1
|
Schulz EG. BREACHing new grounds in fragile X syndrome: Trinucleotide expansion linked to genome-wide heterochromatin domains and genome misfolding. Mol Cell 2024; 84:413-414. [PMID: 38307002 DOI: 10.1016/j.molcel.2023.12.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/04/2024]
Abstract
In a recent study in Cell, Malachowski et al.1 show that the trinucleotide expansion in the FMR1 gene underlying fragile X syndrome triggers formation of large heterochromatin domains across the genome, resulting in the repression of synaptic genes housed within these domains.
Collapse
Affiliation(s)
- Edda G Schulz
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
2
|
Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [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: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
Collapse
Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
| |
Collapse
|
3
|
Cao Y, Tian W, Wu J, Song X, Cao L, Luan X. DNA hypermethylation of NOTCH2NLC in neuronal intranuclear inclusion disease: a case-control study. J Neurol 2022; 269:6049-6057. [PMID: 35857137 DOI: 10.1007/s00415-022-11272-y] [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: 03/31/2022] [Revised: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND GGC repeat expansions in NOTCH2NLC gene have been recently proposed to cause neuronal intranuclear inclusion disease (NIID) via prevailing gain-of-function mechanism (protein and RNA toxicity). Nevertheless, increasing evidences suggest that epigenetics can also play a role in the pathogenesis of repeat-mediated disorders. METHODS In this study, using MethylTarget sequencing, we performed a quantitative analysis of the methylation status of 68 CpG sites located around the NOTCH2NLC promoter in 25 NIID patients and 25 age- and gender-matched healthy controls. We further explored the correlation of DNA methylation (DNAm) status with disease features and performed receiver operating characteristic (ROC) analysis. RESULTS DNAm levels of GGC repeats and adjacent CpG islands were higher in the NIID patients than in controls, independent of gender and family history. DNAm levels at 4 CpG sites (CpG_207, CpG_421, GpG_473 and CpG_523) were negatively correlated with age at onset, and DNAm levels at 7 CpG sites (CpG_25, CpG_298, CpG_336, CpG_374, CpG_411, CpG_421 and CpG_473) were positively correlated with GGC repeats. NIID patients had concomitant system symptoms besides nervous system symptoms, and negative correlations between NOTCH2NLC DNAm levels and the number of multi-systemic involvement were observed in the study. The area under the ROC curve at NOTCH2NLC DNAm level reached to 0.733 for the best cutoff point of 0.012. CONCLUSIONS Our findings suggested the aberrant DNAm status of the NOTCH2NLC promoter in NIID, and we explored the link between DNAm levels and disease features quantitatively for the first time, which may help to further explore pathogenic mechanism.
Collapse
Affiliation(s)
- Yuwen Cao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wotu Tian
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jingying Wu
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xingwang Song
- Institute of Neuroscience and Department of Neurology, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Cao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Xinghua Luan
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| |
Collapse
|
4
|
Nelson RS, Dammer EB, Santiago JV, Seyfried NT, Rangaraju S. Brain Cell Type-Specific Nuclear Proteomics Is Imperative to Resolve Neurodegenerative Disease Mechanisms. Front Neurosci 2022; 16:902146. [PMID: 35784845 PMCID: PMC9243337 DOI: 10.3389/fnins.2022.902146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 01/19/2023] Open
Abstract
Neurodegenerative diseases (NDs) involve complex cellular mechanisms that are incompletely understood. Emerging findings have revealed that disruption of nuclear processes play key roles in ND pathogenesis. The nucleus is a nexus for gene regulation and cellular processes that together, may underlie pathomechanisms of NDs. Furthermore, many genetic risk factors for NDs encode proteins that are either present in the nucleus or are involved in nuclear processes (for example, RNA binding proteins, epigenetic regulators, or nuclear-cytoplasmic transport proteins). While recent advances in nuclear transcriptomics have been significant, studies of the nuclear proteome in brain have been relatively limited. We propose that a comprehensive analysis of nuclear proteomic alterations of various brain cell types in NDs may provide novel biological and therapeutic insights. This may be feasible because emerging technical advances allow isolation and investigation of intact nuclei from post-mortem frozen human brain tissue with cell type-specific and single-cell resolution. Accordingly, nuclei of various brain cell types harbor unique protein markers which can be used to isolate cell-type specific nuclei followed by down-stream proteomics by mass spectrometry. Here we review the literature providing a rationale for investigating proteomic changes occurring in nuclei in NDs and then highlight the potential for brain cell type-specific nuclear proteomics to enhance our understanding of distinct cellular mechanisms that drive ND pathogenesis.
Collapse
Affiliation(s)
- Ruth S. Nelson
- Department of Neurology, Emory University, Atlanta, GA, United States
| | - Eric B. Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, United States
| | | | | | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, United States,*Correspondence: Srikant Rangaraju
| |
Collapse
|
5
|
Marsh JI, Hu H, Petereit J, Bayer PE, Valliyodan B, Batley J, Nguyen HT, Edwards D. Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1443-1455. [PMID: 35141762 PMCID: PMC9033719 DOI: 10.1007/s00122-022-04045-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/22/2022] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.
Collapse
Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Jakob Petereit
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Babu Valliyodan
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia.
| |
Collapse
|
6
|
Visconti VV, Centofanti F, Fittipaldi S, Macrì E, Novelli G, Botta A. Epigenetics of Myotonic Dystrophies: A Minireview. Int J Mol Sci 2021; 22:ijms222212594. [PMID: 34830473 PMCID: PMC8623789 DOI: 10.3390/ijms222212594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 12/14/2022] Open
Abstract
Myotonic dystrophy type 1 and 2 (DM1 and DM2) are two multisystemic autosomal dominant disorders with clinical and genetic similarities. The prevailing paradigm for DMs is that they are mediated by an in trans toxic RNA mechanism, triggered by untranslated CTG and CCTG repeat expansions in the DMPK and CNBP genes for DM1 and DM2, respectively. Nevertheless, increasing evidences suggest that epigenetics can also play a role in the pathogenesis of both diseases. In this review, we discuss the available information on epigenetic mechanisms that could contribute to the DMs outcome and progression. Changes in DNA cytosine methylation, chromatin remodeling and expression of regulatory noncoding RNAs are described, with the intent of depicting an epigenetic signature of DMs. Epigenetic biomarkers have a strong potential for clinical application since they could be used as targets for therapeutic interventions avoiding changes in DNA sequences. Moreover, understanding their clinical significance may serve as a diagnostic indicator in genetic counselling in order to improve genotype–phenotype correlations in DM patients.
Collapse
Affiliation(s)
- Virginia Veronica Visconti
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Federica Centofanti
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Simona Fittipaldi
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Elisa Macrì
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
- IRCCS (Institute for Treatment and Research) Neuromed, 86077 Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
- Correspondence: ; Tel.: +39-6-7259-6078
| |
Collapse
|
7
|
Morales F, Corrales E, Zhang B, Vásquez M, Santamaría-Ulloa C, Quesada H, Sirito M, Estecio MR, Monckton DG, Krahe R. Myotonic dystrophy type 1 (DM1) clinical sub-types and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent. Hum Mol Genet 2021; 31:262-274. [PMID: 34432028 DOI: 10.1093/hmg/ddab243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a complex disease with a wide spectrum of symptoms. The exact relationship between mutant CTG repeat expansion size and clinical outcome remains unclear. DM1 congenital patients (CDM) inherit the largest expanded alleles, which are associated with abnormal and increased DNA methylation flanking the CTG repeat. However, DNA methylation at the DMPK locus remains understudied. Its relationship to DM1 clinical subtypes, expansion size and age-at-onset is not yet completely understood. Using pyrosequencing-based methylation analysis on 225 blood DNA samples from Costa Rican DM1 patients, we determined that the size of the estimated progenitor allele length (ePAL) is not only a good discriminator between CDM and non-CDM cases (with an estimated threshold at 653 CTG repeats), but also for all DM1 clinical subtypes. Secondly, increased methylation at both CTCF sites upstream and downstream of the expansion was almost exclusively present in CDM cases. Thirdly, levels of abnormal methylation were associated with clinical subtype, age and ePAL, with strong correlations between these variables. Fourthly, both ePAL and the intergenerational expansion size were significantly associated with methylation status. Finally, methylation status was associated with ePAL and maternal inheritance, with almost exclusively maternal transmission of CDM. In conclusion, increased DNA methylation at the CTCF sites flanking the DM1 expansion could be linked to ePAL, and both increased methylation and the ePAL could be considered biomarkers for the CDM phenotype.
Collapse
Affiliation(s)
- Fernando Morales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Eyleen Corrales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Baili Zhang
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Melissa Vásquez
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Carolina Santamaría-Ulloa
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Hazel Quesada
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Mario Sirito
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Marcos R Estecio
- Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Ralf Krahe
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| |
Collapse
|
8
|
Eiras MC, Pinheiro DP, Romcy KAM, Ferriani RA, Reis RMD, Furtado CLM. Polycystic Ovary Syndrome: the Epigenetics Behind the Disease. Reprod Sci 2021; 29:680-694. [PMID: 33826098 DOI: 10.1007/s43032-021-00516-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/21/2021] [Indexed: 10/21/2022]
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders, affecting approximately 5-20% of women of reproductive age. PCOS is a multifactorial, complex, and heterogeneous disease, characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovaries, which may lead to impaired fertility. Besides the reproductive outcomes, multiple comorbidities, such as metabolic disturbances, insulin resistance, obesity, diabetes, and cardiovascular disease, are associated with PCOS. In addition to the clear genetic basis, epigenetic alterations may also play a central role in PCOS outcomes, as environmental and hormonal alterations directly affect clinical manifestations and PCOS development. Here, we highlighted the epigenetic modifications in the multiplicity of clinical manifestations, as well as environmental epigenetic disruptors, as intrauterine hormonal and metabolic alterations affecting embryo development and the adulthood lifestyle, which may contribute to PCOS development. Additionally, we also discussed the new approaches for future studies and potential epigenetic biomarkers for the treatment of associated comorbidities and improvement in quality of life of women with PCOS.
Collapse
Affiliation(s)
- Matheus Credendio Eiras
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Av Bandeirantes, 3900, Ribeirão Preto, São Paulo, 14049-900, SP, Brazil
| | - Daniel Pascoalino Pinheiro
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Coronel Nunes de Melo, 1000, Rodolfo Teófilo, Fortaleza, 60430-275, CE, Brazil
| | - Kalil Andrade Mubarac Romcy
- Drug Research and Development Center, Postgraduate Program in Medical and Surgical Sciences, Federal University of Ceara, Coronel Nunes de Melo, 1000, Rodolfo Teófilo, Fortaleza, CE, 60430-275, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Av Bandeirantes, 3900, Ribeirão Preto, São Paulo, 14049-900, SP, Brazil
| | - Rosana Maria Dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Av Bandeirantes, 3900, Ribeirão Preto, São Paulo, 14049-900, SP, Brazil.
| | - Cristiana Libardi Miranda Furtado
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Av Bandeirantes, 3900, Ribeirão Preto, São Paulo, 14049-900, SP, Brazil. .,Drug Research and Development Center, Postgraduate Program in Medical and Surgical Sciences, Federal University of Ceara, Coronel Nunes de Melo, 1000, Rodolfo Teófilo, Fortaleza, CE, 60430-275, Brazil.
| |
Collapse
|
9
|
Macken WL, Vandrovcova J, Hanna MG, Pitceathly RDS. Applying genomic and transcriptomic advances to mitochondrial medicine. Nat Rev Neurol 2021; 17:215-230. [PMID: 33623159 DOI: 10.1038/s41582-021-00455-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has increased our understanding of the molecular basis of many primary mitochondrial diseases (PMDs). Despite this progress, many patients with suspected PMD remain without a genetic diagnosis, which restricts their access to in-depth genetic counselling, reproductive options and clinical trials, in addition to hampering efforts to understand the underlying disease mechanisms. Although they represent a considerable improvement over their predecessors, current methods for sequencing the mitochondrial and nuclear genomes have important limitations, and molecular diagnostic techniques are often manual and time consuming. However, recent advances in genomics and transcriptomics offer realistic solutions to these challenges. In this Review, we discuss the current genetic testing approach for PMDs and the opportunities that exist for increased use of whole-genome NGS of nuclear and mitochondrial DNA (mtDNA) in the clinical environment. We consider the possible role for long-read approaches in sequencing of mtDNA and in the identification of novel nuclear genomic causes of PMDs. We examine the expanding applications of RNA sequencing, including the detection of cryptic variants that affect splicing and gene expression and the interpretation of rare and novel mitochondrial transfer RNA variants.
Collapse
Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK.
| |
Collapse
|
10
|
Vilema-Enríquez G, Quinlan R, Kilfeather P, Mazzone R, Saqlain S, Del Molino Del Barrio I, Donato A, Corda G, Li F, Vedadi M, Németh AH, Brennan PE, Wade-Martins R. Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich's ataxia patient cells. J Biol Chem 2020; 295:17973-17985. [PMID: 33028632 PMCID: PMC7939392 DOI: 10.1074/jbc.ra120.015533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich's ataxia (FRDA) are linked to epigenetic modification of the FXN locus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation of FXN expression and represent a novel therapeutic target. Using a human FXN-GAA-Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. We found that pharmacological inhibition of the SUV4-20 methyltransferases by the tool compound A-196 increased the expression of FXN by ∼1.5-fold in the reporter cell line. In several FRDA cell lines and patient-derived primary peripheral blood mononuclear cells, A-196 increased FXN expression by up to 2-fold, an effect not seen in WT cells. SUV4-20 inhibition was accompanied by a reduction in H4K20me2 and H4K20me3 and an increase in H4K20me1, but only modest (1.4-7.8%) perturbation in genome-wide expression was observed. Finally, based on the structural activity relationship and crystal structure of A-196, novel small molecule A-196 analogs were synthesized and shown to give a 20-fold increase in potency for increasing FXN expression. Overall, our results suggest that histone methylation is important in the regulation of FXN expression and highlight SUV4-20 H1 as a potential novel therapeutic target for FRDA.
Collapse
Affiliation(s)
| | - Robert Quinlan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter Kilfeather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Roberta Mazzone
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Saba Saqlain
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Annalidia Donato
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Gabriele Corda
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Trust, Oxford, United Kingdom
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
11
|
Mystery of Expansion: DNA Metabolism and Unstable Repeats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:101-124. [PMID: 32383118 DOI: 10.1007/978-3-030-41283-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The mammalian genome mostly contains repeated sequences. Some of these repeats are in the regulatory elements of genes, and their instability, particularly the propensity to change the repeat unit number, is responsible for 36 well-known neurodegenerative human disorders. The mechanism of repeat expansion has been an unsolved question for more than 20 years. There are a few hypotheses describing models of mutation development. Every hypothesis is based on assumptions about unusual secondary structures that violate DNA metabolism processes in the cell. Some models are based on replication errors, and other models are based on mismatch repair or base excision repair errors. Additionally, it has been shown that epigenetic regulation of gene expression can influence the probability and frequency of expansion. In this review, we consider the molecular bases of repeat expansion disorders and discuss possible mechanisms of repeat expansion during cell metabolism.
Collapse
|
12
|
Sherzai M, Valle A, Perry N, Kalef-Ezra E, Al-Mahdawi S, Pook M, Anjomani Virmouni S. HMTase Inhibitors as a Potential Epigenetic-Based Therapeutic Approach for Friedreich's Ataxia. Front Genet 2020; 11:584. [PMID: 32582297 PMCID: PMC7291394 DOI: 10.3389/fgene.2020.00584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/14/2020] [Indexed: 12/17/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disorder caused by a homozygous GAA repeat expansion mutation in intron 1 of the frataxin gene (FXN), which instigates reduced transcription. As a consequence, reduced levels of frataxin protein lead to mitochondrial iron accumulation, oxidative stress, and ultimately cell death; particularly in dorsal root ganglia (DRG) sensory neurons and the dentate nucleus of the cerebellum. In addition to neurological disability, FRDA is associated with cardiomyopathy, diabetes mellitus, and skeletal deformities. Currently there is no effective treatment for FRDA and patients die prematurely. Recent findings suggest that abnormal GAA expansion plays a role in histone modification, subjecting the FXN gene to heterochromatin silencing. Therefore, as an epigenetic-based therapy, we investigated the efficacy and tolerability of two histone methyltransferase (HMTase) inhibitor compounds, BIX0194 (G9a-inhibitor) and GSK126 (EZH2-inhibitor), to specifically target and reduce H3K9me2/3 and H3K27me3 levels, respectively, in FRDA fibroblasts. We show that a combination treatment of BIX0194 and GSK126, significantly increased FXN gene expression levels and reduced the repressive histone marks. However, no increase in frataxin protein levels was observed. Nevertheless, our results are still promising and may encourage to investigate HMTase inhibitors with other synergistic epigenetic-based therapies for further preliminary studies.
Collapse
Affiliation(s)
- Mursal Sherzai
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Adamo Valle
- Energy Metabolism and Nutrition, Research Institute of Health Sciences (IUNICS) and Health Research Institute of Balearic Islands (IdISBa), University of Balearic Islands, Palma de Mallorca, Spain.,Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Nicholas Perry
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Ester Kalef-Ezra
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sara Anjomani Virmouni
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| |
Collapse
|
13
|
DNA Hypermethylation and Unstable Repeat Diseases: A Paradigm of Transcriptional Silencing to Decipher the Basis of Pathogenic Mechanisms. Genes (Basel) 2020; 11:genes11060684. [PMID: 32580525 PMCID: PMC7348995 DOI: 10.3390/genes11060684] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
Unstable repeat disorders comprise a variable group of incurable human neurological and neuromuscular diseases caused by an increase in the copy number of tandem repeats located in various regions of their resident genes. It has become clear that dense DNA methylation in hyperexpanded non-coding repeats induces transcriptional silencing and, subsequently, insufficient protein synthesis. However, the ramifications of this paradigm reveal a far more profound role in disease pathogenesis. This review will summarize the significant progress made in a subset of non-coding repeat diseases demonstrating the role of dense landscapes of 5-methylcytosine (5mC) as a common disease modifier. However, the emerging findings suggest context-dependent models of 5mC-mediated silencing with distinct effects of excessive DNA methylation. An in-depth understanding of the molecular mechanisms underlying this peculiar group of human diseases constitutes a prerequisite that could help to discover novel pathogenic repeat loci, as well as to determine potential therapeutic targets. In this regard, we report on a brief description of advanced strategies in DNA methylation profiling for the identification of unstable Guanine-Cytosine (GC)-rich regions and on promising examples of molecular targeted therapies for Fragile X disease (FXS) and Friedrich ataxia (FRDA) that could pave the way for the application of this technique in other hypermethylated expansion disorders.
Collapse
|
14
|
Fernández-Frías I, Pérez-Luz S, Díaz-Nido J. Analysis of Putative Epigenetic Regulatory Elements in the FXN Genomic Locus. Int J Mol Sci 2020; 21:E3410. [PMID: 32408537 PMCID: PMC7279236 DOI: 10.3390/ijms21103410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/05/2020] [Accepted: 05/09/2020] [Indexed: 12/22/2022] Open
Abstract
Friedreich´s ataxia (FRDA) is an autosomal recessive disease caused by an abnormally expanded Guanine-Adenine-Adenine (GAA) repeat sequence within the first intron of the frataxin gene (FXN). The molecular mechanisms associated with FRDA are still poorly understood and most studies on FXN gene regulation have been focused on the region around the minimal promoter and the region in which triplet expansion occurs. Nevertheless, since there could be more epigenetic changes involved in the reduced levels of FXN transcripts, the aim of this study was to obtain a more detailed view of the possible regulatory elements by analyzing data from ENCODE and Roadmap consortia databases. This bioinformatic analysis indicated new putative regulatory regions within the FXN genomic locus, including exons, introns, and upstream and downstream regions. Moreover, the region next to the end of intron 4 is of special interest, since the enhancer signals in FRDA-affected tissues are weak or absent in this region, whilst they are strong in the rest of the analyzed tissues. Therefore, these results suggest that there could be a direct relationship between the absence of enhancer sequences in this specific region and their predisposition to be affected in this pathology.
Collapse
Affiliation(s)
- Iván Fernández-Frías
- Departamento Biología Molecular and Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (I.F.-F.); (J.D.-N.)
- Instituto Investigación Sanitaria Puerta de Hierro-Majadahonda, 28222 Madrid, Spain
| | - Sara Pérez-Luz
- Departamento Biología Molecular and Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (I.F.-F.); (J.D.-N.)
- Instituto Investigación Sanitaria Puerta de Hierro-Majadahonda, 28222 Madrid, Spain
| | - Javier Díaz-Nido
- Departamento Biología Molecular and Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (I.F.-F.); (J.D.-N.)
- Instituto Investigación Sanitaria Puerta de Hierro-Majadahonda, 28222 Madrid, Spain
| |
Collapse
|
15
|
Verma AK, Khan E, Mishra SK, Mishra A, Charlet-Berguerand N, Kumar A. Curcumin Regulates the r(CGG) exp RNA Hairpin Structure and Ameliorate Defects in Fragile X-Associated Tremor Ataxia Syndrome. Front Neurosci 2020; 14:295. [PMID: 32317919 PMCID: PMC7155420 DOI: 10.3389/fnins.2020.00295] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Fragile X-associated tremor ataxia syndrome is an untreatable neurological and neuromuscular disorder caused by unstable expansion of 55–200 CGG nucleotide repeats in 5′ UTR of Fragile X intellectual disability 1 (FMR1) gene. The expansion of CGG repeats in the FMR1 mRNA elicits neuronal cell toxicity through two main pathogenic mechanisms. First, mRNA with CGG expanded repeats sequester specific RNA regulatory proteins resulting in splicing alterations and formation of ribonuclear inclusions. Second, repeat-associated non-canonical translation (RANT) of the CGG expansion produces a toxic homopolymeric protein, FMRpolyG. Very few small molecules are known to modulate these pathogenic events, limiting the therapeutic possibilities for FXTAS. Here, we found that a naturally available biologically active small molecule, Curcumin, selectively binds to CGG RNA repeats. Interestingly, Curcumin improves FXTAS associated alternative splicing defects and decreases the production and accumulation of FMRpolyG protein inclusion. Furthermore, Curcumin decreases cell cytotoxicity promptly by expression of CGG RNA in FXTAS cell models. In conclusion, our data suggest that small molecules like Curcumin and its derivatives may be explored as a potential therapeutic strategy against the debilitating repeats associated neurodegenerative disorders.
Collapse
Affiliation(s)
- Arun Kumar Verma
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Nicolas Charlet-Berguerand
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, Strasbourg, France
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| |
Collapse
|
16
|
Gottesfeld JM. Molecular Mechanisms and Therapeutics for the GAA·TTC Expansion Disease Friedreich Ataxia. Neurotherapeutics 2019; 16:1032-1049. [PMID: 31317428 PMCID: PMC6985418 DOI: 10.1007/s13311-019-00764-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Friedreich ataxia (FRDA), the most common inherited ataxia, is caused by transcriptional silencing of the nuclear FXN gene, encoding the essential mitochondrial protein frataxin. Currently, there is no approved therapy for this fatal disorder. Gene silencing in FRDA is due to hyperexpansion of the triplet repeat sequence GAA·TTC in the first intron of the FXN gene, which results in chromatin histone modifications consistent with heterochromatin formation. Frataxin is involved in mitochondrial iron homeostasis and the assembly and transfer of iron-sulfur clusters to various mitochondrial enzymes and components of the electron transport chain. Frataxin insufficiency leads to progressive spinocerebellar neurodegeneration, causing symptoms of gait and limb ataxia, slurred speech, muscle weakness, sensory loss, and cardiomyopathy in many patients, resulting in death in early adulthood. Numerous approaches are being taken to find a treatment for FRDA, including excision or correction of the repeats by genome engineering methods, gene activation with small molecules or artificial transcription factors, delivery of frataxin to affected cells by protein replacement therapy, gene therapy, or small molecules to increase frataxin protein levels, and therapies aimed at countering the cellular consequences of reduced frataxin. This review will summarize the mechanisms involved in repeat-mediated gene silencing and recent efforts aimed at development of therapeutics.
Collapse
Affiliation(s)
- Joel M Gottesfeld
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA.
| |
Collapse
|
17
|
|
18
|
Eimer H, Sureshkumar S, Singh Yadav A, Kraupner-Taylor C, Bandaranayake C, Seleznev A, Thomason T, Fletcher SJ, Gordon SF, Carroll BJ, Balasubramanian S. RNA-Dependent Epigenetic Silencing Directs Transcriptional Downregulation Caused by Intronic Repeat Expansions. Cell 2018; 174:1095-1105.e11. [PMID: 30057112 DOI: 10.1016/j.cell.2018.06.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 04/20/2018] [Accepted: 06/22/2018] [Indexed: 01/07/2023]
Abstract
Transcriptional downregulation caused by intronic triplet repeat expansions underlies diseases such as Friedreich's ataxia. This downregulation of gene expression is coupled with epigenetic changes, but the underlying mechanisms are unknown. Here, we show that an intronic GAA/TTC triplet expansion within the IIL1 gene of Arabidopsis thaliana results in accumulation of 24-nt short interfering RNAs (siRNAs) and repressive histone marks at the IIL1 locus, which in turn causes its transcriptional downregulation and an associated phenotype. Knocking down DICER LIKE-3 (DCL3), which produces 24-nt siRNAs, suppressed transcriptional downregulation of IIL1 and the triplet expansion-associated phenotype. Furthermore, knocking down additional components of the RNA-dependent DNA methylation (RdDM) pathway also suppressed both transcriptional downregulation of IIL1 and the repeat expansion-associated phenotype. Thus, our results show that triplet repeat expansions can lead to local siRNA biogenesis, which in turn downregulates transcription through an RdDM-dependent epigenetic modification.
Collapse
Affiliation(s)
- Hannes Eimer
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | | | - Champa Bandaranayake
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Andrei Seleznev
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Tamblyn Thomason
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Stephen J Fletcher
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia QLD 4072, Australia
| | | | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia QLD 4072, Australia
| | | |
Collapse
|
19
|
Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System. Stem Cells Int 2018; 2018:7834175. [PMID: 30123293 PMCID: PMC6079388 DOI: 10.1155/2018/7834175] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/04/2018] [Accepted: 03/27/2018] [Indexed: 12/26/2022] Open
Abstract
Epigenetics classically refers to the inheritable changes of hereditary information without perturbing DNA sequences. Understanding mechanisms of how epigenetic factors contribute to inheritable phenotype changes and cell identity will pave the way for us to understand diverse biological processes. In recent years, the emergence of CRISPR/Cas9 technology has provided us with new routes to the epigenetic field. In this review, novel epigenetic techniques utilizing the CRISPR/Cas9 system are the main contents to be discussed, including epigenome editing, temporal and spatial control of epigenetic effectors, noncoding RNA manipulation, chromatin in vivo imaging, and epigenetic element screening.
Collapse
|
20
|
Barik S. Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias. Heliyon 2017; 3:e00492. [PMID: 29387823 PMCID: PMC5772840 DOI: 10.1016/j.heliyon.2017.e00492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 11/18/2022] Open
Abstract
A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.
Collapse
|
21
|
Guo J, Chen L, Li GM. DNA mismatch repair in trinucleotide repeat instability. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1087-1092. [PMID: 29075942 DOI: 10.1007/s11427-017-9186-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 09/30/2017] [Indexed: 11/29/2022]
Abstract
Trinucleotide repeat expansions cause over 30 severe neuromuscular and neurodegenerative disorders, including Huntington's disease, myotonic dystrophy type 1, and fragile X syndrome. Although previous studies have substantially advanced the understanding of the disease biology, many key features remain unknown. DNA mismatch repair (MMR) plays a critical role in genome maintenance by removing DNA mismatches generated during DNA replication. However, MMR components, particularly mismatch recognition protein MutSβ and its interacting factors MutLα and MutLγ, have been implicated in trinucleotide repeat instability. In this review, we will discuss the roles of these key MMR proteins in promoting trinucleotide repeat instability.
Collapse
Affiliation(s)
- Jinzhen Guo
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Luping Chen
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
22
|
Williams J, Smith F, Kumar S, Vijayan M, Reddy PH. Are microRNAs true sensors of ageing and cellular senescence? Ageing Res Rev 2017; 35:350-363. [PMID: 27903442 PMCID: PMC5357446 DOI: 10.1016/j.arr.2016.11.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/11/2016] [Accepted: 11/18/2016] [Indexed: 12/14/2022]
Abstract
All living beings are programmed to death due to aging and age-related processes. Aging is a normal process of every living species. While all cells are inevitably progressing towards death, many disease processes accelerate the aging process, leading to senescence. Pathologies such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, cardiovascular disease, cancer, and skin diseases have been associated with deregulated aging. Healthy aging can delay onset of all age-related diseases. Genetics and epigenetics are reported to play large roles in accelerating and/or delaying the onset of age-related diseases. Cellular mechanisms of aging and age-related diseases are not completely understood. However, recent molecular biology discoveries have revealed that microRNAs (miRNAs) are potential sensors of aging and cellular senescence. Due to miRNAs capability to bind to the 3' untranslated region (UTR) of mRNA of specific genes, miRNAs can prevent the translation of specific genes. The purpose of our article is to highlight recent advancements in miRNAs and their involvement in cellular changes in aging and senescence. Our article discusses the current understanding of cellular senescence, its interplay with miRNAs regulation, and how they both contribute to disease processes.
Collapse
Affiliation(s)
- Justin Williams
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States
| | - Flint Smith
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States
| | - Subodh Kumar
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States
| | - Murali Vijayan
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States
| | - P Hemachandra Reddy
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States; Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States; Neuroscience & Pharmacology Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States; Neurology Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States; Speech, Language and Hearing Sciences Departments, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, United States; Garrison Institute on Aging, South West Campus, Texas Tech University Health Sciences Center, 6630 S. Quaker Suite E, MS 7495, Lubbock, TX 79413, United States.
| |
Collapse
|
23
|
Abstract
Epigenome editing aims for an introduction or removal of chromatin marks at a defined genomic region using artificial EpiEffectors resulting in a modulation of the activity of the targeted functional DNA elements. Rationally designed EpiEffectors consist of a targeting DNA-binding module (such as a zinc finger protein, TAL effector, or CRISPR/Cas complex) and usually, but not exclusively, a catalytic domain of a chromatin-modifying enzyme. Epigenome editing opens a completely new strategy for basic research of the central nervous system and causal treatment of psychiatric and neurological diseases, because rewriting of epigenetic information can lead to the direct and durable control of the expression of disease-associated genes. Here, we review current advances in the design of locus- and allele-specific DNA-binding modules, approaches for spatial, and temporal control of EpiEffectors and discuss some examples of existing and propose new potential therapeutic strategies based on epigenome editing for treatment of neurodegenerative and psychiatric diseases. These include the targeted silencing of disease-associated genes or activation of neuroprotective genes which may be applied in Alzheimer's and Parkinson's diseases or the control of addiction and depression. Moreover, we discuss allele-specific epigenome editing as novel therapeutic approach for imprinting disorders, Huntington's disease and Rett syndrome.
Collapse
|
24
|
Jones L, Houlden H, Tabrizi SJ. DNA repair in the trinucleotide repeat disorders. Lancet Neurol 2017; 16:88-96. [PMID: 27979358 DOI: 10.1016/s1474-4422(16)30350-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/22/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inherited diseases caused by unstable repeated DNA sequences are rare, but together represent a substantial cause of morbidity. Trinucleotide repeat disorders are severe, usually life-shortening, neurological disorders caused by nucleotide expansions, and most have no disease-modifying treatments. Longer repeat expansions are associated with genetic anticipation (ie, earlier disease onset in successive generations), although the differences in age at onset are not entirely accounted for by repeat length. Such phenotypic variation within disorders implies the existence of additional modifying factors in pathways that can potentially be modulated to treat disease. RECENT DEVELOPMENTS A genome-wide association study detected genetic modifiers of age at onset in Huntington's disease. Similar findings were seen in the spinocerebellar ataxias, indicating an association between DNA damage-response and repair pathways and the age at onset of disease. These studies also suggest that a common genetic mechanism modulates age at onset across polyglutamine diseases and could extend to other repeat expansion disorders. Genetic defects in DNA repair underlie other neurodegenerative disorders (eg, ataxia-telangiectasia), and DNA double-strand breaks are crucial to the modulation of early gene expression, which provides a mechanistic link between DNA repair and neurodegeneration. Mismatch and base-excision repair are important in the somatic expansion of repeated sequences in mouse models of trinucleotide repeat disorders, and somatic expansion of the expanded CAG tract in HTT correlates with age at onset of Huntington's disease and other trinucleotide repeat disorders. WHERE NEXT?: To understand the common genetic architecture of trinucleotide repeat disorders and any further genetic susceptibilities in individual disorders, genetic analysis with increased numbers of variants and sample sizes is needed, followed by sequencing approaches to define the phenotype-modifying variants. The findings must then be translated into cell biology analyses to elucidate the mechanisms through which the genetic variants operate. Genes that have roles in the DNA damage response could underpin a common DNA repeat-based mechanism and provide new therapeutic targets (and hence therapeutics) in multiple trinucleotide repeat disorders.
Collapse
Affiliation(s)
- Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK.
| | - Henry Houlden
- Department of Molecular Neuroscience and MRC Centre for Neuromuscular Diseases, Institute of Neurology, Queen Square, London, UK
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, UK
| |
Collapse
|