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Ryu J, Statz JP, Chan W, Oyama K, Custer M, Wienisch M, Chen R, Hanna CB, Hennebold JD. Generation of Rhesus Macaque Embryos with Expanded CAG Trinucleotide Repeats in the Huntingtin Gene. Cells 2024; 13:829. [PMID: 38786052 PMCID: PMC11119628 DOI: 10.3390/cells13100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Huntington's disease (HD) arises from expanded CAG repeats in exon 1 of the Huntingtin (HTT) gene. The resultant misfolded HTT protein accumulates within neuronal cells, negatively impacting their function and survival. Ultimately, HTT accumulation results in cell death, causing the development of HD. A nonhuman primate (NHP) HD model would provide important insight into disease development and the generation of novel therapies due to their genetic and physiological similarity to humans. For this purpose, we tested CRISPR/Cas9 and a single-stranded DNA (ssDNA) containing expanded CAG repeats in introducing an expanded CAG repeat into the HTT gene in rhesus macaque embryos. Analyses were conducted on arrested embryos and trophectoderm (TE) cells biopsied from blastocysts to assess the insertion of the ssDNA into the HTT gene. Genotyping results demonstrated that 15% of the embryos carried an expanded CAG repeat. The integration of an expanded CAG repeat region was successfully identified in five blastocysts, which were cryopreserved for NHP HD animal production. Some off-target events were observed in biopsies from the cryopreserved blastocysts. NHP embryos were successfully produced, which will help to establish an NHP HD model and, ultimately, may serve as a vital tool for better understanding HD's pathology and developing novel treatments.
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Affiliation(s)
- Junghyun Ryu
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
| | - John P. Statz
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
| | - William Chan
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
| | - Kiana Oyama
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
| | - Maggie Custer
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
| | - Martin Wienisch
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA;
| | | | - Carol B. Hanna
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
- Assisted Reproductive Technologies Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jon D. Hennebold
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.); (J.P.S.); (W.C.); (K.O.); (M.C.); (C.B.H.)
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
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Nasheuer HP, Meaney AM, Hulshoff T, Thiele I, Onwubiko NO. Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism. Int J Mol Sci 2024; 25:588. [PMID: 38203759 PMCID: PMC10779431 DOI: 10.3390/ijms25010588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Replication protein A (RPA) is a heterotrimeric protein complex and the main single-stranded DNA (ssDNA)-binding protein in eukaryotes. RPA has key functions in most of the DNA-associated metabolic pathways and DNA damage signalling. Its high affinity for ssDNA helps to stabilise ssDNA structures and protect the DNA sequence from nuclease attacks. RPA consists of multiple DNA-binding domains which are oligonucleotide/oligosaccharide-binding (OB)-folds that are responsible for DNA binding and interactions with proteins. These RPA-ssDNA and RPA-protein interactions are crucial for DNA replication, DNA repair, DNA damage signalling, and the conservation of the genetic information of cells. Proteins such as ATR use RPA to locate to regions of DNA damage for DNA damage signalling. The recruitment of nucleases and DNA exchange factors to sites of double-strand breaks are also an important RPA function to ensure effective DNA recombination to correct these DNA lesions. Due to its high affinity to ssDNA, RPA's removal from ssDNA is of central importance to allow these metabolic pathways to proceed, and processes to exchange RPA against downstream factors are established in all eukaryotes. These faceted and multi-layered functions of RPA as well as its role in a variety of human diseases will be discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
| | - Anna Marie Meaney
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
| | - Timothy Hulshoff
- Molecular Systems Physiology Group, School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Ines Thiele
- Molecular Systems Physiology Group, School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Nichodemus O. Onwubiko
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
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LoTempio J, Delot E, Vilain E. Benchmarking long-read genome sequence alignment tools for human genomics applications. PeerJ 2023; 11:e16515. [PMID: 38130927 PMCID: PMC10734412 DOI: 10.7717/peerj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023] Open
Abstract
Background The utility of long-read genome sequencing platforms has been shown in many fields including whole genome assembly, metagenomics, and amplicon sequencing. Less clear is the applicability of long reads to reference-guided human genomics, which is the foundation of genomic medicine. Here, we benchmark available platform-agnostic alignment tools on datasets from nanopore and single-molecule real-time platforms to understand their suitability in producing a genome representation. Results For this study, we leveraged publicly-available data from sample NA12878 generated on Oxford Nanopore and sample NA24385 on Pacific Biosciences platforms. We employed state of the art sequence alignment tools including GraphMap2, long-read aligner (LRA), Minimap2, CoNvex Gap-cost alignMents for Long Reads (NGMLR), and Winnowmap2. Minimap2 and Winnowmap2 were computationally lightweight enough for use at scale, while GraphMap2 was not. NGMLR took a long time and required many resources, but produced alignments each time. LRA was fast, but only worked on Pacific Biosciences data. Each tool widely disagreed on which reads to leave unaligned, affecting the end genome coverage and the number of discoverable breakpoints. No alignment tool independently resolved all large structural variants (1,001-100,000 base pairs) present in the Database of Genome Variants (DGV) for sample NA12878 or the truthset for NA24385. Conclusions These results suggest a combined approach is needed for LRS alignments for human genomics. Specifically, leveraging alignments from three tools will be more effective in generating a complete picture of genomic variability. It should be best practice to use an analysis pipeline that generates alignments with both Minimap2 and Winnowmap2 as they are lightweight and yield different views of the genome. Depending on the question at hand, the data available, and the time constraints, NGMLR and LRA are good options for a third tool. If computational resources and time are not a factor for a given case or experiment, NGMLR will provide another view, and another chance to resolve a case. LRA, while fast, did not work on the nanopore data for our cluster, but PacBio results were promising in that those computations completed faster than Minimap2. Due to its significant burden on computational resources and slow run time, Graphmap2 is not an ideal tool for exploration of a whole human genome generated on a long-read sequencing platform.
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Affiliation(s)
- Jonathan LoTempio
- Institute for Clinical and Translational Science, University of California, Irvine, CA, United States of America
- International Research Laboratory (IRL2006) “Epigenetics, Data, Politics (EpiDaPo)”, Centre National de la Recherche Scientifique, Washington, DC, United States of America
| | - Emmanuele Delot
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, United States of America
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, United States of America
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, CA, United States of America
- International Research Laboratory (IRL2006) “Epigenetics, Data, Politics (EpiDaPo)”, Centre National de la Recherche Scientifique, Washington, DC, United States of America
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Rani A, Saini V, Patra P, Prashar T, Pandey RK, Mishra A, Jha HC. Epigallocatechin Gallate: A Multifaceted Molecule for Neurological Disorders and Neurotropic Viral Infections. ACS Chem Neurosci 2023; 14:2968-2980. [PMID: 37590965 DOI: 10.1021/acschemneuro.3c00368] [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] [Indexed: 08/19/2023] Open
Abstract
Epigallocatechin-3-gallate (EGCG), a polyphenolic moiety found in green tea extracts, exhibits pleiotropic bioactivities to combat many diseases including neurological ailments. These neurological diseases include Alzheimer's disease, multiple sclerosis, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. For instance, in the case of Alzheimer's disease, the formation of a β-sheet in the region of the 10th-21st amino acids was significantly reduced in EGCG-induced oligomeric samples of Aβ40. Its interference induces the formation of Aβ structures with an increase in intercenter-of-mass distances, reduction in interchain/intrachain contacts, reduction in β-sheet propensity, and increase in α-helix. Besides, numerous neurotropic viruses are known to instigate or aggravate neurological ailments. It exerts an effect on the oxidative damage caused in neurodegenerative disorders by acting on GSK3-β, PI3K/Akt, and downstream signaling pathways via caspase-3 and cytochrome-c. EGCG also diminishes these viral-mediated effects, such as EGCG delayed HSV-1 infection by blocking the entry for virions, inhibitory effects on NS3/4A protease or NS5B polymerase of HCV and potent inhibitor of ZIKV NS2B-NS3pro/NS3 serine protease (NS3-SP). It showed a reduction in the neurotoxic properties of HIV-gp120 and Tat in the presence of IFN-γ. EGCG also involves numerous viral-mediated inflammatory cascades, such as JAK/STAT. Nonetheless, it also inhibits the Epstein-Barr virus replication protein (Zta and Rta). Moreover, it also impedes certain viruses (influenza A and B strains) by hijacking the endosomal and lysosomal compartments. Therefore, the current article aims to describe the importance of EGCG in numerous neurological diseases and its inhibitory effect against neurotropic viruses.
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Affiliation(s)
- Annu Rani
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552, Indore India
| | - Vaishali Saini
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552, Indore India
| | - Priyanka Patra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552, Indore India
| | - Tanish Prashar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu India
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Karwar, 342030, Jodhpur India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552, Indore India
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Kamitsuka PJ, Ghanem MM, Ziar R, McDonald SE, Thomas MG, Kwakye GF. Defective Mitochondrial Dynamics and Protein Degradation Pathways Underlie Cadmium-Induced Neurotoxicity and Cell Death in Huntington's Disease Striatal Cells. Int J Mol Sci 2023; 24:ijms24087178. [PMID: 37108341 PMCID: PMC10139096 DOI: 10.3390/ijms24087178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Exposure to heavy metals, including cadmium (Cd), can induce neurotoxicity and cell death. Cd is abundant in the environment and accumulates in the striatum, the primary brain region selectively affected by Huntington's disease (HD). We have previously reported that mutant huntingtin protein (mHTT) combined with chronic Cd exposure induces oxidative stress and promotes metal dyshomeostasis, resulting in cell death in a striatal cell model of HD. To understand the effect of acute Cd exposure on mitochondrial health and protein degradation pathways, we hypothesized that expression of mHTT coupled with acute Cd exposure would cooperatively alter mitochondrial bioenergetics and protein degradation mechanisms in striatal STHdh cells to reveal novel pathways that augment Cd cytotoxicity and HD pathogenicity. We report that mHTT cells are significantly more susceptible to acute Cd-induced cell death as early as 6 h after 40 µM CdCl2 exposure compared with wild-type (WT). Confocal microscopy, biochemical assays, and immunoblotting analysis revealed that mHTT and acute Cd exposure synergistically impair mitochondrial bioenergetics by reducing mitochondrial potential and cellular ATP levels and down-regulating the essential pro-fusion proteins MFN1 and MFN2. These pathogenic effects triggered cell death. Furthermore, Cd exposure increases the expression of autophagic markers, such as p62, LC3, and ATG5, and reduces the activity of the ubiquitin-proteasome system to promote neurodegeneration in HD striatal cells. Overall, these results reveal a novel mechanism to further establish Cd as a pathogenic neuromodulator in striatal HD cells via Cd-triggered neurotoxicity and cell death mediated by an impairment in mitochondrial bioenergetics and autophagy with subsequent alteration in protein degradation pathways.
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Affiliation(s)
- Paul J Kamitsuka
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Marwan M Ghanem
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Rania Ziar
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Sarah E McDonald
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Morgan G Thomas
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Gunnar F Kwakye
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
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6
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Salari M, Beladi Moghadam N, Soleimani S, Etemadifar M. Atypical parkinsonism can be a presenting feature of late‐onset Huntington's disease. Clin Case Rep 2022; 10:e6014. [PMID: 35846909 PMCID: PMC9272221 DOI: 10.1002/ccr3.6014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/05/2022] [Accepted: 06/19/2022] [Indexed: 11/30/2022] Open
Abstract
Huntington's disease is a progressive neurodegenerative disease that typically manifests with Choreic movements, psychological disorders, and cognitive decline. Some patients can initially present atypical movements other than the usual symptoms, such as parkinsonism, ataxia, and dystonia. In this report, we present an HD patient who presented with atypical parkinsonism.
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Affiliation(s)
- Mehri Salari
- Department of Neurology Shohada Tajrish Hospital Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Nahid Beladi Moghadam
- Department of Neurology, Imam Hossein Hospital Shahid Beheshti University of Medical Science Tehran Iran
| | - Sevim Soleimani
- Student research Committee, faculty of Medicine Shahid Beheshti University of Medical Science Shahid Beheshti Medical University Tehran Iran
| | - Masoud Etemadifar
- Department of Neurosurgery, School of Medicine Isfahan University of Medical Science Isfahan Iran
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7
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Coelho P, Fão L, Mota S, Rego AC. Mitochondrial function and dynamics in neural stem cells and neurogenesis: Implications for neurodegenerative diseases. Ageing Res Rev 2022; 80:101667. [PMID: 35714855 DOI: 10.1016/j.arr.2022.101667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/21/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022]
Abstract
Mitochondria have been largely described as the powerhouse of the cell and recent findings demonstrate that this organelle is fundamental for neurogenesis. The mechanisms underlying neural stem cells (NSCs) maintenance and differentiation are highly regulated by both intrinsic and extrinsic factors. Mitochondrial-mediated switch from glycolysis to oxidative phosphorylation, accompanied by mitochondrial remodeling and dynamics are vital to NSCs fate. Deregulation of mitochondrial proteins, mitochondrial DNA, function, fission/fusion and metabolism underly several neurodegenerative diseases; data show that these impairments are already present in early developmental stages and NSC fate decisions. However, little is known about mitochondrial role in neurogenesis. In this Review, we describe the recent evidence covering mitochondrial role in neurogenesis, its impact in selected neurodegenerative diseases, for which aging is the major risk factor, and the recent advances in stem cell-based therapies that may alleviate neurodegenerative disorders-related neuronal deregulation through improvement of mitochondrial function and dynamics.
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Affiliation(s)
- Patrícia Coelho
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal.
| | - Lígia Fão
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal; FMUC- Faculty of Medicine, University of Coimbra Polo 3, Coimbra, Portugal.
| | - Sandra Mota
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal; III, Institute of Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.
| | - A Cristina Rego
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal; FMUC- Faculty of Medicine, University of Coimbra Polo 3, Coimbra, Portugal.
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8
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Srinivasan E, Ram V, Rajasekaran R. A review on Huntington protein Insight into protein aggregation and therapeutic interventions. Curr Drug Metab 2022; 23:260-282. [PMID: 35319359 DOI: 10.2174/1389200223666220321103942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/13/2021] [Accepted: 01/15/2022] [Indexed: 11/22/2022]
Abstract
Huntington disease (HD) is a distressing, innate neurodegenerative disease that descends from CAG repeat expansion in the huntingtin gene causing behavioral changes, motor dysfunction, and dementia in children and adults. Mutation in huntingtin (HTT) protein has been suggested to cause neuron loss in the cortex and striatum through various mechanisms including abnormal regulation of transcription, proteasomal dysfunction, post-translational modification, and other events, regulating toxicity. Pathogenesis of HD involves cleavage of the huntingtin protein followed by the neuronal accumulation of its aggregated form. Several research groups made possible efforts to reduce huntingtin gene expression, protein accumulation, and protein aggregation using inhibitors and molecular chaperones as developing drugs against HD. Herein, we review the mechanism proposed towards the formation of HTT protein aggregation and the impact of therapeutic strategies for the treatment of HD.
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Affiliation(s)
- E Srinivasan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore - 632014, Tamil Nadu, India
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai - 602105, Tamil Nadu, India
| | - Vavish Ram
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore - 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore - 632014, Tamil Nadu, India
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9
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Bang S, Lee S, Choi N, Kim HN. Emerging Brain-Pathophysiology-Mimetic Platforms for Studying Neurodegenerative Diseases: Brain Organoids and Brains-on-a-Chip. Adv Healthc Mater 2021; 10:e2002119. [PMID: 34028201 DOI: 10.1002/adhm.202002119] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/25/2021] [Indexed: 12/13/2022]
Abstract
Neurodegenerative diseases are a group of disorders characterized by progressive degeneration of the structural and functional integrity of the central and peripheral nervous systems. Millions of people suffer from degenerative brain diseases worldwide, and the mortality continues to increase every year, causing a growing demand for knowledge of the underlying mechanisms and development of therapeutic targets. Conventional 2D-based cell culture platforms and animal models cannot fully recapitulate the pathophysiology, and this has limited the capability for estimating drug efficacy. Recently, engineered platforms, including brain organoids and brain-on-a-chip, have emerged. They mimic the physiology of brain tissue and reflect the fundamental pathophysiological signatures of neurodegenerative diseases, such as the accumulation of neurotoxic proteins, structural abnormalities, and functional loss. In this paper, recent advances in brain-mimetic platforms and their potential for modeling features of neurodegenerative diseases in vitro are reviewed. The development of a physiologically relevant model should help overcome unresolved neurodegenerative diseases.
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Affiliation(s)
- Seokyoung Bang
- Brain Science Institute Korea Institute of Science and Technology (KIST) Seoul 02792 Republic of Korea
| | - Songhyun Lee
- Department of Medical Engineering Yonsei University College of Medicine Seoul 03722 Republic of Korea
| | - Nakwon Choi
- Brain Science Institute Korea Institute of Science and Technology (KIST) Seoul 02792 Republic of Korea
- KU‐KIST Graduate School of Converging Science and Technology Korea University Seoul 02841 Republic of Korea
| | - Hong Nam Kim
- Brain Science Institute Korea Institute of Science and Technology (KIST) Seoul 02792 Republic of Korea
- Division of Bio‐Medical Science & Technology KIST School Korea University of Science and Technology (UST) Seoul 02792 Republic of Korea
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10
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Kozlov E, Shidlovskii YV, Gilmutdinov R, Schedl P, Zhukova M. The role of CPEB family proteins in the nervous system function in the norm and pathology. Cell Biosci 2021; 11:64. [PMID: 33789753 PMCID: PMC8011179 DOI: 10.1186/s13578-021-00577-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/19/2021] [Indexed: 12/29/2022] Open
Abstract
Posttranscriptional gene regulation includes mRNA transport, localization, translation, and regulation of mRNA stability. CPEB (cytoplasmic polyadenylation element binding) family proteins bind to specific sites within the 3′-untranslated region and mediate poly- and deadenylation of transcripts, activating or repressing protein synthesis. As part of ribonucleoprotein complexes, the CPEB proteins participate in mRNA transport and localization to different sub-cellular compartments. The CPEB proteins are evolutionarily conserved and have similar functions in vertebrates and invertebrates. In the nervous system, the CPEB proteins are involved in cell division, neural development, learning, and memory. Here we consider the functional features of these proteins in the nervous system of phylogenetically distant organisms: Drosophila, a well-studied model, and mammals. Disruption of the CPEB proteins functioning is associated with various pathologies, such as autism spectrum disorder and brain cancer. At the same time, CPEB gene regulation can provide for a recovery of the brain function in patients with fragile X syndrome and Huntington's disease, making the CPEB genes promising targets for gene therapy.
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Affiliation(s)
- Eugene Kozlov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
| | - Yulii V Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334.,Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia, 119992
| | - Rudolf Gilmutdinov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544-1014, USA
| | - Mariya Zhukova
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334.
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11
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Rosseto SM, Alarcon TA, Rocha DMC, Ribeiro FM, Ferguson SSG, Martins-Silva C, Muniz MR, Costa PF, Guimarães DA, Pires RGW. DYNLT1 gene expression is downregulated in whole blood of patients at different Huntington's disease stages. Neurol Sci 2020; 42:1963-1967. [PMID: 32995988 DOI: 10.1007/s10072-020-04772-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/25/2020] [Indexed: 11/29/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG nucleotide expansion, which encodes the amino acid glutamine, in the huntingtin gene. HD is characterized by motor, cognitive, and psychiatric dysfunctions. In a previous study, we showed by qPCR that some genes altered in an HD mouse model were also altered in blood of HD patients. These alterations were mainly with respect to the dynein family. Therefore, this study aimed to investigate whether dynein light chain Tctex type 1 (DYNLT1) is altered in HD patients and if there is a correlation between DYNLT1 gene expression changes and disease progression. We assessed the DYNLT1 gene expression in the blood of 19 HD patients and 20 healthy age-matched controls. Also, in 6 of these patients, we analyzed the DYNLT1 expression at two time points, 3 years apart. The DYNLT1 gene expression in the whole blood of HD patients was significantly downregulated and this difference was widened in later stages. These data suggest that DYNLT1 could emerge as a peripheral prognostic indicator in HD and, also, might be a target for potential intervention in the future.
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Affiliation(s)
- S M Rosseto
- Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - T A Alarcon
- Laboratory of Molecular and Behavioral Neurobiology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - D M C Rocha
- Department of Pharmaceutical Sciences, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, 29043-900, Brazil
| | - F M Ribeiro
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - S S G Ferguson
- Department of Cellular and Molecular Medicine, Brain and Mind Research Institute and Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - C Martins-Silva
- Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil.,Laboratory of Molecular and Behavioral Neurobiology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - M R Muniz
- Department of Clinical Medicine, Health Science Center, Federal University of Espírito Santo, Espírito Santo, Brazil
| | - P F Costa
- Department of Physiotherapy, School of Sciences, Santa Casa de Misericordia de Vitoria, Vitória, ES, Brazil
| | - D A Guimarães
- Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil.,Department of Pharmaceutical Sciences, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, 29043-900, Brazil
| | - Rita G W Pires
- Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil. .,Laboratory of Molecular and Behavioral Neurobiology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil. .,Department of Physiological Sciences, Health Sciences Center, Federal University of Espirito Santo, Vitória, ES, 29043-910, Brazil.
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12
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Das L, Nanda S, Das JK. Hereditary disease prediction in eukaryotic DNA: an adaptive signal processing approach. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1179-1199. [PMID: 32571139 DOI: 10.1080/15257770.2020.1780440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Hereditary disease prediction in eukaryotic DNA using signal processing approaches is an incredible work in bioinformatics. Researchers of various fields are trying to put forth a noninvasive approach to forecast the disease-related genes. As diseased genes are more random than the healthy ones, in this work, a comparison of the diseased gene is made against the healthy ones. An adaptive signal processing method like functional link artificial neural network-based Levenberg-Marquardt filter has been proposed in this regard. For parameter upgradation, the algorithm is modified using particle swarm optimization. Here, disease genes are discriminated from healthy ones based on the magnitude of mean square error (MSE), which is calculated through the adaptive filter. The performance of the algorithm is inspected by computing some evaluation parameters. Since accuracy is the prime concern, authors in this work have taken an attempt to improve the accuracy level compared to the existing methods. Taking the reference gene as healthy, the overall process is accomplished by categorizing the diseased and healthy targets with MSE value at a threshold of 0.012. The proposed technique predicts the test gene sets successfully.
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Affiliation(s)
- Lopamudra Das
- School of Electronics Engineering, KIIT University, Bhubaneswar, Odisha, India
| | - Sarita Nanda
- School of Electronics Engineering, KIIT University, Bhubaneswar, Odisha, India
| | - J K Das
- School of Electronics Engineering, KIIT University, Bhubaneswar, Odisha, India
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13
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Caillaud M, Laisney M, Bejanin A, Scherer-Gagou C, Bonneau D, Duclos H, Eustache F, Verny C, Desgranges B, Allain P. Specific cognitive theory of mind and behavioral dysfunctions in early manifest Huntington disease: a case report. Neurocase 2020; 26:36-41. [PMID: 31771445 DOI: 10.1080/13554794.2019.1696837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Huntington's disease (HD) is a devastating illness, associated with progressive motor, behavioral and cognitive dysfunctions. However, some studies emphasized that social cognition impairment could occur prior to the onset of these other symptoms. Here, we report the case of a 47 years old patient with early manifest HD, whose complaint was mainly related to the behavioral sphere. He exhibited a significant impairment of Theory of Mind abilities as well as behavioral, and discrete motor symptoms without noticeable cognitive decline. This case study suggests that social cognition impairments and behavioral changes could be in some cases a feature of the disease and may represent a major disability, in early stages of manifest HD.
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Affiliation(s)
- Marie Caillaud
- Laboratoire de Psychologie des Pays de la Loire (LPPL), EA 4638, Angers, France.,Normandie Univ, UNICAEN, PSL Universités Paris, EPHE, INSERM, U1077, CHU de Caen, GIP Cyceron, Caen, France
| | - Mickael Laisney
- Normandie Univ, UNICAEN, PSL Universités Paris, EPHE, INSERM, U1077, CHU de Caen, GIP Cyceron, Caen, France
| | - Alexandre Bejanin
- Normandie Univ, UNICAEN, PSL Universités Paris, EPHE, INSERM, U1077, CHU de Caen, GIP Cyceron, Caen, France
| | - Clarisse Scherer-Gagou
- Centre National de Référence pour les Maladies Neurogénétiques de l'Adulte, Département de Neurologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Dominique Bonneau
- Centre National de Référence pour les Maladies Neurogénétiques de l'Adulte, Département de Neurologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Harmony Duclos
- Normandie Univ, UNICAEN, PSL Universités Paris, EPHE, INSERM, U1077, CHU de Caen, GIP Cyceron, Caen, France
| | - Francis Eustache
- Normandie Univ, UNICAEN, PSL Universités Paris, EPHE, INSERM, U1077, CHU de Caen, GIP Cyceron, Caen, France
| | - Christophe Verny
- Centre National de Référence pour les Maladies Neurogénétiques de l'Adulte, Département de Neurologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Béatrice Desgranges
- Normandie Univ, UNICAEN, PSL Universités Paris, EPHE, INSERM, U1077, CHU de Caen, GIP Cyceron, Caen, France
| | - Philippe Allain
- Laboratoire de Psychologie des Pays de la Loire (LPPL), EA 4638, Angers, France.,Centre National de Référence pour les Maladies Neurogénétiques de l'Adulte, Département de Neurologie, Centre Hospitalier Universitaire d'Angers, Angers, France
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14
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Abstract
Between the 1930s and 1950s, scientists developed key principles of population genetics to try and explain the aging process. Almost a century later, these aging theories, including antagonistic pleiotropy and mutation accumulation, have been experimentally validated in animals. Although the theories have been much harder to test in humans despite research dating back to the 1970s, recent research is closing this evidence gap. Here we examine the strength of evidence for antagonistic pleiotropy in humans, one of the leading evolutionary explanations for the retention of genetic risk variation for non-communicable diseases. We discuss the analytical tools and types of data that are used to test for patterns of antagonistic pleiotropy and provide a primer of evolutionary theory on types of selection as a guide for understanding this mechanism and how it may manifest in other diseases. We find an abundance of non-experimental evidence for antagonistic pleiotropy in many diseases. In some cases, several studies have independently found corroborating evidence for this mechanism in the same or related sets of diseases including cancer and neurodegenerative diseases. Recent studies also suggest antagonistic pleiotropy may be involved in cardiovascular disease and diabetes. There are also compelling examples of disease risk variants that confer fitness benefits ranging from resistance to other diseases or survival in extreme environments. This provides increasingly strong support for the theory that antagonistic pleiotropic variants have enabled improved fitness but have been traded for higher burden of disease later in life. Future research in this field is required to better understand how this mechanism influences contemporary disease and possible consequences for their treatment.
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15
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An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. J Mol Evol 2019; 88:104-119. [PMID: 31522275 DOI: 10.1007/s00239-019-09911-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Copy number variants (CNVs), deletions and duplications of segments of DNA, account for at least five times more variable base pairs in humans than single-nucleotide variants. Several common CNVs were shown to change coding and regulatory sequences and thus dramatically affect adaptive phenotypes involving immunity, perception, metabolism, skin structure, among others. Some of these CNVs were also associated with susceptibility to cancer, infection, and metabolic disorders. These observations raise the possibility that CNVs are a primary contributor to human phenotypic variation and consequently evolve under selective pressures. Indeed, locus-specific haplotype-level analyses revealed signatures of natural selection on several CNVs. However, more traditional tests of selection which are often applied to single-nucleotide variation often have diminished statistical power when applied to CNVs because they often do not show strong linkage disequilibrium with nearby variants. Recombination-based formation mechanisms of CNVs lead to frequent recurrence and gene conversion events, breaking the linkage disequilibrium involving CNVs. Similar methodological challenges also prevent routine genome-wide association studies to adequately investigate the impact of CNVs on heritable human disease. Thus, we argue that the full relevance of CNVs to human health and evolution is yet to be elucidated. We further argue that a holistic investigation of formation mechanisms within an evolutionary framework would provide a powerful framework to understand the functional and biomedical impact of CNVs. In this paper, we review several cases where studies reveal diverse evolutionary histories and unexpected functional consequences of CNVs. We hope that this review will encourage further work on CNVs by both evolutionary and medical geneticists.
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16
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Areal LB, Pereira LP, Ribeiro FM, Olmo IG, Muniz MR, do Carmo Rodrigues M, Costa PF, Martins-Silva C, Ferguson SSG, Guimarães DAM, Pires RGW. Role of Dynein Axonemal Heavy Chain 6 Gene Expression as a Possible Biomarker for Huntington's Disease: a Translational Study. J Mol Neurosci 2017; 63:342-348. [PMID: 29019003 DOI: 10.1007/s12031-017-0984-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/04/2017] [Indexed: 11/27/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder characterized by motor dysfunction, cognitive deficits, and psychiatric symptoms. The primary genetic cause is an expansion of cytosine adenine guanine (CAG) nucleotides of the huntingtin gene, which codes an important protein involved with neuronal signaling. The severity of HD correlates with the number of CAG repeats and individuals with longer expansions have an earlier onset and more severe symptoms. A microarray study conducted by our research group showed alteration in DNAH6 gene (encoding dynein axonemal heavy chain 6). DNAH6 belongs to dynein family, whose members are constituents of the microtubule-associated motor proteins and is downregulated in the striatum of a HD mouse model (knockin HdhQ111/Q111). In this manner, our goal was to confirm these downregulations in the mouse model and verify if the same alteration in the axonemal DNAH6 gene expression is observed in blood samples of HD patients. Blood samples were collected from 17 patients with clinical diagnosis of HD and 12 healthy individuals and RNA extracted for qPCR analysis. Microarray data were confirmed by qPCR in knockin HdhQ111/Q111, and DNAH6 was severely decreased in those mice, as compared to control mice (HdhQ20/Q20). Notably, decreased expression of DNAH6 gene was also observed in HD patients when compared to control group and negatively correlates with the CAG expansion. Although further studies are necessary to underlie the molecular mechanisms of dynein-htt interaction, this data highlights DNAH6 as a potential new blood marker for HD.
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Affiliation(s)
- Lorena B Areal
- Laboratory of Molecular and Behavioral Neurobiology, Health Sciences Center, Federal University of Espirito Santo, Vitória, ES, Brazil.,Graduate Program in Neuroscience, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lorraine P Pereira
- Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Fabiola M Ribeiro
- Graduate Program in Neuroscience, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Isabella G Olmo
- Graduate Program in Neuroscience, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcelo R Muniz
- Department of Clinical Medicine, Health Science Center, Federal University of Espírito Santo, Vitória, Brazil
| | - Maria do Carmo Rodrigues
- Department of Clinical Medicine, Health Science Center, Federal University of Espírito Santo, Vitória, Brazil
| | - Patrik F Costa
- Department of Physiotherapy, School of Sciences, Santa Casa de Misericordia de Vitoria, Vitória, ES, Brazil
| | - Cristina Martins-Silva
- Laboratory of Molecular and Behavioral Neurobiology, Health Sciences Center, Federal University of Espirito Santo, Vitória, ES, Brazil.,Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Stephen S G Ferguson
- Department of Cellular and Molecular Medicine, Brain and Mind Research Institute and Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Daniela A M Guimarães
- Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Rita G W Pires
- Laboratory of Molecular and Behavioral Neurobiology, Health Sciences Center, Federal University of Espirito Santo, Vitória, ES, Brazil. .,Graduate Program in Neuroscience, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Graduate Program in Biochemistry and Pharmacology, Health Sciences Center, Federal University of Espírito Santo, Vitória, ES, Brazil. .,Department of Physiological Sciences, Health Science Center, Federal University of Espírito Santo, Marechal Campos Avenue, 1468, Vitória, ES, 29043-910, Brazil.
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17
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Rao DN, Dryden DTF, Bheemanaik S. Type III restriction-modification enzymes: a historical perspective. Nucleic Acids Res 2014; 42:45-55. [PMID: 23863841 PMCID: PMC3874151 DOI: 10.1093/nar/gkt616] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 05/28/2013] [Accepted: 06/24/2013] [Indexed: 11/12/2022] Open
Abstract
Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.
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Affiliation(s)
- Desirazu N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India and School of Chemistry, The King’s Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, Scotland, UK
| | - David T. F. Dryden
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India and School of Chemistry, The King’s Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, Scotland, UK
| | - Shivakumara Bheemanaik
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India and School of Chemistry, The King’s Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, Scotland, UK
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18
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Ma L, Chen K, Clarke DJ, Nortcliffe CP, Wilson GG, Edwardson JM, Morton AJ, Jones AC, Dryden DTF. Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats. Nucleic Acids Res 2013; 41:4999-5009. [PMID: 23525471 PMCID: PMC3643589 DOI: 10.1093/nar/gkt176] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The type II restriction endonuclease TseI recognizes the DNA target sequence 5′-G^CWGC-3′ (where W = A or T) and cleaves after the first G to produce fragments with three-base 5′-overhangs. We have determined that it is a dimeric protein capable of cleaving not only its target sequence but also one containing A:A or T:T mismatches at the central base pair in the target sequence. The cleavage of targets containing these mismatches is as efficient as cleavage of the correct target sequence containing a central A:T base pair. The cleavage mechanism does not apparently use a base flipping mechanism as found for some other type II restriction endonuclease recognizing similarly degenerate target sequences. The ability of TseI to cleave targets with mismatches means that it can cleave the unusual DNA hairpin structures containing A:A or T:T mismatches formed by the repetitive DNA sequences associated with Huntington’s disease (CAG repeats) and myotonic dystrophy type 1 (CTG repeats).
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Affiliation(s)
- Long Ma
- EaStChem School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
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19
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Gupta YK, Yang L, Chan SH, Samuelson JC, Xu SY, Aggarwal AK. Structural insights into the assembly and shape of Type III restriction-modification (R-M) EcoP15I complex by small-angle X-ray scattering. J Mol Biol 2012; 420:261-8. [PMID: 22560991 DOI: 10.1016/j.jmb.2012.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/25/2012] [Accepted: 04/27/2012] [Indexed: 11/25/2022]
Abstract
EcoP15I is the prototype of the Type III restriction enzyme family, composed of two modification (Mod) subunits to which two (or one) restriction (Res) subunits are then added. The Mod subunits are responsible for DNA recognition and methylation, while the Res subunits are responsible for ATP hydrolysis and cleavage. Despite extensive biochemical and genetic studies, there is still no structural information on Type III restriction enzymes. We present here small-angle X-ray scattering (SAXS) and analytical ultracentrifugation analysis of the EcoP15I holoenzyme and the Mod(2) subcomplex. We show that the Mod(2) subcomplex has a relatively compact shape with a radius of gyration (R(G)) of ∼37.4 Å and a maximal dimension of ∼110 Å. The holoenzyme adopts an elongated crescent shape with an R(G) of ∼65.3 Å and a maximal dimension of ∼218 Å. From reconstructed SAXS envelopes, we postulate that Mod(2) is likely docked in the middle of the holoenzyme with a Res subunit at each end. We discuss the implications of our model for EcoP15I action, whereby the Res subunits may come together and form a "sliding clamp" around the DNA.
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Affiliation(s)
- Yogesh K Gupta
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
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20
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Carter AJR, Nguyen AQ. Antagonistic pleiotropy as a widespread mechanism for the maintenance of polymorphic disease alleles. BMC MEDICAL GENETICS 2011; 12:160. [PMID: 22151998 PMCID: PMC3254080 DOI: 10.1186/1471-2350-12-160] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 12/12/2011] [Indexed: 11/12/2022]
Abstract
BACKGROUND Many serious diseases have a genetic basis which, from an evolutionary point of view, should have been selected against, resulting in very low frequencies. The remarkable sustained prevalence of a number of disease-associated alleles is therefore surprising. We believe that antagonistic pleiotropy, when multiple effects of a gene have opposing effects on fitness (e.g., sickle cell disease), may be more widespread than typically considered. We hypothesize that, rather than being an exception to the rule of genetic disorders, antagonistic pleiotropy may be common. METHODS We surveyed the medical literature in order to determine whether sufficient evidence exists to reassess the nature of antagonistic pleiotropy; from being considered an unusual scenario to one that is anticipated. We also used a simple population genetic model to examine the feasibility of antagonistic pleiotropy to act as a mechanism to maintain polymorphism for serious genetic disorders even if the benefits are subtle. RESULTS We identified a number of examples of antagonistic pleiotropy where the deleterious effect, the beneficial effect, and the exact molecular cause have been demonstrated. We also identified putative cases in which there is circumstantial evidence or a strong reason to expect antagonistic pleiotropy in a genetic disorder. The population genetic model demonstrates that alleles with severe deleterious health effects can be maintained at medically relevant frequencies with only minor beneficial pleiotropic effects. CONCLUSION We believe that our identification of several cases of antagonistic pleiotropy, despite the lack of research on this question and the varied natures of the types of these disorders, speaks to both the underappreciated nature of this phenomenon and its potentially fundamental importance. If antagonistic pleiotropy is as common as our research suggests, this may explain why so many serious diseases, even apparently environmentally caused ones, have a genetic component. Furthermore, acceptance of a genome full of antagonistically pleiotropic genetic interactions poses important implications for clinical treatment and disease prevention research, especially genetically based therapies.
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Affiliation(s)
- Ashley JR Carter
- Biology Department, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, USA
| | - Andrew Q Nguyen
- Biology Department, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, USA
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21
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López Castel A, Nakamori M, Thornton CA, Pearson CE. Identification of restriction endonucleases sensitive to 5-cytosine methylation at non-CpG sites, including expanded (CAG)n/(CTG)n repeats. Epigenetics 2011; 6:416-20. [PMID: 21364324 DOI: 10.4161/epi.6.4.14953] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Most epigenetic studies assess methylation of 5'-CpG-3' sites but recent evidence indicates that non-CpG cytosine methylation occurs at high levels in humans and other species. This is most prevalent at 5'-CHG-3', where H = A, C or T, and it preferentially occurs at 5'-CpA-3' and 5'-CpT-3' sites. With the goal of facilitating the detection of non-CpG methylation, the restriction endonucleases ApeKI, BbvI, EcoP15I, Fnu 4HI, MwoI and TseI were assessed for their sensitivity to 5-methylcytosine at GpCpA, GpCpT, GpCpC or GpCpG sites, where methylation is catalyzed by the DNA 5-cytosine 5'-GpC-3' methyltransferase M.CviPI. We tested a variety of sequences including various plasmid-based sites, a cloned disease-associated (CAG)83•(CTG)83 repeat and in vitro synthesized tracts of only (CAG)500•(CTG)500 or (CAG)800•(CTG)800. The repeat tracts are enriched for the preferred CpA and CpT motifs. We found that none of the tested enzymes can cleave their recognition sequences when they are 5'-GpC-3' methylated. A genomic site known to convert its non-CpG methylation levels upon C2C12 differentiation was confirmed through the use of these enzymes. These enzymes can be useful in rapidly and easily determining the most common non-CpG methylation status in various sequence contexts, as well as at expansions of (CAG)n•(CTG)n repeat tracts associated with diseases like myotonic dystrophy and Huntington disease.
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Affiliation(s)
- Arturo López Castel
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
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22
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Duzdevich D, Li J, Whang J, Takahashi H, Takeyasu K, Dryden DTF, Morton AJ, Edwardson JM. Unusual structures are present in DNA fragments containing super-long Huntingtin CAG repeats. PLoS One 2011; 6:e17119. [PMID: 21347256 PMCID: PMC3037965 DOI: 10.1371/journal.pone.0017119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/21/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the R6/2 mouse model of Huntington's disease (HD), expansion of the CAG trinucleotide repeat length beyond about 300 repeats induces a novel phenotype associated with a reduction in transcription of the transgene. METHODOLOGY/PRINCIPAL FINDINGS We analysed the structure of polymerase chain reaction (PCR)-generated DNA containing up to 585 CAG repeats using atomic force microscopy (AFM). As the number of CAG repeats increased, an increasing proportion of the DNA molecules exhibited unusual structural features, including convolutions and multiple protrusions. At least some of these features are hairpin loops, as judged by cross-sectional analysis and sensitivity to cleavage by mung bean nuclease. Single-molecule force measurements showed that the convoluted DNA was very resistant to untangling. In vitro replication by PCR was markedly reduced, and TseI restriction enzyme digestion was also hindered by the abnormal DNA structures. However, significantly, the DNA gained sensitivity to cleavage by the Type III restriction-modification enzyme, EcoP15I. CONCLUSIONS/SIGNIFICANCE "Super-long" CAG repeats are found in a number of neurological diseases and may also appear through CAG repeat instability. We suggest that unusual DNA structures associated with super-long CAG repeats decrease transcriptional efficiency in vitro. We also raise the possibility that if these structures occur in vivo, they may play a role in the aetiology of CAG repeat diseases such as HD.
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Affiliation(s)
- Daniel Duzdevich
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Jinliang Li
- Laragen, Inc., Culver City, California, United States of America
| | - Jhoon Whang
- Laragen, Inc., Culver City, California, United States of America
| | - Hirohide Takahashi
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Kunio Takeyasu
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - David T. F. Dryden
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, United Kingdom
| | - A. Jennifer Morton
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AJM); (JME)
| | - J. Michael Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AJM); (JME)
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23
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Dryden DTF, Edwardson JM, Henderson RM. DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements. Nucleic Acids Res 2011; 39:4525-31. [PMID: 21310716 PMCID: PMC3113558 DOI: 10.1093/nar/gkq1285] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Much insight into the interactions of DNA and enzymes has been obtained using a number of single-molecule techniques. However, recent results generated using two of these techniques-atomic force microscopy (AFM) and magnetic tweezers (MT)-have produced apparently contradictory results when applied to the action of the ATP-dependent type III restriction endonucleases on DNA. The AFM images show extensive looping of the DNA brought about by the existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT experiments show no evidence for looping being a requirement for DNA cleavage, but instead support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs, leading to cleavage. Not only do these two methods appear to disagree, but also the models derived from them have difficulty explaining some ensemble biochemical results on DNA cleavage. In this 'Survey and Summary', we describe several different models put forward for the action of type III restriction enzymes and their inadequacies. We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes.
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Affiliation(s)
- David T F Dryden
- School of Chemistry, The King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK.
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24
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Pérez-Bello D, Xu Z, Higginson-Clarke D, Rojas AMR, Le W, Rodríguez-Tanty C. DNA-labelled cytidine assay for the quantification of CAG repeats. J Neurosci Methods 2008; 169:201-7. [DOI: 10.1016/j.jneumeth.2007.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 10/12/2007] [Accepted: 10/30/2007] [Indexed: 10/22/2022]
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Raghavendra NK, Rao DN. Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I--usefulness in SAGE. Biochem Biophys Res Commun 2006; 334:803-11. [PMID: 16026759 DOI: 10.1016/j.bbrc.2005.06.171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2005] [Accepted: 06/28/2005] [Indexed: 11/21/2022]
Abstract
While it has been demonstrated that AdoMet is required for DNA cleavage by Type III restriction enzymes, here we show that in the presence of exogenous AdoMet, the head-to-head oriented recognition sites are cleaved only on a supercoiled DNA. On a linear DNA, exogenous AdoMet strongly drives methylation while inhibiting cleavage reaction. Strikingly, AdoMet analogue sinefungin results in cleavage at all recognition sites irrespective of the topology of DNA. The cleavage reaction in the presence of sinefungin is ATP dependent. The site of cleavage is comparable with that in the presence of AdoMet. The use of EcoP15I restriction in presence of sinefungin as an improved tool for serial analysis of gene expression is discussed.
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Gao H, Kong J. The microsatellites and minisatellites in the genome of Fenneropenaeus chinensis. ACTA ACUST UNITED AC 2006; 16:426-36. [PMID: 16287622 DOI: 10.1080/10425170500354359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Through two-time sequencing randomly in Fenneropenaeus chinensis, 2,597,000 bp cumulative length random genomic sequences about occupying 1.23 per thousand of the entire genome are obtained, in which the length of the first time sequencing is 884,000 bp, by cutting the genome DNA with Sau3AI enzyme, and the second is 1,713,000 bp by breaking the genome DNA with the physical method, ultrasonic. Using tandem repeat finder (TRF) soft to analyze the sequences, 4,588 tandem repeats are found, in which the number of microsatellites (1-6 bp) is 3,888, and 700 for minisatellites ( >or= 7 bp). The cumulative length of repeats is 305,555 bp, accounting for 11.72% of total cumulative sequence length, in which the cumulative length of microsatellites is 232,979 bp, accounting for 8.97% of total sequence length, and greater than those of other organisms, such as human and mosquito, etc. The dinucleotide repeat type is dominant in which the dominant repeat class is AT. The second abundant repeat type is trinucleotide, of which the dominant repeat class is AAT. Interestingly, of all of repeat types, the repeat numbers and repeat classes of primer number repeat types, such as pentanucleotide, heptanucleotide, elevennucleotide, etc. are less than those of repeat types beside them. The phenomena may involve the genesis and the evolution of microsatellites and minisatellites.
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Affiliation(s)
- Huan Gao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR of China
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Möncke-Buchner E, Mackeldanz P, Krüger DH, Reuter M. Overexpression and affinity chromatography purification of the Type III restriction endonuclease EcoP15I for use in transcriptome analysis. J Biotechnol 2005; 114:99-106. [PMID: 15464603 DOI: 10.1016/j.jbiotec.2004.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 06/29/2004] [Indexed: 11/19/2022]
Abstract
The Type III restriction endonuclease EcoP15I is a multifunctional hetero-oligomeric enzyme that recognizes the non-symmetric DNA sequence 5'-CAGCAG. For efficient cleavage, EcoP15I needs the interaction with two copies of the recognition sequence that have to be inversely oriented in the DNA double strand. The enzyme cuts the upper DNA strand 25-26 bp and the lower DNA strand 27-28 bp, respectively, downstream of the recognition sequence-a distinct feature that makes the enzyme particularly valuable for gene expression profiling methods relying on the SAGE procedure (Matsumura et al., PNAS 100, 15718, 2003). Because the broader use of this transcriptome analysis method requires the availability of larger amounts of restriction endonuclease EcoP15I and the enzyme is not commercially available, we have cloned the genes coding for the EcoP15I restriction endonuclease into pQE-16 plasmid vector that provides the enzyme with a C-terminal 6xHis-tag. After Ni-NTA affinity chromatography and ion exchange chromatography on heparin sepharose, we obtained 5mg homogeneous EcoP15I per gram cell pellet within 1-2 day(s). Moreover, the C-terminally 6xHis-tagged EcoP15I restriction endonuclease shows comparable enzymatic activity as the untagged enzyme.
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Reich S, Gössl I, Reuter M, Rabe JP, Krüger DH. Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I. J Mol Biol 2004; 341:337-43. [PMID: 15276827 DOI: 10.1016/j.jmb.2004.06.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 06/15/2004] [Accepted: 06/15/2004] [Indexed: 11/28/2022]
Abstract
Type III restriction enzymes are multifunctional heterooligomeric enzymes that cleave DNA at a fixed position downstream of a non-symmetric recognition site. For effective DNA cleavage these restriction enzymes need the presence of two unmethylated, inversely oriented recognition sites in the DNA molecule. DNA cleavage was proposed to result from ATP-dependent DNA translocation, which is expected to induce DNA loop formation, and collision of two enzyme-DNA complexes. We used scanning force microscopy to visualise the protein interaction with linear DNA molecules containing two EcoP15I recognition sites in inverse orientation. In the presence of the cofactors ATP and Mg(2+), EcoP15I molecules were shown to bind specifically to the recognition sites and to form DNA loop structures. One of the origins of the protein-clipped DNA loops was shown to be located at an EcoP15I recognition site, the other origin had an unspecific position in between the two EcoP15I recognition sites. The data demonstrate for the first time DNA translocation by the Type III restriction enzyme EcoP15I using scanning force microscopy. Moreover, our study revealed differences in the DNA-translocation processes mediated by Type I and Type III restriction enzymes.
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Affiliation(s)
- Stefanie Reich
- Institute of Virology (Helmut-Ruska-Haus), Charité Medical School, Humboldt University, Schumannstr. 20-21, D-10117 Berlin, Germany
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