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Dudley-Fraser J, Rittinger K. It's a TRIM-endous view from the top: the varied roles of TRIpartite Motif proteins in brain development and disease. Front Mol Neurosci 2023; 16:1287257. [PMID: 38115822 PMCID: PMC10728303 DOI: 10.3389/fnmol.2023.1287257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
The tripartite motif (TRIM) protein family members have been implicated in a multitude of physiologies and pathologies in different tissues. With diverse functions in cellular processes including regulation of signaling pathways, protein degradation, and transcriptional control, the impact of TRIM dysregulation can be multifaceted and complex. Here, we focus on the cellular and molecular roles of TRIMs identified in the brain in the context of a selection of pathologies including cancer and neurodegeneration. By examining each disease in parallel with described roles in brain development, we aim to highlight fundamental common mechanisms employed by TRIM proteins and identify opportunities for therapeutic intervention.
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Affiliation(s)
- Jane Dudley-Fraser
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom
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Kim J, Choi TI, Park S, Kim MH, Kim CH, Lee S. Rnf220 cooperates with Zc4h2 to specify spinal progenitor domains. Development 2018; 145:145/17/dev165340. [DOI: 10.1242/dev.165340] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/13/2018] [Indexed: 11/20/2022]
Abstract
ABSTRACT
During early embryonic development of the spinal cord, graded sonic hedgehog signaling establishes distinct ventral progenitor domains by regulating the spatiotemporal expression of fate-specifying transcription factors. However, regulation of their protein stability remains incompletely understood. Here, we show that RNF220, an E3 ubiquitin ligase, plays crucial roles in the generation of the ventral progenitor domains, which produce ventral interneurons and motor neurons, by targeting key transcription factors including Dbx1/2 and Nkx2.2 for degradation. Surprisingly, RNF220 interacts with, and is co-expressed with, a zinc-finger protein ZC4H2, and they cooperate to degrade Dbx1/2 and Nkx2.2. RNF220-null mice show widespread alterations of ventral progenitor domains, including the loss of the p2 domain that produces V2 interneurons. Knockdown of RNF220 and ZC4H2 in the chick spinal cord downregulates expression of the V2 interneuronal marker Chx10. Co-expression of RNF220 and ZC4H2 further promotes the ability of Nkx6.1 to induce ectopic Chx10+ V2 interneurons. Our results uncover a novel regulatory pathway in establishing distinct progenitor domains through modulating the protein stability of transcription factors. Our results provide insights into the molecular mechanism by which ZC4H2 mutations lead to human syndromes characterized by delayed motor development.
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Affiliation(s)
- Jumee Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon 34134, Korea
| | - Shinhye Park
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Korea
| | - Seunghee Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea
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Regulation of REST levels overcomes dysregulation of neural stem cell differentiation caused by disruption of polyubiquitin gene Ubb. Biochem Biophys Res Commun 2017; 486:171-177. [PMID: 28285139 DOI: 10.1016/j.bbrc.2017.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/07/2017] [Indexed: 11/23/2022]
Abstract
Reduced levels of cellular ubiquitin (Ub) caused by disruption of the polyubiquitin gene Ubb lead to dysregulated differentiation of neural stem/progenitor cells (NSCs) and apoptosis in cells cultured in vitro. However, the underlying mechanisms responsible for these phenotypes in Ub-deficient cells have not been studied extensively. In the present study, we found that levels of repressor element-1 silencing transcription factor (REST) are elevated in Ubb-/- cells. To determine whether dysregulation of NSC differentiation is caused by the increased REST levels, we investigated the effect of reduced REST levels in Ubb-/- cells. Rest knockdown was found to increase the expression of the neuronal marker βIII-tubulin (TUJ1) and restore the expression pattern of the early neuronal marker α-internexin (α-INX) in Ubb-/- cells. Furthermore, Rest knockdown reduced Ub deficiency-induced apoptosis in cells cultured in vitro. Therefore, our study validates that cellular Ub levels are crucial for precise control of the levels of regulatory proteins such as REST during neurogenesis. We propose that regulation of Rest levels is a promising approach to overcome dysregulation of NSC differentiation caused by disruption of the polyubiquitin gene Ubb.
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Zhao Y, Alexandrov PN, Jaber V, Lukiw WJ. Deficiency in the Ubiquitin Conjugating Enzyme UBE2A in Alzheimer's Disease (AD) is Linked to Deficits in a Natural Circular miRNA-7 Sponge (circRNA; ciRS-7). Genes (Basel) 2016; 7:genes7120116. [PMID: 27929395 PMCID: PMC5192492 DOI: 10.3390/genes7120116] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/18/2016] [Accepted: 11/30/2016] [Indexed: 12/15/2022] Open
Abstract
Our understanding of the highly specialized functions for small non-coding single-stranded RNA (ssRNA) in the transcriptome of the human central nervous system (CNS) continues to evolve. Circular RNAs (circRNAs), a recently discovered class of ssRNA enriched in the brain and retina, are extremely stable and intrinsically resilient to degradation by exonuclease. Conventional methods of ssRNA, microRNA (miRNA), or messenger RNA (mRNA) detection and quantitation requiring free ribonucleotide ends may have considerably underestimated the quantity and significance of CNS circRNA in the CNS. Highly-specific small ssRNAs, such as the ~23 nucleotide (nt) Homo sapien microRNA-7 (hsa-miRNA-7; chr 9q21.32), are not only abundant in the human limbic system but are, in addition, associated with a ~1400 nt circRNA for miRNA-7 (ciRS-7) in the same anatomical region. Structurally, ciRS-7 contains about ~70 tandem anti-miRNA-7 sequences and acts as an endogenous, anti-complementary miRNA-7 “sponge” that attracts, binds, and, hence, quenches, natural miRNA-7 functions. Using a combination of DNA and miRNA array technologies, enhanced LED-Northern and Western blot hybridization, and the magnesium-dependent exoribonuclease and circRNA-sensitive probe RNaseR, here we provide evidence of a significantly misregulated ciRS-7-miRNA-7-UBE2A circuit in sporadic Alzheimer’s disease (AD) neocortex (Brodmann A22) and hippocampal CA1. Deficits in ciRS-7-mediated “sponging events”, resulting in excess ambient miRNA-7 appear to drive the selective down-regulation in the expression of miRNA-7-sensitive mRNA targets, such as that encoding the ubiquitin conjugating enzyme E2A (UBE2A; chr Xq24). UBE2A, which normally serves as a central effector in the ubiquitin-26S proteasome system, coordinates the clearance of amyloid peptides via proteolysis, is known to be depleted in sporadic AD brain and, hence, contributes to amyloid accumulation and the formation of senile plaque deposits. Dysfunction of circRNA-miRNA-mRNA regulatory systems appears to represent another important layer of epigenetic control over pathogenic gene expression programs in the human CNS that are targeted by the sporadic AD process.
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Affiliation(s)
- Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA.
- Department of Anatomy and Cell Biology, Louisiana State University Health Science Center, New Orleans, LA 70112, USA.
| | | | - Vivian Jaber
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA.
| | - Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA.
- Department of Ophthalmology, Louisiana State University Health Science Center, New Orleans, LA 70112, USA.
- Department of Neurology, Louisiana State University Health Science Center, New Orleans, LA 70112, USA.
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Fuller HR, Mandefro B, Shirran SL, Gross AR, Kaus AS, Botting CH, Morris GE, Sareen D. Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Have Reduced Expression of Proteins Important in Neuronal Development. Front Cell Neurosci 2016; 9:506. [PMID: 26793058 PMCID: PMC4707261 DOI: 10.3389/fncel.2015.00506] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/15/2015] [Indexed: 11/15/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an inherited neuromuscular disease primarily characterized by degeneration of spinal motor neurons, and caused by reduced levels of the SMN protein. Previous studies to understand the proteomic consequences of reduced SMN have mostly utilized patient fibroblasts and animal models. We have derived human motor neurons from type I SMA and healthy controls by creating their induced pluripotent stem cells (iPSCs). Quantitative mass spectrometry of these cells revealed increased expression of 63 proteins in control motor neurons compared to respective fibroblasts, whereas 30 proteins were increased in SMA motor neurons vs. their fibroblasts. Notably, UBA1 was significantly decreased in SMA motor neurons, supporting evidence for ubiquitin pathway defects. Subcellular distribution of UBA1 was predominantly cytoplasmic in SMA motor neurons in contrast to nuclear in control motor neurons; suggestive of neurodevelopmental abnormalities. Many of the proteins that were decreased in SMA motor neurons, including beta III-tubulin and UCHL1, were associated with neurodevelopment and differentiation. These neuron-specific consequences of SMN depletion were not evident in fibroblasts, highlighting the importance of iPSC technology. The proteomic profiles identified here provide a useful resource to explore the molecular consequences of reduced SMN in motor neurons, and for the identification of novel biomarker and therapeutic targets for SMA.
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Affiliation(s)
- Heidi R Fuller
- Wolfson Centre for Inherited Neuromuscular Disease, The Robert Jones and Agnes Hunt Orthopaedic HospitalOswestry, UK; Institute for Science and Technology in Medicine, Keele UniversityStaffordshire, UK
| | - Berhan Mandefro
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical CenterLos Angeles, CA, USA; iPSC Core, The David and Janet Polak Foundation Stem Cell Core LaboratoryLos Angeles, CA, USA
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews Fife, UK
| | - Andrew R Gross
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Anjoscha S Kaus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews Fife, UK
| | - Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, The Robert Jones and Agnes Hunt Orthopaedic HospitalOswestry, UK; Institute for Science and Technology in Medicine, Keele UniversityStaffordshire, UK
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical CenterLos Angeles, CA, USA; iPSC Core, The David and Janet Polak Foundation Stem Cell Core LaboratoryLos Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical CenterLos Angeles, CA, USA
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Saritas-Yildirim B, Pliner HA, Ochoa A, Silva EM. Genome-Wide Identification and Expression of Xenopus F-Box Family of Proteins. PLoS One 2015; 10:e0136929. [PMID: 26327321 PMCID: PMC4556705 DOI: 10.1371/journal.pone.0136929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/11/2015] [Indexed: 02/05/2023] Open
Abstract
Protein degradation via the multistep ubiquitin/26S proteasome pathway is a rapid way to alter the protein profile and drive cell processes and developmental changes. Many key regulators of embryonic development are targeted for degradation by E3 ubiquitin ligases. The most studied family of E3 ubiquitin ligases is the SCF ubiquitin ligases, which use F-box adaptor proteins to recognize and recruit target proteins. Here, we used a bioinformatics screen and phylogenetic analysis to identify and annotate the family of F-box proteins in the Xenopus tropicalis genome. To shed light on the function of the F-box proteins, we analyzed expression of F-box genes during early stages of Xenopus development. Many F-box genes are broadly expressed with expression domains localized to diverse tissues including brain, spinal cord, eye, neural crest derivatives, somites, kidneys, and heart. All together, our genome-wide identification and expression profiling of the Xenopus F-box family of proteins provide a foundation for future research aimed to identify the precise role of F-box dependent E3 ubiquitin ligases and their targets in the regulatory circuits of development.
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Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Hannah A. Pliner
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Angelica Ochoa
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Elena M. Silva
- Department of Biology, Georgetown University, Washington, DC, United States of America
- * E-mail:
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Saritas-Yildirim B, Childers CP, Elsik CG, Silva EM. Identification of REST targets in the Xenopus tropicalis genome. BMC Genomics 2015; 16:380. [PMID: 25971704 PMCID: PMC4430910 DOI: 10.1186/s12864-015-1591-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 04/28/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A major role of REST (repressor element-1 silencing transcription factor) is to inhibit the expression of neuronal genes in neural stem cells and non-neuronal cells by binding to a 21 bp consensus sequence and recruiting epigenetic and regulatory cofactors to gene regulatory regions. In neural stem cells, REST silences differentiation-promoting genes to prevent their premature expression and is central to the regulation of neurogenesis and the balance of neural stem cells and neurons. RESULTS To understand the role of REST in vertebrate neurogenesis, we performed a genome-wide screen for REST targets in Xenopus tropicalis. We identified 742 neuron-restrictive silencer elements (NRSE) associated with 1396 genes that are enriched in neuronal function. Comparative analyses revealed that characteristics of NRSE motifs in frog are similar to those in mammals in terms of the distance to target genes, frequency of motifs and the repertoire of putative target genes. In addition, we identified four F-box ubiquitin ligases as putative REST targets and determined that they are expressed in neuronal tissues during Xenopus development. CONCLUSION We identified a conserved core of putative target genes in human, mouse and frog that may be fundamental to REST function in vertebrates. We demonstrate that NRSE sites are associated with both protein-coding genes and lncRNAs in the human genome. Furthermore, we demonstrate that REST binding sites are abundant in low gene-occupancy regions of the human genome but this is not due to an increased association with non-coding RNAs. Our findings identify novel targets of REST and broaden the known mechanism of REST-mediated silencing in neurogenesis.
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Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
| | - Christopher P Childers
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Christine G Elsik
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. .,Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
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Sanz AL, Míguez DG. Dual R-Smads interplay in the regulation of vertebrate neurogenesis. NEUROGENESIS 2014. [DOI: 10.4161/neur.29529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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