. [PMID: 27213019 PMCID: PMC4875624 DOI: 10.1186/s13148-016-0214-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) is a highly abundant chromosomal protein within the brain. It is hence not surprising that perturbations in its genome-wide distribution, and at particular loci within this tissue, can result in widespread neurological disorders that transcend the early implications of this protein in Rett syndrome (RTT). Yet, the details of its role and involvement in chromatin organization are still poorly understood. This paper focuses on what is known to date about all of this with special emphasis on the relation to different epigenetic modifications (DNA methylation, histone acetylation/ubiquitination, MeCP2 phosphorylation and miRNA). We showcase all of the above in two particular important neurological functional alterations in the brain: depression (major depressive disorder [MDD]) and cocaine addiction, both of which affect the MeCP2 homeostasis and result in significant changes in the overall levels of these epigenetic marks.
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Affiliation(s)
- Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6 Canada
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41
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Roque A, Ponte I, Suau P. Post-translational modifications of the intrinsically disordered terminal domains of histone H1: effects on secondary structure and chromatin dynamics. Chromosoma 2016; 126:83-91. [DOI: 10.1007/s00412-016-0591-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 01/14/2023]
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42
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Gruet A, Dosnon M, Blocquel D, Brunel J, Gerlier D, Das RK, Bonetti D, Gianni S, Fuxreiter M, Longhi S, Bignon C. Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions. FEBS J 2016; 283:576-94. [PMID: 26684000 DOI: 10.1111/febs.13631] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/22/2015] [Accepted: 12/15/2015] [Indexed: 12/13/2022]
Abstract
Despite the partial disorder-to-order transition that intrinsically disordered proteins often undergo upon binding to their partners, a considerable amount of residual disorder may be retained in the bound form, resulting in a fuzzy complex. Fuzzy regions flanking molecular recognition elements may enable partner fishing through non-specific, transient contacts, thereby facilitating binding, but may also disfavor binding through various mechanisms. So far, few computational or experimental studies have addressed the effect of fuzzy appendages on partner recognition by intrinsically disordered proteins. In order to shed light onto this issue, we used the interaction between the intrinsically disordered C-terminal domain of the measles virus (MeV) nucleoprotein (NTAIL ) and the X domain (XD) of the viral phosphoprotein as model system. After binding to XD, the N-terminal region of NTAIL remains conspicuously disordered, with α-helical folding taking place only within a short molecular recognition element. To study the effect of the N-terminal fuzzy region on NTAIL /XD binding, we generated N-terminal truncation variants of NTAIL , and assessed their binding abilities towards XD. The results revealed that binding increases with shortening of the N-terminal fuzzy region, with this also being observed with hsp70 (another MeV NTAIL binding partner), and for the homologous NTAIL /XD pairs from the Nipah and Hendra viruses. Finally, similar results were obtained when the MeV NTAIL fuzzy region was replaced with a highly dissimilar artificial disordered sequence, supporting a sequence-independent inhibitory effect of the fuzzy region.
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Affiliation(s)
- Antoine Gruet
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Marion Dosnon
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - David Blocquel
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Joanna Brunel
- Centre International de Recherche en Infectiologie, INSERM U1111, Centre National de la Recherche Scientifique, UMR 5308, Université Lyon 1, Lyon, France
| | - Denis Gerlier
- Centre International de Recherche en Infectiologie, INSERM U1111, Centre National de la Recherche Scientifique, UMR 5308, Université Lyon 1, Lyon, France
| | - Rahul K Das
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St Louis, MO, USA
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, Rome, Italy.,Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Monika Fuxreiter
- Hungarian Academy of Sciences, Momentum Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary
| | - Sonia Longhi
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Christophe Bignon
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
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43
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Kucukkal TG, Yang Y, Uvarov O, Cao W, Alexov E. Impact of Rett Syndrome Mutations on MeCP2 MBD Stability. Biochemistry 2015; 54:6357-68. [PMID: 26418480 PMCID: PMC9871983 DOI: 10.1021/acs.biochem.5b00790] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Rett syndrome causing missense mutations in the methyl-CpG-binding domain (MBD) of methyl CpG-binding protein 2 (MeCP2) were investigated both in silico and in vitro to reveal their effect on protein stability. It is demonstrated that the vast majority of frequently occurring mutations in the human population indeed alter the MBD folding free energy by a fraction of a kcal/mol up to more than 1 kcal/mol. While the absolute magnitude of the change of the free energy is small, the effect on the MBD functionality may be substantial since the folding free energy of MBD is about 2 kcal/mol only. Thus, it is emphasized that the effect of mutations on protein integrity should be evaluated with respect to the wild-type folding free energy but not with the absolute value of the folding free energy change. Furthermore, it was observed that the magnitude of the effect is correlated neither with the burial of the mutation sites nor with the basic amino acid physicochemical property change. Mutations that strongly perturb the immediate structural features were found to have little effect on folding free energy, while very conservative mutations resulted in large changes of the MBD stability. This observation was attributed to the protein's ability to structurally relax and reorganize to reduce the effect of mutation. Comparison between in silico and in vitro results indicated that some Web servers perform relatively well, while the free energy perturbation approach frequently overpredicts the magnitude of the free energy change especially when a charged amino acid is involved.
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Affiliation(s)
- Tugba G Kucukkal
- Department of Physics, Clemson University, 118 Kinard Laboratory, Clemson, SC 29634, USA
| | - Ye Yang
- Department of Genetics and Biochemistry, Clemson University, 049 Life Sciences Facility, Clemson, SC 29634, USA
| | - Olga Uvarov
- Department of Genetics and Biochemistry, Clemson University, 049 Life Sciences Facility, Clemson, SC 29634, USA
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, 049 Life Sciences Facility, Clemson, SC 29634, USA,Weiguo Cao: , Tel: 864-656-4176; Fax: 864-656-6879, Alexov: , Tel: 864-908-4796, Fax: 864-656-0805
| | - Emil Alexov
- Department of Physics, Clemson University, 118 Kinard Laboratory, Clemson, SC 29634, USA,Weiguo Cao: , Tel: 864-656-4176; Fax: 864-656-6879, Alexov: , Tel: 864-908-4796, Fax: 864-656-0805
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44
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Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies. Int J Mol Sci 2015; 16:19040-54. [PMID: 26287166 PMCID: PMC4581285 DOI: 10.3390/ijms160819040] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/15/2015] [Accepted: 08/04/2015] [Indexed: 12/13/2022] Open
Abstract
The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution.
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45
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Abstract
Two severe, progressive neurological disorders characterized by intellectual disability, autism, and developmental regression, Rett syndrome and MECP2 duplication syndrome, result from loss and gain of function, respectively, of the same critical gene, methyl-CpG-binding protein 2 (MECP2). Neurons acutely require the appropriate dose of MECP2 to function properly but do not die in its absence or overexpression. Instead, neuronal dysfunction can be reversed in a Rett syndrome mouse model if MeCP2 function is restored. Thus, MECP2 disorders provide a unique window into the delicate balance of neuronal health, the power of mouse models, and the importance of chromatin regulation in mature neurons. In this Review, we will discuss the clinical profiles of MECP2 disorders, the knowledge acquired from mouse models of the syndromes, and how that knowledge is informing current and future clinical studies.
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46
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Fuzzy complexes: Specific binding without complete folding. FEBS Lett 2015; 589:2533-42. [PMID: 26226339 DOI: 10.1016/j.febslet.2015.07.022] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 12/17/2022]
Abstract
Specific molecular recognition is assumed to require a well-defined set of contacts and devoid of conformational and interaction ambiguities. Growing experimental evidence demonstrates however, that structural multiplicity or dynamic disorder can be retained in protein complexes, termed as fuzziness. Fuzzy regions establish alternative contacts between specific partners usually via transient interactions. Nature often tailors the dynamic properties of these segments via post-translational modifications or alternative splicing to fine-tune affinity. Most experimentally characterized fuzzy complexes are involved in regulation of gene-expression, signal transduction and cell-cycle regulation. Fuzziness is also characteristic to viral protein complexes, cytoskeleton structure, and surprisingly in a few metabolic enzymes. A plausible role of fuzzy complexes in increasing half-life of intrinsically disordered proteins is also discussed.
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47
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MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome. Proc Natl Acad Sci U S A 2015; 112:5509-14. [PMID: 25870282 DOI: 10.1073/pnas.1505909112] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Epigenetic mechanisms, such as DNA methylation, regulate transcriptional programs to afford the genome flexibility in responding to developmental and environmental cues in health and disease. A prime example involving epigenetic dysfunction is the postnatal neurodevelopmental disorder Rett syndrome (RTT), which is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MeCP2). Despite decades of research, it remains unclear how MeCP2 regulates transcription or why RTT features appear 6-18 months after birth. Here we report integrated analyses of genomic binding of MeCP2, gene-expression data, and patterns of DNA methylation. In addition to the expected high-affinity binding to methylated cytosine in the CG context (mCG), we find a distinct epigenetic pattern of substantial MeCP2 binding to methylated cytosine in the non-CG context (mCH, where H = A, C, or T) in the adult brain. Unexpectedly, we discovered that genes that acquire elevated mCH after birth become preferentially misregulated in mouse models of MeCP2 disorders, suggesting that MeCP2 binding at mCH loci is key for regulating neuronal gene expression in vivo. This pattern is unique to the maturing and adult nervous system, as it requires the increase in mCH after birth to guide differential MeCP2 binding among mCG, mCH, and nonmethylated DNA elements. Notably, MeCP2 binds mCH with higher affinity than nonmethylated identical DNA sequences to influence the level of Bdnf, a gene implicated in the pathophysiology of RTT. This study thus provides insight into the molecular mechanism governing MeCP2 targeting and sheds light on the delayed onset of RTT symptoms.
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48
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Desai MA, Webb HD, Sinanan LM, Scarsdale JN, Walavalkar NM, Ginder GD, Williams DC. An intrinsically disordered region of methyl-CpG binding domain protein 2 (MBD2) recruits the histone deacetylase core of the NuRD complex. Nucleic Acids Res 2015; 43:3100-13. [PMID: 25753662 PMCID: PMC4381075 DOI: 10.1093/nar/gkv168] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 12/20/2022] Open
Abstract
The MBD2-NuRD (Nucleosome Remodeling and Deacetylase) complex is an epigenetic reader of DNA methylation that regulates genes involved in normal development and neoplastic diseases. To delineate the architecture and functional interactions of the MBD2-NuRD complex, we previously solved the structures of MBD2 bound to methylated DNA and a coiled-coil interaction between MBD2 and p66α that recruits the CHD4 nucleosome remodeling protein to the complex. The work presented here identifies novel structural and functional features of a previously uncharacterized domain of MBD2 (MBD2IDR). Biophysical analyses show that the MBD2IDR is an intrinsically disordered region (IDR). However, despite this inherent disorder, MBD2IDR increases the overall binding affinity of MBD2 for methylated DNA. MBD2IDR also recruits the histone deacetylase core components (RbAp48, HDAC2 and MTA2) of NuRD through a critical contact region requiring two contiguous amino acid residues, Arg(286) and Leu(287). Mutating these residues abrogates interaction of MBD2 with the histone deacetylase core and impairs the ability of MBD2 to repress the methylated tumor suppressor gene PRSS8 in MDA-MB-435 breast cancer cells. These findings expand our knowledge of the multi-dimensional interactions of the MBD2-NuRD complex that govern its function.
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Affiliation(s)
- Megha A Desai
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Heather D Webb
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Leander M Sinanan
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Neel Scarsdale
- Institute of Structural Biology and Drug Design, Center for the Study of Biological Complexity, and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ninad M Walavalkar
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gordon D Ginder
- Departments of Internal Medicine, Human and Molecular Genetics, and Microbiology and Immunology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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49
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Abstract
Rett syndrome (RTT) is a severe neurological disorder caused by mutations in the X-linked gene MECP2 (methyl-CpG-binding protein 2). Two decades of research have fostered the view that MeCP2 is a multifunctional chromatin protein that integrates diverse aspects of neuronal biology. More recently, studies have focused on specific RTT-associated mutations within the protein. This work has yielded molecular insights into the critical functions of MeCP2 that promise to simplify our understanding of RTT pathology.
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Affiliation(s)
- Matthew J Lyst
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Adrian Bird
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
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50
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Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:746157. [PMID: 26064184 PMCID: PMC4431600 DOI: 10.1155/2015/746157] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/11/2015] [Indexed: 12/25/2022]
Abstract
Rett Syndrome (RTT) is a progressive neurodevelopmental disease affecting females. RTT is caused by mutations in the MECP2 gene and various amino acid substitutions have been identified clinically in different domains of the multifunctional MeCP2 protein encoded by this gene. The R133C variant in the methylated-CpG-binding domain (MBD) of MeCP2 is the second most common disease-causing mutation in the MBD. Comparative molecular dynamics simulations of R133C mutant and wild-type MBD have been performed to understand the impact of the mutation on structure, dynamics, and interactions of the protein and subsequently understand the disease mechanism. Two salt bridges within the protein and two critical hydrogen bonds between the protein and DNA are lost upon the R133C mutation. The mutation was found to weaken the interaction with DNA and also cause loss of helicity within the 141-144 region. The structural, dynamical, and energetical consequences of R133C mutation were investigated in detail at the atomic resolution. Several important implications of this have been shown regarding protein stability and hydration dynamics as well as its interaction with DNA. The results are in agreement with previous experimental studies and further provide atomic level understanding of the molecular origin of RTT associated with R133C variant.
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