1
|
Wei Z, Yang B, Wang H, Lv S, Chen H, Liu D. Caloric restriction, Sirtuins, and cardiovascular diseases. Chin Med J (Engl) 2024; 137:921-935. [PMID: 38527930 PMCID: PMC11046024 DOI: 10.1097/cm9.0000000000003056] [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: 10/11/2023] [Indexed: 03/27/2024] Open
Abstract
ABSTRACT Caloric restriction (CR) is a well-established dietary intervention known to extend healthy lifespan and exert positive effects on aging-related diseases, including cardiovascular conditions. Sirtuins, a family of nicotinamide adenine dinucleotide (NAD + )-dependent histone deacetylases, have emerged as key regulators of cellular metabolism, stress responses, and the aging process, serving as energy status sensors in response to CR. However, the mechanism through which CR regulates Sirtuin function to ameliorate cardiovascular disease remains unclear. This review not only provided an overview of recent research investigating the interplay between Sirtuins and CR, specifically focusing on their potential implications for cardiovascular health, but also provided a comprehensive summary of the benefits of CR for the cardiovascular system mediated directly via Sirtuins. CR has also been shown to have considerable impact on specific metabolic organs, leading to the production of small molecules that enter systemic circulation and subsequently regulate Sirtuin activity within the cardiovascular system. The direct and indirect effects of CR offer a potential mechanism for Sirtuin modulation and subsequent cardiovascular protection. Understanding the interplay between CR and Sirtuins will provide new insights for the development of interventions to prevent and treat cardiovascular diseases.
Collapse
Affiliation(s)
- Ziyu Wei
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Bo Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Huiyu Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Shuangjie Lv
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Houzao Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Depei Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| |
Collapse
|
2
|
Ivessa AS, Singh S. The increase in cell death rates in caloric restricted cells of the yeast helicase mutant rrm3 is Sir complex dependent. Sci Rep 2023; 13:17832. [PMID: 37857740 PMCID: PMC10587150 DOI: 10.1038/s41598-023-45125-z] [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: 11/29/2022] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Calorie restriction (CR), which is a reduction in calorie intake without malnutrition, usually extends lifespan and improves tissue integrity. This report focuses on the relationship between nuclear genomic instability and dietary-restriction and its effect on cell survival. We demonstrate that the cell survival rates of the genomic instability yeast mutant rrm3 change under metabolic restricted conditions. Rrm3 is a DNA helicase, chromosomal replication slows (and potentially stalls) in its absence with increased rates at over 1400 natural pause sites including sites within ribosomal DNA and tRNA genes. Whereas rrm3 mutant cells have lower cell death rates compared to wild type (WT) in growth medium containing normal glucose levels (i.e., 2%), under CR growth conditions cell death rates increase in the rrm3 mutant to levels, which are higher than WT. The silent-information-regulatory (Sir) protein complex and mitochondrial oxidative stress are required for the increase in cell death rates in the rrm3 mutant when cells are transferred from growth medium containing 2% glucose to CR-medium. The Rad53 checkpoint protein is highly phosphorylated in the rrm3 mutant in response to genomic instability in growth medium containing 2% glucose. Under CR, Rad53 phosphorylation is largely reduced in the rrm3 mutant in a Sir-complex dependent manner. Since CR is an adjuvant treatment during chemotherapy, which may target genomic instability in cancer cells, our studies may gain further insight into how these therapy strategies can be improved.
Collapse
Affiliation(s)
- Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA.
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA
| |
Collapse
|
3
|
Duregon E, Fernandez ME, Martinez Romero J, Di Germanio C, Cabassa M, Voloshchuk R, Ehrlich-Mora MR, Moats JM, Wong S, Bosompra O, Rudderow A, Morrell CH, Camandola S, Price NL, Aon MA, Bernier M, de Cabo R. Prolonged fasting times reap greater geroprotective effects when combined with caloric restriction in adult female mice. Cell Metab 2023; 35:1179-1194.e5. [PMID: 37437544 PMCID: PMC10369303 DOI: 10.1016/j.cmet.2023.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/27/2023] [Accepted: 05/08/2023] [Indexed: 07/14/2023]
Abstract
Emerging new evidence highlights the importance of prolonged daily fasting periods for the health and survival benefits of calorie restriction (CR) and time-restricted feeding (TRF) in male mice; however, little is known about the impact of these feeding regimens in females. We placed 14-month-old female mice on five different dietary regimens, either CR or TRF with different feeding windows, and determined the effects of these regimens on physiological responses, progression of neoplasms and inflammatory diseases, serum metabolite levels, and lifespan. Compared with TRF feeding, CR elicited a robust systemic response, as it relates to energetics and healthspan metrics, a unique serum metabolomics signature in overnight fasted animals, and was associated with an increase in lifespan. These results indicate that daytime (rest-phase) feeding with prolonged fasting periods initiated late in life confer greater benefits when combined with imposed lower energy intake.
Collapse
Affiliation(s)
- Eleonora Duregon
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Maria Emilia Fernandez
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jorge Martinez Romero
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Clara Di Germanio
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Meaghan Cabassa
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Romaniya Voloshchuk
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Margaux R Ehrlich-Mora
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jacqueline M Moats
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sarah Wong
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Oye Bosompra
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Annamaria Rudderow
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Christopher H Morrell
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Simonetta Camandola
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Miguel A Aon
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
4
|
Xie S, Choudhari S, Wu CL, Abramson K, Corcoran D, Gregory SG, Thimmapuram J, Guilak F, Little D. Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction. FASEB J 2023; 37:e22785. [PMID: 36794668 PMCID: PMC10561192 DOI: 10.1096/fj.202201413r] [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: 08/31/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023]
Abstract
The epigenome of stem cells occupies a critical interface between genes and environment, serving to regulate expression through modification by intrinsic and extrinsic factors. We hypothesized that aging and obesity, which represent major risk factors for a variety of diseases, synergistically modify the epigenome of adult adipose stem cells (ASCs). Using integrated RNA- and targeted bisulfite-sequencing in murine ASCs from lean and obese mice at 5- and 12-months of age, we identified global DNA hypomethylation with either aging or obesity, and a synergistic effect of aging combined with obesity. The transcriptome of ASCs in lean mice was relatively stable to the effects of age, but this was not true in obese mice. Functional pathway analyses identified a subset of genes with critical roles in progenitors and in diseases of obesity and aging. Specifically, Mapt, Nr3c2, App, and Ctnnb1 emerged as potential hypomethylated upstream regulators in both aging and obesity (AL vs. YL and AO vs. YO), and App, Ctnnb1, Hipk2, Id2, and Tp53 exhibited additional effects of aging in obese animals. Furthermore, Foxo3 and Ccnd1 were potential hypermethylated upstream regulators of healthy aging (AL vs. YL), and of the effects of obesity in young animals (YO vs. YL), suggesting that these factors could play a role in accelerated aging with obesity. Finally, we identified candidate driver genes that appeared recurrently in all analyses and comparisons undertaken. Further mechanistic studies are needed to validate the roles of these genes capable of priming ASCs for dysfunction in aging- and obesity-associated pathologies.
Collapse
Affiliation(s)
- Shaojun Xie
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
| | - Sulbha Choudhari
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
- Advanced Biomedical Computational Science, Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, MD 2170
| | - Chia-Lung Wu
- Department of Orthopaedics and Rehabilitation, Center for Musculoskeletal Research, University of Rochester, Rochester, NY, 14611
| | - Karen Abramson
- Duke Molecular Physiology Institute, 300 North Duke Street, Durham, NC 27701
| | - David Corcoran
- Genomic Analysis and Bioinformatics Shared Resource, Duke Center for Genomic and Computational Biology, 101 Science Drive, Duke University Medical Center Box 3382, Durham, NC 27708
- Lineberger Bioinformatics Core, 5200 Marsico Hall, University of North Carolina-Chapel Hill, Chapel Hill, NC 27516
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, 300 North Duke Street, Durham, NC 27701
- Department of Neurology, Duke University School of Medicine, 311 Research Drive, Durham, NC 27710
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University in St. Louis, 4515 McKinley Ave., St. Louis, MO 63110
- Shriners Hospitals for Children – St. Louis, 4400 Clayton Ave, St. Louis Missouri 63110
| | - Dianne Little
- Departments of Basic Medical Sciences and Biomedical Engineering, Purdue University, 2186 Lynn Hall, 625 Harrison St, West Lafayette, IN 47907-2026
| |
Collapse
|
5
|
Jusic A, Thomas PB, Wettinger SB, Dogan S, Farrugia R, Gaetano C, Tuna BG, Pinet F, Robinson EL, Tual-Chalot S, Stellos K, Devaux Y. Noncoding RNAs in age-related cardiovascular diseases. Ageing Res Rev 2022; 77:101610. [PMID: 35338919 DOI: 10.1016/j.arr.2022.101610] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/28/2022] [Accepted: 03/15/2022] [Indexed: 11/01/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the adult population worldwide and represent a severe economic burden and public health concern. The majority of human genes do not code for proteins. However, noncoding transcripts play important roles in ageing that significantly increases the risk for CVDs. Noncoding RNAs (ncRNAs) are critical regulators of multiple biological processes related to ageing such as oxidative stress, mitochondrial dysfunction and chronic inflammation. NcRNAs are also involved in pathophysiological developments within the cardiovascular system including arrhythmias, cardiac hypertrophy, fibrosis, myocardial infarction and heart failure. In this review article, we cover the roles of ncRNAs in cardiovascular ageing and disease as well as their potential therapeutic applications in CVDs.
Collapse
|
6
|
Advances in transcriptome analysis of human brain aging. Exp Mol Med 2020; 52:1787-1797. [PMID: 33244150 PMCID: PMC8080664 DOI: 10.1038/s12276-020-00522-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Aging is associated with gradual deterioration of physiological and biochemical functions, including cognitive decline. Transcriptome profiling of brain samples from individuals of varying ages has identified the whole-transcriptome changes that underlie age-associated cognitive declines. In this review, we discuss transcriptome-based research on human brain aging performed by using microarray and RNA sequencing analyses. Overall, decreased synaptic function and increased immune function are prevalent in most regions of the aged brain. Age-associated gene expression changes are also cell dependent and region dependent and are affected by genotype. In addition, the transcriptome changes that occur during brain aging include different splicing events, intersample heterogeneity, and altered levels of various types of noncoding RNAs. Establishing transcriptome-based hallmarks of human brain aging will improve the understanding of cognitive aging and neurodegenerative diseases and eventually lead to interventions that delay or prevent brain aging.
Collapse
|
7
|
Liu YP, Wan J, Long F, Tian J, Zhang C. circPVT1 Facilitates Invasion and Metastasis by Regulating miR-205-5p/c-FLIP Axis in Osteosarcoma. Cancer Manag Res 2020; 12:1229-1240. [PMID: 32110097 PMCID: PMC7035890 DOI: 10.2147/cmar.s231872] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/28/2019] [Indexed: 11/25/2022] Open
Abstract
Background As a key subtype of non-coding RNAs, circular RNA (circRNA) has been well documented to play a key role in the tumorigenesis of osteosarcoma (OS). circPVT1 was revealed to participate in the progression of multiple human tumors; however, the roles of circPVT1 in OS invasion and metastasis and its potential mechanisms remain elusive. Methods RNA expression in OS tissues and cells was examined by qRT-PCR, protein expression was measured by Western blot. circPVT1 knockdown in vitro was achieved by transfecting OS cells with specific siRNAs. OS cell proliferation was assessed via CCK-8 and colony formation assays. OS cell migration and invasion were evaluated by transwell assay. Interaction between miR-205-5p and circPVT1 or c-FLIP was validated through dual-luciferase reporter assay. Rescue experiments were performed to explore the regulatory net among circPVT1, miR-205-5p and c-FLIP in OS progression in vitro. Results circPVT1 and c-FLIP were highly expressed, while miR-205-5p was lowly expressed in OS tissues and cell lines. Knockdown of circPVT1 repressed cell proliferation, migration and invasion via inhibiting epithelial–mesenchymal transition (EMT) in OS. circPVT1 functioned as a sponge of miR-205-5p, and c-FLIP was targeted by miR-205-5p in OS cells. Furthermore, circPVT1 indirectly regulated c-FLIP expression through competitively binding to miR-205-5p. Inhibition of miR-205-5p or overexpression of c-FLIP abolished the effects of si-circPVT1 on cell proliferation, migration and invasion. Conclusion Our study demonstrated circPVT1 functions as a sponge for miR-205-5p to promote c-FLIP expression, thereby enhancing EMT and inducing OS invasion and metastasis in vitro, implying that circPVT1 might be a potential therapeutic target for further clinical therapy of OS.
Collapse
Affiliation(s)
- Yu-Peng Liu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, People's Republic of China
| | - Jun Wan
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, People's Republic of China
| | - Feng Long
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, People's Republic of China
| | - Jian Tian
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, People's Republic of China
| | - Can Zhang
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, People's Republic of China
| |
Collapse
|
8
|
Barja G. Towards a unified mechanistic theory of aging. Exp Gerontol 2019; 124:110627. [DOI: 10.1016/j.exger.2019.05.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/08/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
|
9
|
Hall AC, Ostrowski LA, Mekhail K. Phase Separation as a Melting Pot for DNA Repeats. Trends Genet 2019; 35:589-600. [DOI: 10.1016/j.tig.2019.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
|
10
|
Conserved Pbp1/Ataxin-2 regulates retrotransposon activity and connects polyglutamine expansion-driven protein aggregation to lifespan-controlling rDNA repeats. Commun Biol 2018; 1:187. [PMID: 30417124 PMCID: PMC6218562 DOI: 10.1038/s42003-018-0187-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022] Open
Abstract
Ribosomal DNA (rDNA) repeat instability and protein aggregation are thought to be two major and independent drivers of cellular aging. Pbp1, the yeast ortholog of human ATXN2, maintains rDNA repeat stability and lifespan via suppression of RNA-DNA hybrids. ATXN2 polyglutamine expansion drives neurodegeneration causing spinocerebellar ataxia type 2 and promoting amyotrophic lateral sclerosis. Here, molecular characterization of Pbp1 revealed that its knockout or subjection to disease-modeling polyQ expansion represses Ty1 (Transposons of Yeast) retrotransposons by respectively promoting Trf4-depedendent RNA turnover and Ty1 Gag protein aggregation. This aggregation, but not its impact on retrotransposition, compromises rDNA repeat stability and shortens lifespan by hyper-activating Trf4-dependent turnover of intergenic ncRNA within the repeats. We uncover a function for the conserved Pbp1/ATXN2 proteins in the promotion of retrotransposition, create and describe powerful yeast genetic models of ATXN2-linked neurodegenerative diseases, and connect the major aging mechanisms of rDNA instability and protein aggregation.
Collapse
|
11
|
Donaldson ME, Ostrowski LA, Goulet KM, Saville BJ. Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression. BMC Genomics 2017; 18:340. [PMID: 28464849 PMCID: PMC5414199 DOI: 10.1186/s12864-017-3720-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Biotrophic fungal plant pathogens cause billions of dollars in losses to North American crops annually. The model for functional investigation of these fungi is Ustilago maydis. Its 20.5 Mb annotated genome sequence has been an excellent resource for investigating biotrophic plant pathogenesis. Expressed-sequence tag libraries and microarray hybridizations have provided insight regarding the type of transcripts produced by U. maydis but these analyses were not comprehensive and there were insufficient data for transcriptome comparison to other smut fungi. To improve transcriptome annotation and enable comparative analyses, comprehensive strand-specific RNA-seq was performed on cell-types of three related smut species: U. maydis (common smut of corn), Ustilago hordei (covered smut of barley), and Sporisorium reilianum (head smut of corn). Results In total, >1 billion paired-end sequence reads were obtained from haploid cell, dikaryon and teliospore RNA of U. maydis, haploid cell RNA of U. hordei, and haploid and dikaryon cell RNA of S. reilianum. The sequences were assembled into transfrags using Trinity, and updated gene models were created using PASA and categorized with Cufflinks Cuffcompare. Representative genes that were predicted for the first time with these RNA-seq analyses and genes with novel annotation features were independently assessed by reverse transcriptase PCR. The analyses indicate hundreds more predicted proteins, relative to the previous genome annotation, could be produced by U. maydis from altered transcript forms, and that the number of non-coding RNAs produced, including transcribed intergenic sequences and natural antisense transcripts, approximately equals the number of mRNAs. This high representation of non-coding RNAs appears to be a conserved feature of the smut fungi regardless of whether they have RNA interference machinery. Approximately 50% of the identified NATs were conserved among the smut fungi. Conclusions Overall, these analyses revealed: 1) smut genomes encode a number of transcriptional units that is twice the number of annotated protein-coding genes, 2) a small number of intergenic transcripts may encode proteins with characteristics of fungal effectors, 3) the vast majority of intergenic and antisense transcripts do not contain ORFs, 4) a large proportion of the identified antisense transcripts were detected at orthologous loci among the smut fungi, and 5) there is an enrichment of functional categories among orthologous loci that suggests antisense RNAs could have a genome-wide, non-RNAi-mediated, influence on gene expression in smut fungi. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3720-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada
| | - Lauren A Ostrowski
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada.,Present Address: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Kristi M Goulet
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada
| | - Barry J Saville
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada. .,Forensic Science Program, Trent University, Peterborough, K9L 0G2, ON, Canada.
| |
Collapse
|
12
|
Affiliation(s)
- Aamir Ahmad
- Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Av, Mobile, AL, USA
| |
Collapse
|