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Vriend J, Liu XQ. Survival-Related Genes on Chromosomes 6 and 17 in Medulloblastoma. Int J Mol Sci 2024; 25:7506. [PMID: 39062749 PMCID: PMC11277021 DOI: 10.3390/ijms25147506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Survival of Medulloblastoma (MB) depends on various factors, including the gene expression profiles of MB tumor tissues. In this study, we identified 967 MB survival-related genes (SRGs) using a gene expression dataset and the Cox proportional hazards regression model. Notably, the SRGs were over-represented on chromosomes 6 and 17, known for the abnormalities monosomy 6 and isochromosome 17 in MB. The most significant SRG was HMGA1 (high mobility group AT-hook 1) on chromosome 6, which is a known oncogene and a histone H1 competitor. High expression of HMGA1 was associated with worse survival, primarily in the Group 3γ subtype. The high expression of HMGA1 was unrelated to any known somatic copy number alteration. Most SRGs on chromosome 17p were associated with low expression in Group 4β, the MB subtype, with 93% deletion of 17p and 98% copy gain of 17q. GO enrichment analysis showed that both chromosomes 6 and 17 included SRGs related to telomere maintenance and provided a rationale for testing telomerase inhibitors in Group 3 MBs. We conclude that HMGA1, along with other SRGs on chromosomes 6 and 17, warrant further investigation as potential therapeutic targets in selected subgroups or subtypes of MB.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xiao-Qing Liu
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
- Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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2
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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3
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Saleh O, Albakri K, Altiti A, Abutair I, Shalan S, Mohd OB, Negida A, Mushtaq G, Kamal MA. The Role of Non-coding RNAs in Alzheimer's Disease: Pathogenesis, Novel Biomarkers, and Potential Therapeutic Targets. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:731-745. [PMID: 37211844 DOI: 10.2174/1871527322666230519113201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/23/2023]
Abstract
Long non-coding RNAs (IncRNAs) are regulatory RNA transcripts that have recently been associated with the onset of many neurodegenerative illnesses, including Alzheimer's disease (AD). Several IncRNAs have been found to be associated with AD pathophysiology, each with a distinct mechanism. In this review, we focused on the role of IncRNAs in the pathogenesis of AD and their potential as novel biomarkers and therapeutic targets. Searching for relevant articles was done using the PubMed and Cochrane library databases. Studies had to be published in full text in English in order to be considered. Some IncRNAs were found to be upregulated, while others were downregulated. Dysregulation of IncRNAs expression may contribute to AD pathogenesis. Their effects manifest as the synthesis of beta-amyloid (Aβ) plaques increases, thereby altering neuronal plasticity, inducing inflammation, and promoting apoptosis. Despite the need for more investigations, IncRNAs could potentially increase the sensitivity of early detection of AD. Until now, there has been no effective treatment for AD. Hence, InRNAs are promising molecules and may serve as potential therapeutic targets. Although several dysregulated AD-associated lncRNAs have been discovered, the functional characterization of most lncRNAs is still lacking.
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Affiliation(s)
- Othman Saleh
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
- Medical Research Group of Egypt, Cairo, Egypt
| | | | - Iser Abutair
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Suhaib Shalan
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | | | - Ahmed Negida
- Medical Research Group of Egypt, Cairo, Egypt
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Ave, Boston, MA, 02115, USA
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
- Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Gohar Mushtaq
- Center for Scientific Research, Faculty of Medicine, Idlib University, Idlib, Syria
| | - Mohammad A Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Daffodil Smart City, Birulia 1216, Bangladesh
- Enzymoics, 7 Peterlee place, Hebersham, NSW 2770, Novel Global Community Educational Foundation, Hebersham, Australia
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4
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Li X, Wang Y, Deng S, Zhu G, Wang C, Johnson NA, Zhang Z, Tirado CR, Xu Y, Metang LA, Gonzalez J, Mukherji A, Ye J, Yang Y, Peng W, Tang Y, Hofstad M, Xie Z, Yoon H, Chen L, Liu X, Chen S, Zhu H, Strand D, Liang H, Raj G, He HH, Mendell JT, Li B, Wang T, Mu P. Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer. Cancer Cell 2023; 41:1427-1449.e12. [PMID: 37478850 PMCID: PMC10530398 DOI: 10.1016/j.ccell.2023.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 05/24/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Abstract
Tumor mutational burden and heterogeneity has been suggested to fuel resistance to many targeted therapies. The cytosine deaminase APOBEC proteins have been implicated in the mutational signatures of more than 70% of human cancers. However, the mechanism underlying how cancer cells hijack the APOBEC mediated mutagenesis machinery to promote tumor heterogeneity, and thereby foster therapy resistance remains unclear. We identify SYNCRIP as an endogenous molecular brake which suppresses APOBEC-driven mutagenesis in prostate cancer (PCa). Overactivated APOBEC3B, in SYNCRIP-deficient PCa cells, is a key mutator, representing the molecular source of driver mutations in some frequently mutated genes in PCa, including FOXA1, EP300. Functional screening identifies eight crucial drivers for androgen receptor (AR)-targeted therapy resistance in PCa that are mutated by APOBEC3B: BRD7, CBX8, EP300, FOXA1, HDAC5, HSF4, STAT3, and AR. These results uncover a cell-intrinsic mechanism that unleashes APOBEC-driven mutagenesis, which plays a significant role in conferring AR-targeted therapy resistance in PCa.
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Affiliation(s)
- Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guanghui Zhu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Nickolas A Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zeda Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yaru Xu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lauren A Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Julisa Gonzalez
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Atreyi Mukherji
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuqiu Yang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei Peng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yitao Tang
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Mia Hofstad
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhiqun Xie
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Heewon Yoon
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Liping Chen
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xihui Liu
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Hong Zhu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Douglas Strand
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ganesh Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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5
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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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6
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Lan Z, Chen Y, Jin J, Xu Y, Zhu X. Long Non-coding RNA: Insight Into Mechanisms of Alzheimer's Disease. Front Mol Neurosci 2022; 14:821002. [PMID: 35095418 PMCID: PMC8795976 DOI: 10.3389/fnmol.2021.821002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD), a heterogeneous neurodegenerative disorder, is the most common cause of dementia accounting for an estimated 60–80% of cases. The pathogenesis of AD remains unclear, and no curative treatment is available so far. Increasing evidence has revealed a vital role of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs), in AD. LncRNAs contribute to the pathogenesis of AD via modulating amyloid production, Tau hyperphosphorylation, mitochondrial dysfunction, oxidative stress, synaptic impairment and neuroinflammation. This review describes the biological functions and mechanisms of lncRNAs in AD, indicating that lncRNAs may provide potential therapeutic targets for the diagnosis and treatment of AD.
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Affiliation(s)
- Zhen Lan
- Department of Neurology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
| | - Yanting Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, the Affiliated Hospital of Nanjing University Medical School, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Jiali Jin
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, the Affiliated Hospital of Nanjing University Medical School, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, the Affiliated Hospital of Nanjing University Medical School, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
- Institute of Brain Sciences, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
- Nanjing Neuropsychiatry Clinic Medical Center, Nanjing, China
| | - Xiaolei Zhu
- Department of Neurology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, the Affiliated Hospital of Nanjing University Medical School, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
- Institute of Brain Sciences, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
- Nanjing Neuropsychiatry Clinic Medical Center, Nanjing, China
- *Correspondence: Xiaolei Zhu
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7
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Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci 2021; 8:696438. [PMID: 34395528 PMCID: PMC8362101 DOI: 10.3389/fmolb.2021.696438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.
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Affiliation(s)
- Elisabeth Lata
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Karine Choquet
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Francis Sagliocco
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Martin Teichmann
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
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8
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Keihani S, Kluever V, Fornasiero EF. Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function. Molecules 2021; 26:molecules26133951. [PMID: 34203457 PMCID: PMC8272081 DOI: 10.3390/molecules26133951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.
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9
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Gillentine MA, Wang T, Hoekzema K, Rosenfeld J, Liu P, Guo H, Kim CN, De Vries BBA, Vissers LELM, Nordenskjold M, Kvarnung M, Lindstrand A, Nordgren A, Gecz J, Iascone M, Cereda A, Scatigno A, Maitz S, Zanni G, Bertini E, Zweier C, Schuhmann S, Wiesener A, Pepper M, Panjwani H, Torti E, Abid F, Anselm I, Srivastava S, Atwal P, Bacino CA, Bhat G, Cobian K, Bird LM, Friedman J, Wright MS, Callewaert B, Petit F, Mathieu S, Afenjar A, Christensen CK, White KM, Elpeleg O, Berger I, Espineli EJ, Fagerberg C, Brasch-Andersen C, Hansen LK, Feyma T, Hughes S, Thiffault I, Sullivan B, Yan S, Keller K, Keren B, Mignot C, Kooy F, Meuwissen M, Basinger A, Kukolich M, Philips M, Ortega L, Drummond-Borg M, Lauridsen M, Sorensen K, Lehman A, Lopez-Rangel E, Levy P, Lessel D, Lotze T, Madan-Khetarpal S, Sebastian J, Vento J, Vats D, Benman LM, Mckee S, Mirzaa GM, Muss C, Pappas J, Peeters H, Romano C, Elia M, Galesi O, Simon MEH, van Gassen KLI, Simpson K, Stratton R, Syed S, Thevenon J, Palafoll IV, Vitobello A, Bournez M, Faivre L, Xia K, Earl RK, Nowakowski T, Bernier RA, Eichler EE. Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders. Genome Med 2021; 13:63. [PMID: 33874999 PMCID: PMC8056596 DOI: 10.1186/s13073-021-00870-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype-phenotype correlations, with clinical characterization remaining a bottleneck for understanding NDDs. Most disease-associated Mendelian genes are members of gene families, and we hypothesize that those with related molecular function share clinical presentations. METHODS We tested our hypothesis by considering gene families that have multiple members with an enrichment of de novo variants among NDDs, as determined by previous meta-analyses. One of these gene families is the heterogeneous nuclear ribonucleoproteins (hnRNPs), which has 33 members, five of which have been recently identified as NDD genes (HNRNPK, HNRNPU, HNRNPH1, HNRNPH2, and HNRNPR) and two of which have significant enrichment in our previous meta-analysis of probands with NDDs (HNRNPU and SYNCRIP). Utilizing protein homology, mutation analyses, gene expression analyses, and phenotypic characterization, we provide evidence for variation in 12 HNRNP genes as candidates for NDDs. Seven are potentially novel while the remaining genes in the family likely do not significantly contribute to NDD risk. RESULTS We report 119 new NDD cases (64 de novo variants) through sequencing and international collaborations and combined with published clinical case reports. We consider 235 cases with gene-disruptive single-nucleotide variants or indels and 15 cases with small copy number variants. Three hnRNP-encoding genes reach nominal or exome-wide significance for de novo variant enrichment, while nine are candidates for pathogenic mutations. Comparison of HNRNP gene expression shows a pattern consistent with a role in cerebral cortical development with enriched expression among radial glial progenitors. Clinical assessment of probands (n = 188-221) expands the phenotypes associated with HNRNP rare variants, and phenotypes associated with variation in the HNRNP genes distinguishes them as a subgroup of NDDs. CONCLUSIONS Overall, our novel approach of exploiting gene families in NDDs identifies new HNRNP-related disorders, expands the phenotypes of known HNRNP-related disorders, strongly implicates disruption of the hnRNPs as a whole in NDDs, and supports that NDD subtypes likely have shared molecular pathogenesis. To date, this is the first study to identify novel genetic disorders based on the presence of disorders in related genes. We also perform the first phenotypic analyses focusing on related genes. Finally, we show that radial glial expression of these genes is likely critical during neurodevelopment. This is important for diagnostics, as well as developing strategies to best study these genes for the development of therapeutics.
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Affiliation(s)
- Madelyn A Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Jill Rosenfeld
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Hui Guo
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Bert B A De Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magnus Nordenskjold
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jozef Gecz
- School of Medicine and the Robinson Research Institute, the University of Adelaide at the Women's and Children's Hospital, Adelaide, South Australia, Australia.,Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Agnese Scatigno
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Genetic Unit, Department of Pediatrics, Fondazione MBBM S. Gerardo Hospital, Monza, Italy
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sarah Schuhmann
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Micah Pepper
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | - Heena Panjwani
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | | | - Farida Abid
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paldeep Atwal
- The Atwal Clinic: Genomic & Personalized Medicine, Jacksonville, FL, USA
| | - Carlos A Bacino
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gifty Bhat
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Katherine Cobian
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Jennifer Friedman
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Meredith S Wright
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Florence Petit
- Clinique de Génétique, Hôpital Jeanne de Flandre, Bâtiment Modulaire, CHU, 59037, Lille Cedex, France
| | - Sophie Mathieu
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Alexandra Afenjar
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Celenie K Christensen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kerry M White
- Department of Medical and Molecular Genetics, IU Health, Indianapolis, IN, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Itai Berger
- Pediatric Neurology, Assuta-Ashdod University Hospital, Ashdod, Israel.,Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Edward J Espineli
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Timothy Feyma
- Gillette Children's Specialty Healthcare, Saint Paul, MN, USA
| | - Susan Hughes
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA.,The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA.,Children's Mercy Kansas City, Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Shuang Yan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kory Keller
- Oregon Health & Science University, Corvallis, OR, USA
| | - Boris Keren
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Cyril Mignot
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Alice Basinger
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Mary Kukolich
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Meredith Philips
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Lucia Ortega
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | | | - Mathilde Lauridsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kristina Sorensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital and BC Women's Hospital, Vancouver, BC, Canada
| | | | - Elena Lopez-Rangel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Division of Developmental Pediatrics, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada.,Sunny Hill Health Centre for Children, Vancouver, BC, Canada
| | - Paul Levy
- Department of Pediatrics, The Children's Hospital at Montefiore, Bronx, NY, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Lotze
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Suneeta Madan-Khetarpal
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.,UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jodie Vento
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Divya Vats
- Kaiser Permanente Southern California, Los Angeles, CA, USA
| | | | - Shane Mckee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Candace Muss
- Al Dupont Hospital for Children, Wilmington, DE, USA
| | - John Pappas
- NYU Grossman School of Medicine, Department of Pediatrics, Clinical Genetic Services, New York, NY, USA
| | - Hilde Peeters
- Center for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | | | | | | | - Marleen E H Simon
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Kara Simpson
- Rare Disease Institute, Children's National Health System, Washington, DC, USA
| | - Robert Stratton
- Department of Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Sabeen Syed
- Department of Pediatric Gastroenterology, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Julien Thevenon
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebrón, Barcelona, Spain
| | | | - Antonio Vitobello
- UF Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne and INSERM UMR1231 GAD, Université de Bourgogne Franche-Comté, F-21000, Dijon, France.,INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France
| | - Marie Bournez
- Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Rachel K Earl
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tomasz Nowakowski
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Raphael A Bernier
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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10
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Khudayberdiev S, Soutschek M, Ammann I, Heinze A, Rust MB, Baumeister S, Schratt G. The cytoplasmic SYNCRIP mRNA interactome of mammalian neurons. RNA Biol 2020; 18:1252-1264. [PMID: 33030396 DOI: 10.1080/15476286.2020.1830553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
SYNCRIP, a member of the cellular heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins, regulates various aspects of neuronal development and plasticity. Although SYNCRIP has been identified as a component of cytoplasmic RNA granules in dendrites of mammalian neurons, only little is known about the specific SYNCRIP target mRNAs that mediate its effect on neuronal morphogenesis and function. Here, we present a comprehensive characterization of the cytoplasmic SYNCRIP mRNA interactome using iCLIP in primary rat cortical neurons. We identify hundreds of bona fide SYNCRIP target mRNAs, many of which encode for proteins involved in neurogenesis, neuronal migration and neurite outgrowth. From our analysis, the stabilization of mRNAs encoding for components of the microtubule network, such as doublecortin (Dcx), emerges as a novel mechanism of SYNCRIP function in addition to the previously reported control of actin dynamics. Furthermore, we found that SYNCRIP synergizes with pro-neural miRNAs, such as miR-9. Thus, SYNCRIP appears to promote early neuronal differentiation by a two-tier mechanism involving the stabilization of pro-neural mRNAs by direct 3'UTR interaction and the repression of anti-neural mRNAs in a complex with neuronal miRISC. Together, our findings provide a rationale for future studies investigating the function of SYNCRIP in mammalian brain development and disease.
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Affiliation(s)
- Sharof Khudayberdiev
- Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps-University of Marburg, Marburg, Germany
| | - Michael Soutschek
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Irina Ammann
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Anika Heinze
- Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps-University of Marburg, Marburg, Germany
| | - Marco B Rust
- Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps-University of Marburg, Marburg, Germany
| | - Stefan Baumeister
- Fachbereich Biologie - Protein Analytik, Philipps-Universität Marburg, Marburg, Germany
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
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11
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Titlow J, Robertson F, Järvelin A, Ish-Horowicz D, Smith C, Gratton E, Davis I. Syncrip/hnRNP Q is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation. J Cell Biol 2020; 219:133707. [PMID: 32040548 PMCID: PMC7055005 DOI: 10.1083/jcb.201903135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/21/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
Memory and learning involve activity-driven expression of proteins and cytoskeletal reorganization at new synapses, requiring posttranscriptional regulation of localized mRNA a long distance from corresponding nuclei. A key factor expressed early in synapse formation is Msp300/Nesprin-1, which organizes actin filaments around the new synapse. How Msp300 expression is regulated during synaptic plasticity is poorly understood. Here, we show that activity-dependent accumulation of Msp300 in the postsynaptic compartment of the Drosophila larval neuromuscular junction is regulated by the conserved RNA binding protein Syncrip/hnRNP Q. Syncrip (Syp) binds to msp300 transcripts and is essential for plasticity. Single-molecule imaging shows that msp300 is associated with Syp in vivo and forms ribosome-rich granules that contain the translation factor eIF4E. Elevated neural activity alters the dynamics of Syp and the number of msp300:Syp:eIF4E RNP granules at the synapse, suggesting that these particles facilitate translation. These results introduce Syp as an important early acting activity-dependent regulator of a plasticity gene that is strongly associated with human ataxias.
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Affiliation(s)
- Joshua Titlow
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Aino Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David Ish-Horowicz
- Department of Biochemistry, University of Oxford, Oxford, UK.,Medical Research Council Lab for Molecular Cell Biology, University College London, London, UK
| | - Carlas Smith
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
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12
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Taha MS, Haghighi F, Stefanski A, Nakhaei-Rad S, Kazemein Jasemi NS, Al Kabbani MA, Görg B, Fujii M, Lang PA, Häussinger D, Piekorz RP, Stühler K, Ahmadian MR. Novel FMRP interaction networks linked to cellular stress. FEBS J 2020; 288:837-860. [PMID: 32525608 DOI: 10.1111/febs.15443] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/09/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Silencing of the fragile X mental retardation 1 (FMR1) gene and consequently lack of synthesis of FMR protein (FMRP) are associated with fragile X syndrome, which is one of the most prevalent inherited intellectual disabilities, with additional roles in increased viral infection, liver disease, and reduced cancer risk. FMRP plays critical roles in chromatin dynamics, RNA binding, mRNA transport, and mRNA translation. However, the underlying molecular mechanisms, including the (sub)cellular FMRP protein networks, remain elusive. Here, we employed affinity pull-down and quantitative LC-MS/MS analyses with FMRP. We identified known and novel candidate FMRP-binding proteins as well as protein complexes. FMRP interacted with 180 proteins, 28 of which interacted with its N terminus. Interaction with the C terminus of FMRP was observed for 102 proteins, and 48 proteins interacted with both termini. This FMRP interactome comprises known FMRP-binding proteins, including the ribosomal proteins FXR1P, NUFIP2, Caprin-1, and numerous novel FMRP candidate interacting proteins that localize to different subcellular compartments, including CARF, LARP1, LEO1, NOG2, G3BP1, NONO, NPM1, SKIP, SND1, SQSTM1, and TRIM28. Our data considerably expand the protein and RNA interaction networks of FMRP, which thereby suggest that, in addition to its known functions, FMRP participates in transcription, RNA metabolism, ribonucleoprotein stress granule formation, translation, DNA damage response, chromatin dynamics, cell cycle regulation, ribosome biogenesis, miRNA biogenesis, and mitochondrial organization. Thus, FMRP seems associated with multiple cellular processes both under normal and cell stress conditions in neuronal as well as non-neuronal cell types, as exemplified by its role in the formation of stress granules.
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Affiliation(s)
- Mohamed S Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany.,Research on Children with Special Needs Department, Medical Research Branch, National Research Centre, Cairo, Egypt
| | - Fereshteh Haghighi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Heinrich Heine-University, Düsseldorf, Germany
| | - Saeideh Nakhaei-Rad
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Mohamed Aghyad Al Kabbani
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Boris Görg
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty of the Heinrich Heine-University, Düsseldorf, Germany
| | - Masahiro Fujii
- Division of Virology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Phillip A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine-University, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty of the Heinrich Heine-University, Düsseldorf, Germany
| | - Roland P Piekorz
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich Heine-University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
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13
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Booy EP, McRae EK, Ezzati P, Choi T, Gussakovsky D, McKenna SA. Comprehensive analysis of the BC200 ribonucleoprotein reveals a reciprocal regulatory function with CSDE1/UNR. Nucleic Acids Res 2019; 46:11575-11591. [PMID: 30247708 PMCID: PMC6265466 DOI: 10.1093/nar/gky860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
BC200 is a long non-coding RNA primarily expressed in brain but aberrantly expressed in various cancers. To gain a further understanding of the function of BC200, we performed proteomic analyses of the BC200 ribonucleoprotein (RNP) by transfection of 3′ DIG-labelled BC200. Protein binding partners of the functionally related murine RNA BC1 as well as a scrambled BC200 RNA were also assessed in both human and mouse cell lines. Stringent validation of proteins identified by mass spectrometry confirmed 14 of 84 protein binding partners and excluded eight proteins that did not appreciably bind BC200 in reverse experiments. Gene ontology analyses revealed general roles in RNA metabolic processes, RNA processing and splicing. Protein/RNA interaction sites were mapped with a series of RNA truncations revealing three distinct modes of interaction involving either the 5′ Alu-domain, 3′ A-rich or 3′ C-rich regions. Due to their high enrichment values in reverse experiments, CSDE1 and STRAP were further analyzed demonstrating a direct interaction between CSDE1 and BC200 and indirect binding of STRAP to BC200 via heterodimerization with CSDE1. Knock-down studies identified a reciprocal regulatory relationship between CSDE1 and BC200 and immunofluorescence analysis of BC200 knock-down cells demonstrated a dramatic reorganization of CSDE1 into distinct nuclear foci.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ewan Ks McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Section of Biomedical Proteomics, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba and Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Taegi Choi
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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14
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Choquet K, Forget D, Meloche E, Dicaire MJ, Bernard G, Vanderver A, Schiffmann R, Fabian MR, Teichmann M, Coulombe B, Brais B, Kleinman CL. Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200. J Biol Chem 2019; 294:7445-7459. [PMID: 30898877 PMCID: PMC6509492 DOI: 10.1074/jbc.ra118.006271] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small noncoding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A, encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3–HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has so far been elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c.2554A→G (p.M852V) into human cell lines and assessed its impact on Pol III biogenesis, nuclear import, DNA occupancy, transcription, and protein levels. Transcriptomic profiling uncovered a subset of transcripts vulnerable to Pol III hypofunction, including a global reduction in tRNA levels. The brain cytoplasmic BC200 RNA (BCYRN1), involved in translation regulation, was consistently affected in all our cellular models, including patient-derived fibroblasts. Genomic BC200 deletion in an oligodendroglial cell line led to major transcriptomic and proteomic changes, having a larger impact than those of POLR3A mutations. Upon differentiation, mRNA levels of the MBP gene, encoding myelin basic protein, were significantly decreased in POLR3A-mutant cells. Our findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3–HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease.
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Affiliation(s)
- Karine Choquet
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Diane Forget
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Elisabeth Meloche
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Marie-Josée Dicaire
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Geneviève Bernard
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,Pediatrics, McGill University, Montréal, Québec H3A 0G4, Canada.,the Department of Internal Medicine, Division of Medical Genetics, Montréal Children's Hospital, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Child Health and Human Development Program, and.,MyeliNeuroGene Laboratory, Research Institute, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Departments of Neurology and Neurosurgery and
| | - Adeline Vanderver
- the Division of Neurology, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania 19104
| | - Raphael Schiffmann
- the Institute of Metabolic Disease, Baylor Research Institute, Dallas, Texas 75204
| | - Marc R Fabian
- the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Martin Teichmann
- INSERM U1212-CNRS UMR5320, Université de Bordeaux, Bordeaux, France, and
| | - Benoit Coulombe
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada.,the Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Bernard Brais
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada.,the Departments of Neurology and Neurosurgery and
| | - Claudia L Kleinman
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada, .,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
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15
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Cortini F, Roma F, Villa C. Emerging roles of long non-coding RNAs in the pathogenesis of Alzheimer's disease. Ageing Res Rev 2019; 50:19-26. [PMID: 30610928 DOI: 10.1016/j.arr.2019.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 01/01/2019] [Indexed: 01/02/2023]
Abstract
Alzheimer's disease (AD) is a heterogeneous neurodegenerative disorder and represents the most common form of senile dementia. The pathogenesis of AD is not yet completely understood and no curative treatment is currently available. With the recent advancement in transcriptome-wide profiling approach, several non-coding RNAs (ncRNAs) have been identified. Among them, long non-coding RNAs (lncRNAs), which are long transcripts without apparent protein-coding capacity, have received increasing interest for their involvement in a wide range of biological processes as regulatory molecules. Recent studies have suggested that lncRNAs play a role in AD pathogenesis, although their specific influences in the disorder remain to be largely unknown. Herein, we will summarize the biology and mechanisms of action of the best characterized dysregulated lncRNAs in AD, focusing the attention on their potential role in the disease pathogenesis. A deeper understanding of the molecular mechanisms and the complex network of interactions in which they are implicated should open the doors to new research considering lncRNAs as novel therapeutic targets and prognostic/diagnostic biomarkers.
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Affiliation(s)
- Francesca Cortini
- Department of Clinical Sciences and Community Health, University of Milan, IRCCS Ca' Granda Foundation, Milan, Italy; UOC Occupational Medicine, Department of Medicine Preventive Services, IRCCS Ca Granda Foundation Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesca Roma
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
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16
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Shin H, Kim Y, Kim M, Lee Y. BC200 RNA: An Emerging Therapeutic Target and Diagnostic Marker for Human Cancer. Mol Cells 2018; 41:993-999. [PMID: 30590906 PMCID: PMC6315322 DOI: 10.14348/molcells.2018.0425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
One of the most interesting findings from genome-wide expression analysis is that a considerable amount of noncoding RNA (ncRNA) is present in the cell. Recent studies have identified diverse biological functions of ncRNAs, which are expressed in a much wider array of forms than proteins. Certain ncRNAs associated with diseases, in particular, have attracted research attention as novel therapeutic targets and diagnostic markers. BC200 RNA, a 200-nucleotide ncRNA originally identified as a neuron-specific transcript, is abnormally over-expressed in several types of cancer tissue. A number of recent studies have suggested mechanisms by which abnormal expression of BC200 RNA contributes to the development of cancer. In this article, we first provide a brief review of a recent progress in identifying functions of BC200 RNA in cancer cells, and then offer examples of other ncRNAs as new therapeutic targets and diagnostic markers for human cancer. Finally, we discuss future directions of studies on BC200 RNA for new cancer treatments.
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Affiliation(s)
- Heegwon Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Youngmi Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Meehyein Kim
- Virus Research and Testing Group, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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17
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Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation. Biochem J 2018; 475:2727-2748. [PMID: 30072491 DOI: 10.1042/bcj20180239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 11/17/2022]
Abstract
Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.
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18
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Samson J, Cronin S, Dean K. BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer. Noncoding RNA Res 2018; 3:131-143. [PMID: 30175286 PMCID: PMC6114260 DOI: 10.1016/j.ncrna.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022] Open
Abstract
With the discovery that the level of RNA synthesis in human cells far exceeds what is required to express protein-coding genes, there has been a concerted scientific effort to identify, catalogue and uncover the biological functions of the non-coding transcriptome. Long, non-coding RNAs (lncRNAs) are a diverse group of RNAs with equally wide-ranging biological roles in the cell. An increasing number of studies have reported alterations in the expression of lncRNAs in various cancers, although unravelling how they contribute specifically to the disease is a bigger challenge. Originally described as a brain-specific, non-coding RNA, BC200 (BCYRN1) is a 200-nucleotide, predominantly cytoplasmic lncRNA that has been linked to neurodegenerative disease and several types of cancer. Here we summarise what is known about BC200, primarily from studies in neuronal systems, before turning to a review of recent work that aims to understand how this lncRNA contributes to cancer initiation, progression and metastasis, along with its possible clinical utility as a biomarker or therapeutic target.
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Affiliation(s)
| | | | - K. Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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19
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Tropea D, Hardingham N, Millar K, Fox K. Mechanisms underlying the role of DISC1 in synaptic plasticity. J Physiol 2018; 596:2747-2771. [PMID: 30008190 PMCID: PMC6046077 DOI: 10.1113/jp274330] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/02/2018] [Indexed: 12/11/2022] Open
Abstract
Disrupted in schizophrenia 1 (DISC1) is an important hub protein, forming multimeric complexes by self-association and interacting with a large number of synaptic and cytoskeletal molecules. The synaptic location of DISC1 in the adult brain suggests a role in synaptic plasticity, and indeed, a number of studies have discovered synaptic plasticity impairments in a variety of different DISC1 mutants. This review explores the possibility that DISC1 is an important molecule for organizing proteins involved in synaptic plasticity and examines why mutations in DISC1 impair plasticity. It concentrates on DISC1's role in interacting with synaptic proteins, controlling dendritic structure and cellular trafficking of mRNA, synaptic vesicles and mitochondria. N-terminal directed mutations appear to impair synaptic plasticity through interactions with phosphodiesterase 4B (PDE4B) and hence protein kinase A (PKA)/GluA1 and PKA/cAMP response element-binding protein (CREB) signalling pathways, and affect spine structure through interactions with kalirin 7 (Kal-7) and Rac1. C-terminal directed mutations also impair plasticity possibly through altered interactions with lissencephaly protein 1 (LIS1) and nuclear distribution protein nudE-like 1 (NDEL1), thereby affecting developmental processes such as dendritic structure and spine maturation. Many of the same molecules involved in DISC1's cytoskeletal interactions are also involved in intracellular trafficking, raising the possibility that impairments in intracellular trafficking affect cytoskeletal development and vice versa. While the multiplicity of DISC1 protein interactions makes it difficult to pinpoint a single causal signalling pathway, we suggest that the immediate-term effects of N-terminal influences on GluA1, Rac1 and CREB, coupled with the developmental effects of C-terminal influences on trafficking and the cytoskeleton make up the two main branches of DISC1's effect on synaptic plasticity and dendritic spine stability.
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Affiliation(s)
- Daniela Tropea
- Neurospychiatric GeneticsTrinity Center for Health Sciences and Trinity College Institute of Neuroscience (TCIN)Trinity College DublinDublinIreland
| | - Neil Hardingham
- School of BiosciencesMuseum AvenueCardiff UniversityCardiffUK
| | - Kirsty Millar
- Centre for Genomic & Experimental MedicineMRC Institute of Genetics & Molecular MedicineWestern General HospitalUniversity of EdinburghCrewe RoadEdinburghUK
| | - Kevin Fox
- School of BiosciencesMuseum AvenueCardiff UniversityCardiffUK
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20
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Epigenetic modulation by small molecule compounds for neurodegenerative disorders. Pharmacol Res 2018; 132:135-148. [PMID: 29684672 DOI: 10.1016/j.phrs.2018.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/18/2022]
Abstract
The accumulation of somatic and genetic mutations which altered the structure and coding information of the DNA are the major cause of neurological disorders. However, our recent understanding of molecular mechanisms of 'epigenetic' phenomenon reveals that the modifications of chromatin play a significant role in the development and severity of neurological disorders. These epigenetic processes are dynamic and reversible as compared to genetic ablations which are stable and irreversible. Therefore, targeting these epigenetic processes through small molecule modulators are of great therapeutic potential. To date, large number of small molecule modulators have been discovered which are capable of altering the brain pathology by targeting epigenetic enzymes. In this review, we shall put forward the key studies supporting the role of altered epigenetic processes in neurological disorders with especial emphasis on neurodegenerative disorders. A few small molecule modulators which have been shown to possess promising results in the animal model system of neurological disorders will also be discussed with future perspectives.
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21
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Hu G, Niu F, Humburg BA, Liao K, Bendi S, Callen S, Fox HS, Buch S. Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. Oncotarget 2018; 9:18648-18663. [PMID: 29719633 PMCID: PMC5915100 DOI: 10.18632/oncotarget.24307] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
LncRNAs are long non-coding regulatory RNAs that are longer than 200 nucleotides. One of the major functions of lncRNAs is the regulation of specific gene expression at multiple steps including, recruitment and expression of basal transcription machinery, post-transcriptional modifications and epigenetics [1]. Emerging evidence suggests that lncRNAs also play a critical role in maintaining tissue homeostasis during physiological and pathological conditions, lipid homeostasis, as well as epithelial and smooth muscle cell homeostasis, a topic that has been elegantly reviewed [2-5]. While aberrant expression of lncRNAs has been implicated in several disease conditions, there is paucity of information about their contribution to the etiology of diseases [6]. Several studies have compared the expression of lncRNAs under normal and cancerous conditions and found differential expression of several lncRNAs, suggesting thereby an involvement of lncRNAs in disease processes [7, 8]. Furthermore, the ability of lncRNAs to influence epigenetic changes also underlies their role in disease pathogenesis since epigenetic regulation is known to play a critical role in many human diseases [1]. LncRNAs thus are not only involved in homeostatic functioning but also play a vital role in the progression of many diseases, thereby underscoring their potential as novel therapeutic targets for the alleviation of a variety of human disease conditions.
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Affiliation(s)
- Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Niu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bree A. Humburg
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ke Liao
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sunil Bendi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon Callen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S. Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
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22
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Landskron L, Steinmann V, Bonnay F, Burkard TR, Steinmann J, Reichardt I, Harzer H, Laurenson AS, Reichert H, Knoblich JA. The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells. eLife 2018; 7:31347. [PMID: 29580384 PMCID: PMC5871330 DOI: 10.7554/elife.31347] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor cells display features that are not found in healthy cells. How they become immortal and how their specific features can be exploited to combat tumorigenesis are key questions in tumor biology. Here we describe the long non-coding RNA cherub that is critically required for the development of brain tumors in Drosophila but is dispensable for normal development. In mitotic Drosophila neural stem cells, cherub localizes to the cell periphery and segregates into the differentiating daughter cell. During tumorigenesis, de-differentiation of cherub-high cells leads to the formation of tumorigenic stem cells that accumulate abnormally high cherub levels. We show that cherub establishes a molecular link between the RNA-binding proteins Staufen and Syncrip. As Syncrip is part of the molecular machinery specifying temporal identity in neural stem cells, we propose that tumor cells proliferate indefinitely, because cherub accumulation no longer allows them to complete their temporal neurogenesis program. Many biological signals control how cells grow and divide. However, cancer cells do not obey these growth-restricting signals, and as a result large tumors may develop. Recent experiments have suggested that stem cells – the precursors to the different types of specialized cells found in the body – are particularly important for generating tumors. A stem cell normally divides unequally to form a self-renewing cell and a more specialized cell (often a progenitor cell that will give rise to increasingly specialized cell types). The timing of when the specialization occurs can be key to guiding the ultimately produced cell progenies to their final identity. However, in a tumor cells can retain the ability to self-renew. Ultimately, the resulting ‘tumor stem cells’ become immortal and proliferate indefinitely. It is not fully understood why this uncontrolled proliferation occurs. Just like mammals (including humans), fruit flies can develop tumors. Some of the DNA mutations responsible for tumor development were already identified in flies as early as in the 1970s. This has made fruit flies a well-studied model system for uncovering the principle defects that cause tumors to form. Landskron et al. have now studied the neural stem cells found in brain tumors in fruit flies. Additional DNA mutations were not responsible for these cells becoming immortal. Instead, certain RNA molecules – products that are ‘transcribed’ from the DNA – were present in different amounts in tumor cells. The RNA that showed the greatest increase in tumor cells is a so-called long non-coding RNA named cherub. This RNA molecule has no important role in normal fruit flies, but is critical for tumor formation. Landskron et al. found that during cell division cherub segregates from the neural stem cells to the newly formed progenitor cells, where it breaks down over time. Progenitor cells that contain high levels of cherub give rise to tumor-generating neural stem cells. At the molecular level, cherubhelps two proteins to interact with each other: one called Syncrip that makes the neural stem cells take on a older identity, and another one (Staufen) that tethers it to the cell membrane. By restricting Syncrip to a particular location in the cell, cherub alters the timing of stem cell specialization, which contributes to tumor formation. Overall, the results presented by Landskron et al. reveal a new role for long non-coding RNAs: controlling the localization of the proteins that determine the fate of the cell. They also highlight a critical link between the timing of stem cell development and the proliferation of the cells. Further work is now needed to test whether the same control mechanism works in species other than fruit flies.
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Affiliation(s)
- Lisa Landskron
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Steinmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Francois Bonnay
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas R Burkard
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Jonas Steinmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Ilka Reichardt
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Heike Harzer
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Jürgen A Knoblich
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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23
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Pérez-Boza J, Lion M, Struman I. Exploring the RNA landscape of endothelial exosomes. RNA (NEW YORK, N.Y.) 2018; 24:423-435. [PMID: 29282313 PMCID: PMC5824360 DOI: 10.1261/rna.064352.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/21/2017] [Indexed: 05/05/2023]
Abstract
Exosomes are small extracellular vesicles of around 100 nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids, and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes are still not completely elucidated. In this study, by the use of next-generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and noncoding RNA species found per compartment. We have also discovered a set of unique genes preferentially included (or excluded) into vesicles. Moreover, after studying the enrichment of RNA motifs in the genes unequally distributed between cells and exosomes, we have detected a set of enriched sequences for several classes of RNA. In conclusion, our results provide the basis for studying the involvement of RNA-binding proteins capable of recognizing RNA sequences and their role in the export of RNAs into exosomes.
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Affiliation(s)
- Jennifer Pérez-Boza
- Laboratory of Molecular Angiogenesis, GIGA-R, University of Liège, 4000 Liège, Belgium
| | - Michelle Lion
- Laboratory of Molecular Angiogenesis, GIGA-R, University of Liège, 4000 Liège, Belgium
| | - Ingrid Struman
- Laboratory of Molecular Angiogenesis, GIGA-R, University of Liège, 4000 Liège, Belgium
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24
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Kulkarni S, Ramsuran V, Rucevic M, Singh S, Lied A, Kulkarni V, O'hUigin C, Le Gall S, Carrington M. Posttranscriptional Regulation of HLA-A Protein Expression by Alternative Polyadenylation Signals Involving the RNA-Binding Protein Syncrip. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:3892-3899. [PMID: 29055006 PMCID: PMC5812486 DOI: 10.4049/jimmunol.1700697] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/25/2017] [Indexed: 01/15/2023]
Abstract
Genomic variation in the untranslated region (UTR) has been shown to influence HLA class I expression level and associate with disease outcomes. Sequencing of the 3'UTR of common HLA-A alleles indicated the presence of two polyadenylation signals (PAS). The proximal PAS is conserved, whereas the distal PAS is disrupted within certain alleles by sequence variants. Using 3'RACE, we confirmed expression of two distinct forms of the HLA-A 3'UTR based on use of either the proximal or the distal PAS, which differ in length by 100 bp. Specific HLA-A alleles varied in the usage of the proximal versus distal PAS, with some alleles using only the proximal PAS, and others using both the proximal and distal PAS to differing degrees. We show that the short and the long 3'UTR produced similar mRNA expression levels. However, the long 3'UTR conferred lower luciferase activity as compared with the short form, indicating translation inhibition of the long 3'UTR. RNA affinity pull-down followed by mass spectrometry analysis as well as RNA coimmunoprecipitation indicated differential binding of Syncrip to the long versus short 3'UTR. Depletion of Syncrip by small interfering RNA increased surface expression of an HLA-A allotype that uses primarily the long 3'UTR, whereas an allotype expressing only the short form was unaffected. Furthermore, specific blocking of the proximal 3'UTR reduced surface expression without decreasing mRNA expression. These data demonstrate HLA-A allele-specific variation in PAS usage, which modulates their cell surface expression posttranscriptionally.
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Affiliation(s)
- Smita Kulkarni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139;
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Veron Ramsuran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for the AIDS Programme of Research in South Africa, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; and
| | | | - Sukhvinder Singh
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Alexandra Lied
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Viraj Kulkarni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Colm O'hUigin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
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25
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Santangelo L, Giurato G, Cicchini C, Montaldo C, Mancone C, Tarallo R, Battistelli C, Alonzi T, Weisz A, Tripodi M. The RNA-Binding Protein SYNCRIP Is a Component of the Hepatocyte Exosomal Machinery Controlling MicroRNA Sorting. Cell Rep 2017; 17:799-808. [PMID: 27732855 DOI: 10.1016/j.celrep.2016.09.031] [Citation(s) in RCA: 400] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/06/2016] [Accepted: 09/09/2016] [Indexed: 12/21/2022] Open
Abstract
Despite clear evidence that exosomal microRNAs (miRNAs) are able to modulate the cellular microenvironment and that exosomal RNA cargo selection is deregulated in pathological conditions, the mechanisms controlling specific RNA sorting into extracellular vesicles are still poorly understood. Here, we identified the RNA binding protein SYNCRIP (synaptotagmin-binding cytoplasmic RNA-interacting protein; also known as hnRNP-Q or NSAP1) as a component of the hepatocyte exosomal miRNA sorting machinery. SYNCRIP knockdown impairs sorting of miRNAs in exosomes. Furthermore, SYNCRIP directly binds to specific miRNAs enriched in exosomes sharing a common extra-seed sequence (hEXO motif). The hEXO motif has a role in the regulation of miRNA localization, since embedment of this motif into a poorly exported miRNA enhances its loading into exosomes. This evidence provides insights into the mechanisms of miRNA exosomal sorting process. Moreover, these findings open the way for the possible selective modification of the miRNAs exosomal cargo.
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Affiliation(s)
- Laura Santangelo
- Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Schola Medica Salernitana, University of Salerno, Via Salvador Allende 1, 84081 Baronissi, Italy
| | - Carla Cicchini
- Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
| | - Claudia Montaldo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - Carmine Mancone
- Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Schola Medica Salernitana, University of Salerno, Via Salvador Allende 1, 84081 Baronissi, Italy
| | - Cecilia Battistelli
- Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
| | - Tonino Alonzi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Schola Medica Salernitana, University of Salerno, Via Salvador Allende 1, 84081 Baronissi, Italy
| | - Marco Tripodi
- Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149 Rome, Italy.
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26
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Kim Y, Lee J, Shin H, Jang S, Kim SC, Lee Y. Biosynthesis of brain cytoplasmic 200 RNA. Sci Rep 2017; 7:6884. [PMID: 28761139 PMCID: PMC5537265 DOI: 10.1038/s41598-017-05097-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA), a neuron-specific non-coding RNA, is also highly expressed in a number of tumors of non-neuronal origin. However, the biosynthesis of BC200 RNA remains poorly understood. In this study, we show that the efficient transcription of BC200 RNA requires both internal and upstream promoter elements in cancer cells. The transcription complex seems to interact with a broad range of sequences within the upstream 100-bp region. The cellular levels and half-lives of BC200 RNA were found to differ across various cancer cell types, but there was no significant correlation between these parameters. Exogenously expressed BC200 RNA had a shorter half-life than that observed for the endogenous version in cancer cells, suggesting that BC200 RNA might be protected by some limiting factor(s) in cancer cells. Transient transfection experiments showed that the transcriptional activity of the exogenous BC200 RNA promoter element varied depending on the cancer cell type. However, the promoter activities together with the half-life data could not explain the differences in the levels of BC200 RNA among different cell types, suggesting that there is another level of transcriptional regulation beyond that detected by our transient transfection experiments.
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Affiliation(s)
- Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Sun Chang Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea.
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27
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Quan Z, Zheng D, Qing H. Regulatory Roles of Long Non-Coding RNAs in the Central Nervous System and Associated Neurodegenerative Diseases. Front Cell Neurosci 2017; 11:175. [PMID: 28713244 PMCID: PMC5491930 DOI: 10.3389/fncel.2017.00175] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes. Mounting evidence has indicated dysregulation or mutations in lncRNA gene loci are associated with a variety of CNS-associated neurodegenerative disorders, such as Alzheimer's, Parkinson's, Huntington's diseases, Amyotrophic Lateral Sclerosis and others. However, how lncRNAs contribute to these disorders remains to be further explored and studied. In this review article, we systematically and comprehensively summarize the current studies of lncRNAs, demonstrate the specificity of lncRNAs expressed in the brain, their functions during neural development and expression profiles in major cell types of the CNS, highlight the regulatory mechanisms of several studied lncRNAs that may play essential roles in the pathophysiology of neurodegenerative diseases, and discuss the current challenges and future perspectives of lncRNA studies involved in neurodegenerative and other diseases.
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Affiliation(s)
- Zhenzhen Quan
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Da Zheng
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Hong Qing
- School of Life Science, Beijing Institute of TechnologyBeijing, China
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28
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Choquet K, Yang S, Moir RD, Forget D, Larivière R, Bouchard A, Poitras C, Sgarioto N, Dicaire MJ, Noohi F, Kennedy TE, Rochford J, Bernard G, Teichmann M, Coulombe B, Willis IM, Kleinman CL, Brais B. Absence of neurological abnormalities in mice homozygous for the Polr3a G672E hypomyelinating leukodystrophy mutation. Mol Brain 2017; 10:13. [PMID: 28407788 PMCID: PMC5391615 DOI: 10.1186/s13041-017-0294-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/04/2017] [Indexed: 01/08/2023] Open
Abstract
Recessive mutations in the ubiquitously expressed POLR3A gene cause one of the most frequent forms of childhood-onset hypomyelinating leukodystrophy (HLD): POLR3-HLD. POLR3A encodes the largest subunit of RNA Polymerase III (Pol III), which is responsible for the transcription of transfer RNAs (tRNAs) and a large array of other small non-coding RNAs. In order to study the central nervous system pathophysiology of the disease, we introduced the French Canadian founder Polr3a mutation c.2015G > A (p.G672E) in mice, generating homozygous knock-in (KI/KI) as well as compound heterozygous mice for one Polr3a KI and one null allele (KI/KO). Both KI/KI and KI/KO mice are viable and are able to reproduce. To establish if they manifest a motor phenotype, WT, KI/KI and KI/KO mice were submitted to a battery of behavioral tests over one year. The KI/KI and KI/KO mice have overall normal balance, muscle strength and general locomotion. Cerebral and cerebellar Luxol Fast Blue staining and measurement of levels of myelin proteins showed no significant differences between the three groups, suggesting that myelination is not overtly impaired in Polr3a KI/KI and KI/KO mice. Finally, expression levels of several Pol III transcripts in the brain showed no statistically significant differences. We conclude that the first transgenic mice with a leukodystrophy-causing Polr3a mutation do not recapitulate the childhood-onset HLD observed in the majority of human patients with POLR3A mutations, and provide essential information to guide selection of Polr3a mutations for developing future mouse models of the disease.
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Affiliation(s)
- Karine Choquet
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Sharon Yang
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Robyn D Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Diane Forget
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Roxanne Larivière
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Annie Bouchard
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Christian Poitras
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Nicolas Sgarioto
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Marie-Josée Dicaire
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Forough Noohi
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Timothy E Kennedy
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | | | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, and Pediatrics, McGill University, Montreal, Canada.,Department of Medical Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Martin Teichmann
- INSERM U1212 - CNRS UMR5320, Université de Bordeaux, Bordeaux, France
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada.,Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - Ian M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada. .,Department of Human Genetics, McGill University, Montréal, Québec, Canada.
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29
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Jang S, Shin H, Lee J, Kim Y, Bak G, Lee Y. Regulation of BC200 RNA-mediated translation inhibition by hnRNP E1 and E2. FEBS Lett 2017; 591:393-405. [PMID: 28027391 DOI: 10.1002/1873-3468.12544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 12/28/2022]
Abstract
The long noncoding RNA BC200 (brain cytoplasmic RNA, 200 nucleotides) acts as a translational modulator of local protein synthesis at dendrites. BC200 RNA has been shown to inhibit translation in vitro, but it remains unknown how this translation inhibition might be controlled in a cell. Here, we performed yeast three-hybrid screening and identified hnRNP E1 and hnRNP E2 as BC200 RNA-interacting proteins. We found that: these hnRNA proteins could restore BC200 RNA-inhibited translation; BC200 RNA interacts with hnRNP E1 and E2 mainly through its unique 3' C-rich domain; and the RNA binding specificities and modes of the two proteins differed somewhat. Our results offer new insights into the regulation of BC200 RNA-mediated translation inhibition.
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Affiliation(s)
| | | | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, Korea
| | - Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, Korea
| | - Geunu Bak
- Department of Chemistry, KAIST, Daejeon, Korea
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30
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Barger SW. Gene regulation and genetics in neurochemistry, past to future. J Neurochem 2016; 139 Suppl 2:24-57. [PMID: 27747882 DOI: 10.1111/jnc.13629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/01/2016] [Accepted: 03/30/2016] [Indexed: 12/14/2022]
Abstract
Ask any neuroscientist to name the most profound discoveries in the field in the past 60 years, and at or near the top of the list will be a phenomenon or technique related to genes and their expression. Indeed, our understanding of genetics and gene regulation has ushered in whole new systems of knowledge and new empirical approaches, many of which could not have even been imagined prior to the molecular biology boon of recent decades. Neurochemistry, in the classic sense, intersects with these concepts in the manifestation of neuropeptides, obviously dependent upon the central dogma (the established rules by which DNA sequence is eventually converted into protein primary structure) not only for their conformation but also for their levels and locales of expression. But, expanding these considerations to non-peptide neurotransmitters illustrates how gene regulatory events impact neurochemistry in a much broader sense, extending beyond the neurochemicals that translate electrical signals into chemical ones in the synapse, to also include every aspect of neural development, structure, function, and pathology. From the beginning, the mutability - yet relative stability - of genes and their expression patterns were recognized as potential substrates for some of the most intriguing phenomena in neurobiology - those instances of plasticity required for learning and memory. Near-heretical speculation was offered in the idea that perhaps the very sequence of the genome was altered to encode memories. A fascinating component of the intervening progress includes evidence that the central dogma is not nearly as rigid and consistent as we once thought. And this mutability extends to the potential to manipulate that code for both experimental and clinical purposes. Astonishing progress has been made in the molecular biology of neurochemistry during the 60 years since this journal debuted. Many of the gains in conceptual understanding have been driven by methodological progress, from automated high-throughput sequencing instruments to recombinant-DNA vectors that can convey color-coded genetic modifications in the chromosomes of live adult animals. This review covers the highlights of these advances, both theoretical and technological, along with a brief window into the promising science ahead. This article is part of the 60th Anniversary special issue.
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Affiliation(s)
- Steven W Barger
- Department of Geriatrics, Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA. .,Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, Arkansas, USA.
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31
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Lee HR, Kim TD, Kim HJ, Jung Y, Lee D, Lee KH, Kim DY, Woo KC, Kim KT. Heterogeneous ribonucleoprotein R regulates arylalkylamine N-acetyltransferase synthesis via internal ribosomal entry site-mediated translation in a circadian manner. J Pineal Res 2015; 59:518-29. [PMID: 26444903 DOI: 10.1111/jpi.12284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/02/2015] [Indexed: 01/07/2023]
Abstract
Rhythmic arylalkylamine N-acetyltransferase (AANAT) synthesis is a prominent circadian-controlled response that occurs in most mammals. AANAT is the core enzyme in melatonin production; because melatonin participates in many physiological processes, the regulation of AANAT is an important research topic. In this study, we focused on the role of heterogeneous ribonucleoprotein R (hnRNP R) in the translation of AANAT. A novel RNA-binding protein hnRNP R widely interacted with the 5' untranslated region (UTR) of AANAT mRNA and contributed to translation through an internal ribosomal entry site (IRES). Fine-tuning of AANAT protein synthesis occurred in response to knockdown and overexpression of hnRNP R. Nocturnal elevation of AANAT protein was dependent on the rhythmic changes of hnRNP R, whose levels are elevated in the pineal gland during nighttime. Increases in hnRNP R additionally improved AANAT production in rat pinealocytes under norepinephrine (NE) treatment. These results suggest that cap-independent translation of AANAT mRNA plays a role in the rhythmic synthesis of melatonin through the recruitment of translational machinery to hnRNP R-bound AANAT mRNA.
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Affiliation(s)
- Hwa-Rim Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Tae-Don Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
| | - Hyo-Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Youngseob Jung
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Dohyun Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Kyung-Ha Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Do-Yeon Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Kyung-Chul Woo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
- Newlife Cosmetics R&D Center for Skin Science, Gyeongsansi, Gyeongbuk, Korea
| | - Kyong-Tai Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Korea
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32
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Sosińska P, Mikuła-Pietrasik J, Książek K. The double-edged sword of long non-coding RNA: The role of human brain-specific BC200 RNA in translational control, neurodegenerative diseases, and cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 766:58-67. [DOI: 10.1016/j.mrrev.2015.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/29/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022]
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33
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Kuchler L, Giegerich AK, Sha LK, Knape T, Wong MSK, Schröder K, Brandes RP, Heide H, Wittig I, Brüne B, von Knethen A. SYNCRIP-dependent Nox2 mRNA destabilization impairs ROS formation in M2-polarized macrophages. Antioxid Redox Signal 2014; 21:2483-97. [PMID: 24844655 DOI: 10.1089/ars.2013.5760] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS During sepsis, macrophages are alternatively activated toward an M2-like phenotype on contact with apoptotic cells (ACs) or their secretion products. Simultaneously, NADPH oxidase-dependent reactive oxygen species (ROS) formation is attenuated, thus contributing to immune paralysis. However, the exact mechanism remains elusive. Here, we provide mechanistic insights into diminished mRNA stability of the NADPH oxidase Nox2 on macrophage M2 polarization and therefore reduced ROS formation in sepsis. RESULTS Murine J774A.1 macrophages were stimulated with conditioned medium (CM) of apoptotic T cells, which reduced Nox2 mRNA and protein expression, consequently decreasing ROS production. An mRNA pulldown approach coupled to mass spectrometry analysis identified the RNA-binding protein SYNCRIP attached to the Nox2 mRNA 3' untranslated region (3'UTR). The binding of SYNCRIP to the 3'UTR of Nox2 mRNA is attenuated after treatment with CM of apoptotic T cells, followed by Nox2 mRNA destabilization. In in vivo models of polymicrobial sepsis such as cecal ligation and puncture, SYNCRIP was strongly downregulated, which was associated with a decreased Nox2 expression in peritoneal macrophages. INNOVATION Downregulation of SYNCRIP in macrophages after contact to material of ACs destabilized Nox2 mRNA and impaired ROS formation, thereby contributing to an M2 phenotype shift of macrophages in sepsis. CONCLUSION M2 polarization of macrophages in sepsis results in an attenuated SYNCRIP binding to the 3'UTR of Nox2 mRNA, destabilizing Nox2 mRNA abundance and expression. Consequently, ROS formation needed to fight against recurrent infections is impaired. In conclusion, SYNCRIP-regulated Nox2 mRNA degradation mediates the hypoinflammatory phase of sepsis.
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Affiliation(s)
- Laura Kuchler
- 1 Faculty of Medicine, Institute of Biochemistry I-Pathobiochemistry, Goethe-University Frankfurt , Frankfurt, Germany
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34
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McDermott SM, Yang L, Halstead JM, Hamilton RS, Meignin C, Davis I. Drosophila Syncrip modulates the expression of mRNAs encoding key synaptic proteins required for morphology at the neuromuscular junction. RNA (NEW YORK, N.Y.) 2014; 20:1593-606. [PMID: 25171822 PMCID: PMC4174441 DOI: 10.1261/rna.045849.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/09/2014] [Indexed: 05/24/2023]
Abstract
Localized mRNA translation is thought to play a key role in synaptic plasticity, but the identity of the transcripts and the molecular mechanism underlying their function are still poorly understood. Here, we show that Syncrip, a regulator of localized translation in the Drosophila oocyte and a component of mammalian neuronal mRNA granules, is also expressed in the Drosophila larval neuromuscular junction, where it regulates synaptic growth. We use RNA-immunoprecipitation followed by high-throughput sequencing and qRT-PCR to show that Syncrip associates with a number of mRNAs encoding proteins with key synaptic functions, including msp-300, syd-1, neurexin-1, futsch, highwire, discs large, and α-spectrin. The protein levels of MSP-300, Discs large, and a number of others are significantly affected in syncrip null mutants. Furthermore, syncrip mutants show a reduction in MSP-300 protein levels and defects in muscle nuclear distribution characteristic of msp-300 mutants. Our results highlight a number of potential new players in localized translation during synaptic plasticity in the neuromuscular junction. We propose that Syncrip acts as a modulator of synaptic plasticity by regulating the translation of these key mRNAs encoding synaptic scaffolding proteins and other important components involved in synaptic growth and function.
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Affiliation(s)
- Suzanne M McDermott
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Lu Yang
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - James M Halstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Russell S Hamilton
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Carine Meignin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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35
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Wigington CP, Williams KR, Meers MP, Bassell GJ, Corbett AH. Poly(A) RNA-binding proteins and polyadenosine RNA: new members and novel functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:601-22. [PMID: 24789627 PMCID: PMC4332543 DOI: 10.1002/wrna.1233] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/07/2014] [Accepted: 03/06/2014] [Indexed: 02/05/2023]
Abstract
Poly(A) RNA-binding proteins (Pabs) bind with high affinity and specificity to polyadenosine RNA. Textbook models show a nuclear Pab, PABPN1, and a cytoplasmic Pab, PABPC, where the nuclear PABPN1 modulates poly(A) tail length and the cytoplasmic PABPC stabilizes poly(A) RNA in the cytoplasm and also enhances translation. While these conventional roles are critically important, the Pab family has expanded recently both in number and in function. A number of novel roles have emerged for both PAPBPN1 and PABPC that contribute to the fine-tuning of gene expression. Furthermore, as the characterization of the nucleic acid binding properties of RNA-binding proteins advances, additional proteins that show high affinity and specificity for polyadenosine RNA are being discovered. With this expansion of the Pab family comes a concomitant increase in the potential for Pabs to modulate gene expression. Further complication comes from an expansion of the potential binding sites for Pab proteins as revealed by an analysis of templated polyadenosine stretches present within the transcriptome. Thus, Pabs could influence mRNA fate and function not only by binding to the nontemplated poly(A) tail but also to internal stretches of adenosine. Understanding the diverse functions of Pab proteins is not only critical to understand how gene expression is regulated but also to understand the molecular basis for tissue-specific diseases that occur when Pab proteins are altered. Here we describe both conventional and recently emerged functions for PABPN1 and PABPC and then introduce and discuss three new Pab family members, ZC3H14, hnRNP-Q1, and LARP4.
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Affiliation(s)
- Callie P. Wigington
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kathryn R. Williams
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P. Meers
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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36
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Halstead JM, Lin YQ, Durraine L, Hamilton RS, Ball G, Neely GG, Bellen HJ, Davis I. Syncrip/hnRNP Q influences synaptic transmission and regulates BMP signaling at the Drosophila neuromuscular synapse. Biol Open 2014; 3:839-49. [PMID: 25171887 PMCID: PMC4163661 DOI: 10.1242/bio.20149027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Synaptic plasticity involves the modulation of synaptic connections in response to neuronal activity via multiple pathways. One mechanism modulates synaptic transmission by retrograde signals from the post-synapse that influence the probability of vesicle release in the pre-synapse. Despite its importance, very few factors required for the expression of retrograde signals, and proper synaptic transmission, have been identified. Here, we identify the conserved RNA binding protein Syncrip as a new factor that modulates the efficiency of vesicle release from the motoneuron and is required for correct synapse structure. We show that syncrip is required genetically and its protein product is detected only in the muscle and not in the motoneuron itself. This unexpected non-autonomy is at least partly explained by the fact that Syncrip modulates retrograde BMP signals from the muscle back to the motoneuron. We show that Syncrip influences the levels of the Bone Morphogenic Protein ligand Glass Bottom Boat from the post-synapse and regulates the pre-synapse. Our results highlight the RNA-binding protein Syncrip as a novel regulator of synaptic output. Given its known role in regulating translation, we propose that Syncrip is important for maintaining a balance between the strength of presynaptic vesicle release and postsynaptic translation.
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Affiliation(s)
- James M Halstead
- Department of Biochemistry, South Parks Road, The University of Oxford, Oxford OX1 3QU, UK Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland
| | - Yong Qi Lin
- Howard Hughes Medical Institute, Department of Molecular and Human Genetics, Department of Neuroscience, Program in Developmental Biology, Neurological Research Institute at Baylor College of Medicine, Houston, TX 77030, USA Neuroscience Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Lita Durraine
- Howard Hughes Medical Institute, Department of Molecular and Human Genetics, Department of Neuroscience, Program in Developmental Biology, Neurological Research Institute at Baylor College of Medicine, Houston, TX 77030, USA
| | - Russell S Hamilton
- Department of Biochemistry, South Parks Road, The University of Oxford, Oxford OX1 3QU, UK
| | - Graeme Ball
- Micron Imaging Facility, Department of Biochemistry, South Parks Road, The University of Oxford, Oxford OX1 3QU, UK
| | - Greg G Neely
- Neuroscience Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Hugo J Bellen
- Howard Hughes Medical Institute, Department of Molecular and Human Genetics, Department of Neuroscience, Program in Developmental Biology, Neurological Research Institute at Baylor College of Medicine, Houston, TX 77030, USA
| | - Ilan Davis
- Department of Biochemistry, South Parks Road, The University of Oxford, Oxford OX1 3QU, UK
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37
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Li X, Wu Z, Fu X, Han W. lncRNAs: insights into their function and mechanics in underlying disorders. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 762:1-21. [PMID: 25485593 DOI: 10.1016/j.mrrev.2014.04.002] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 12/14/2022]
Abstract
Genomes of complex organisms are characterized by the pervasive expression of different types of noncoding RNAs (ncRNAs). lncRNAs constitute a large family of long—arbitrarily defined as being longer than 200 nucleotides—ncRNAs that are expressed throughout the cell and that include thousands of different species. While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown at present. Existing examples suggest that lncRNAs have fulfilled a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass signal, decoy, scaffold and guide capacities, derive from folded modular domains in lncRNAs. Early discoveries support a paradigm in which lncRNAs regulate transcription networks via chromatin modulation, but new functions are steadily emerging. Given the biochemical versatility of RNA, lncRNAs may be used for various tasks, including posttranscriptional processing. In addition, long intergenic ncRNAs (lincRNAs) are strongly enriched for trait-associated SNPs, which suggest a new mechanism by which intergenic trait-associated regions might function. Moreover, multiple lines of evidence increasingly link mutations and dysregulations of lncRNAs to diverse human diseases, especially disorders related to aging. In this article, we review the current state of the knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions and mechanisms of action of these molecules. We highlight the growing evidence for the importance of lncRNAs in diverse human disorders and the indications that their dysregulations and mutations underlie some aging-related disorders. Finally, we consider the potential medical implications, and future potential in the application of lncRNAs as therapeutic targets and diagnostic markers.
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Affiliation(s)
- Xiaolei Li
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhiqiang Wu
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaobing Fu
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China; Key Laboratory of Wound Healing and Cell Biology, Institute of Burns, The First Affiliated Hospital to the Chinese PLA General Hospital, Trauma Center of Postgraduate Medical School, Beijing 100037, China.
| | - Weidong Han
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China.
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38
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Vučićević D, Schrewe H, Orom UA. Molecular mechanisms of long ncRNAs in neurological disorders. Front Genet 2014; 5:48. [PMID: 24624135 PMCID: PMC3941653 DOI: 10.3389/fgene.2014.00048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/15/2014] [Indexed: 01/02/2023] Open
Abstract
Long non-coding RNAs (ncRNAs) have added an unexpected layer of complexity in the regulation of gene expression. Mounting evidence now links long ncRNAs to fundamental biological processes such as development and differentiation, and recent research shows important involvement of long ncRNAs in a variety of diseases including neurodegenerative disorders, such as Parkinson’s, Alzheimer’s, spinocerebellar ataxia, and Huntington’s diseases. Furthermore, long ncRNAs are speculated to be implicated in development of psychiatric disorders such as schizophrenia and bipolar disorders. Long ncRNAs contribute to these disorders in diverse ways, from regulation of transcription to modulation of RNA processing and translation. In this review, we describe the diverse mechanisms reported for long ncRNAs, and discuss how they could mechanistically be involved in the development of neurological disorders.
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Affiliation(s)
- Dubravka Vučićević
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Heinrich Schrewe
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Ulf A Orom
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics Berlin, Germany
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39
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Johnson EM, Daniel DC, Gordon J. The pur protein family: genetic and structural features in development and disease. J Cell Physiol 2013; 228:930-7. [PMID: 23018800 PMCID: PMC3747735 DOI: 10.1002/jcp.24237] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/21/2012] [Indexed: 12/19/2022]
Abstract
The Pur proteins are an ancient family of sequence-specific single-stranded nucleic acid-binding proteins. They bind a G-rich element in either single- or double-stranded nucleic acids and are capable of displacing the complementary C-rich strand. Recently several reports have described Pur family member knockouts, mutations, and disease aberrations. Together with a recent crystal structure of Purα, these data reveal conserved structural features of these proteins that have been adapted to serve functions unique to higher eukaryotes. In humans Pur proteins are critical for myeloid cell development, muscle development, and brain development, including trafficking of mRNA to neuronal dendrites. Pur family members have been implicated in diseases as diverse as cancer, premature aging, and fragile-X mental retardation syndrome.
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Affiliation(s)
- Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507-1696, USA.
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Long noncoding RNAs in development and disease of the central nervous system. Trends Genet 2013; 29:461-8. [PMID: 23562612 DOI: 10.1016/j.tig.2013.03.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/25/2013] [Accepted: 03/11/2013] [Indexed: 12/29/2022]
Abstract
The central nervous system (CNS) is a complex biological system composed of numerous cell types working in concert. The intricate development and functioning of this highly ordered structure depends upon exquisite spatial and temporal control of gene expression in the cells comprising the CNS. Thus, gene regulatory networks that control cell fates and functions play critical roles in the CNS. Failure to develop and maintain intricate regulatory networks properly leads to impaired development or neural dysfunction, which might manifest as neurological disorders. Long noncoding RNAs (lncRNAs) are emerging as important components of gene regulatory networks, working in concert with transcription factors and epigenetic regulators of gene expression. Interestingly, many lncRNAs are highly expressed in the adult and developing brain, often showing precise temporal and spatial patterns of expression. This specificity of expression and growing awareness of the importance of lncRNAs suggest that they play key roles in CNS development and function. In this review, we highlight the growing evidence for the importance of lncRNAs in the CNS and the indications that their dysregulation underlies some neurological disorders.
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Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, Hempel M, Horn D, Hoyer J, Joset P, Röpke A, Moog U, Riess A, Thiel CT, Tzschach A, Wiesener A, Wohlleber E, Zweier C, Ekici AB, Zink AM, Rump A, Meisinger C, Grallert H, Sticht H, Schenck A, Engels H, Rappold G, Schröck E, Wieacker P, Riess O, Meitinger T, Reis A, Strom TM. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 2012; 380:1674-82. [PMID: 23020937 DOI: 10.1016/s0140-6736(12)61480-9] [Citation(s) in RCA: 764] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND The genetic cause of intellectual disability in most patients is unclear because of the absence of morphological clues, information about the position of such genes, and suitable screening methods. Our aim was to identify de-novo variants in individuals with sporadic non-syndromic intellectual disability. METHODS In this study, we enrolled children with intellectual disability and their parents from ten centres in Germany and Switzerland. We compared exome sequences between patients and their parents to identify de-novo variants. 20 children and their parents from the KORA Augsburg Diabetes Family Study were investigated as controls. FINDINGS We enrolled 51 participants from the German Mental Retardation Network. 45 (88%) participants in the case group and 14 (70%) in the control group had de-novo variants. We identified 87 de-novo variants in the case group, with an exomic mutation rate of 1·71 per individual per generation. In the control group we identified 24 de-novo variants, which is 1·2 events per individual per generation. More participants in the case group had loss-of-function variants than in the control group (20/51 vs 2/20; p=0·022), suggesting their contribution to disease development. 16 patients carried de-novo variants in known intellectual disability genes with three recurrently mutated genes (STXBP1, SYNGAP1, and SCN2A). We deemed at least six loss-of-function mutations in six novel genes to be disease causing. We also identified several missense alterations with potential pathogenicity. INTERPRETATION After exclusion of copy-number variants, de-novo point mutations and small indels are associated with severe, sporadic non-syndromic intellectual disability, accounting for 45-55% of patients with high locus heterogeneity. Autosomal recessive inheritance seems to contribute little in the outbred population investigated. The large number of de-novo variants in known intellectual disability genes is only partially attributable to known non-specific phenotypes. Several patients did not meet the expected syndromic manifestation, suggesting a strong bias in present clinical syndrome descriptions. FUNDING German Ministry of Education and Research, European Commission 7th Framework Program, and Swiss National Science Foundation.
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Affiliation(s)
- Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schwerzenbach-Zurich, Switzerland
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McDermott SM, Meignin C, Rappsilber J, Davis I. Drosophila Syncrip binds the gurken mRNA localisation signal and regulates localised transcripts during axis specification. Biol Open 2012; 1:488-97. [PMID: 23213441 PMCID: PMC3507208 DOI: 10.1242/bio.2012885] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In the Drosophila oocyte, mRNA transport and localised translation play a fundamental role in axis determination and germline formation of the future embryo. gurken mRNA encodes a secreted TGF-α signal that specifies dorsal structures, and is localised to the dorso-anterior corner of the oocyte via a cis-acting 64 nucleotide gurken localisation signal. Using GRNA chromatography, we characterised the biochemical composition of the ribonucleoprotein complexes that form around the gurken mRNA localisation signal in the oocyte. We identified a number of the factors already known to be involved in gurken localisation and translational regulation, such as Squid and Imp, in addition to a number of factors with known links to mRNA localisation, such as Me31B and Exu. We also identified previously uncharacterised Drosophila proteins, including the fly homologue of mammalian SYNCRIP/hnRNPQ, a component of RNA transport granules in the dendrites of mammalian hippocampal neurons. We show that Drosophila Syncrip binds specifically to gurken and oskar, but not bicoid transcripts. The loss-of-function and overexpression phenotypes of syncrip in Drosophila egg chambers show that the protein is required for correct grk and osk mRNA localisation and translational regulation. We conclude that Drosophila Syncrip is a new factor required for localisation and translational regulation of oskar and gurken mRNA in the oocyte. We propose that Syncrip/SYNCRIP is part of a conserved complex associated with localised transcripts and required for their correct translational regulation in flies and mammals.
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Affiliation(s)
- Suzanne M McDermott
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU , UK ; Present address: Seattle Biomedical Research Institute, 307 Westlake Avenue N, Suite 500, Seattle, WA 98109-5219, USA
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Berger A, Strub K. Multiple Roles of Alu-Related Noncoding RNAs. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:119-46. [PMID: 21287136 DOI: 10.1007/978-3-642-16502-3_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Repetitive Alu and Alu-related elements are present in primates, tree shrews (Scandentia), and rodents and have expanded to 1.3 million copies in the human genome by nonautonomous retrotransposition. Pol III transcription from these elements occurs at low levels under normal conditions but increases transiently after stress, indicating a function of Alu RNAs in cellular stress response. Alu RNAs assemble with cellular proteins into ribonucleoprotein complexes and can be processed into the smaller scAlu RNAs. Alu and Alu-related RNAs play a role in regulating transcription and translation. They provide a source for the biogenesis of miRNAs and, embedded into mRNAs, can be targeted by miRNAs. When present as inverted repeats in mRNAs, they become substrates of the editing enzymes, and their modification causes the nuclear retention of these mRNAs. Certain Alu elements evolved into unique transcription units with specific expression profiles producing RNAs with highly specific cellular functions.
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Affiliation(s)
- Audrey Berger
- Department of Cell Biology, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
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Transcriptomic responses in mouse brain exposed to chronic excess of the neurotransmitter glutamate. BMC Genomics 2010; 11:360. [PMID: 20529287 PMCID: PMC2896956 DOI: 10.1186/1471-2164-11-360] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 06/07/2010] [Indexed: 12/11/2022] Open
Abstract
Background Increases during aging in extracellular levels of glutamate (Glu), the major excitatory neurotransmitter in the brain, may be linked to chronic neurodegenerative diseases. Little is known about the molecular responses of neurons to chronic, moderate increases in Glu levels. Genome-wide gene expression in brain hippocampus was examined in a unique transgenic (Tg) mouse model that exhibits moderate Glu hyperactivity throughout the lifespan, the neuronal Glutamate dehydrogenase (Glud1) mouse, and littermate 9 month-old wild type mice. Results Integrated bioinformatic analyses on transcriptomic data were used to identify bio-functions, pathways and gene networks underlying neuronal responses to increased Glu synaptic release. Bio-functions and pathways up-regulated in Tg mice were those associated with oxidative stress, cell injury, inflammation, nervous system development, neuronal growth, and synaptic transmission. Increased gene expression in these functions and pathways indicated apparent compensatory responses offering protection against stress, promoting growth of neuronal processes (neurites) and re-establishment of synapses. The transcription of a key gene in the neurite growth network, the kinase Ptk2b, was significantly up-regulated in Tg mice as was the activated (phosphorylated) form of the protein. In addition to genes related to neurite growth and synaptic development, those associated with neuronal vesicle trafficking in the Huntington's disease signalling pathway, were also up-regulated. Conclusions This is the first study attempting to define neuronal gene expression patterns in response to chronic, endogenous Glu hyperactivity at brain synapses. The patterns observed were characterized by a combination of responses to stress and stimulation of nerve growth, intracellular transport and recovery.
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Santos SD, Manadas B, Duarte CB, Carvalho AL. Proteomic Analysis of an Interactome for Long-Form AMPA Receptor Subunits. J Proteome Res 2010; 9:1670-82. [DOI: 10.1021/pr900766r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra D. Santos
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Carlos B. Duarte
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Ana Luísa Carvalho
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
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NMR characterization of copper and lipid interactions of the C2B domain of synaptotagmin I-relevance to the non-classical secretion of the human acidic fibroblast growth factor (hFGF-1). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:297-302. [PMID: 19835837 DOI: 10.1016/j.bbamem.2009.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 09/18/2009] [Accepted: 09/30/2009] [Indexed: 11/21/2022]
Abstract
Human fibroblast growth factor (hFGF-1) is a approximately 17 kDa heparin binding cytokine. It lacks the conventional hydrophobic N-terminal signal sequence and is secreted through non-classical secretion routes. Under stress, hFGF-1 is released as a multiprotein complex consisting of hFGF-1, S100A13 (a calcium binding protein), and p40 synaptotagmin (Syt1). Copper (Cu(2+)) is shown to be required for the formation of the multiprotein hFGF-1 release complex (Landriscina et al. ,2001; Di Serio et al., 2008). Syt1, containing the lipid binding C2B domain, is believed to play an important role in the eventual export of the hFGF-1 across the lipid bilayer. In this study, we characterize Cu(2+) and lipid interactions of the C2B domain of Syt1 using multidimensional NMR spectroscopy. The results highlight how Cu(2+) appears to stabilize the protein bound to pS vesicles. Cu(2+) and lipid binding interface mapped using 2D (1)H-(15)N heteronuclear single quantum coherence experiments reveal that residues in beta-strand I contributes to the unique Cu(2+) binding site in the C2B domain. In the absence of metal ions, residues located in Loop II and beta-strand IV contribute to binding to unilamelar pS vesicles. In the presence of Cu(2+), additional residues located in Loops I and III appear to stabilize the protein-lipid interactions. The results of this study provide valuable information towards understanding the molecular mechanism of the Cu(2+)-induced non-classical secretion of hFGF-1.
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