1
|
Zeinoun B, Teixeira MT, Barascu A. TERRA and Telomere Maintenance in the Yeast Saccharomyces cerevisiae. Genes (Basel) 2023; 14:genes14030618. [PMID: 36980890 PMCID: PMC10048448 DOI: 10.3390/genes14030618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Telomeres are structures made of DNA, proteins and RNA found at the ends of eukaryotic linear chromosomes. These dynamic nucleoprotein structures protect chromosomal tips from end-to-end fusions, degradation, activation of damage checkpoints and erroneous DNA repair events. Telomeres were thought to be transcriptionally silent regions because of their constitutive heterochromatin signature until telomeric long non-coding RNAs (LncRNAs) were discovered. One of them, TERRA (TElomeric Repeat-containing RNA), starts in the subtelomeric regions towards the chromosome ends from different telomeres and has been extensively studied in many evolutionarily distant eukaryotes. Changes in TERRA’s expression can lead to telomeric dysfunction, interfere with the replicative machinery and impact telomere length. TERRA also co-localizes in vivo with telomerase, and can form RNA:DNA hybrid structures called R-loops, which have been implicated in the onset of senescence and the alternative lengthening of telomere (ALT) pathway. Yet, the molecular mechanisms involving TERRA, as well as its function, remain elusive. Here, we review the current knowledge of TERRA transcription, structure, expression, regulation and its multiple telomeric and extra-telomeric functions in the budding yeast Saccharomyces cerevisiae.
Collapse
|
2
|
Tea Polyphenols as Prospective Natural Attenuators of Brain Aging. Nutrients 2022; 14:nu14153012. [PMID: 35893865 PMCID: PMC9332553 DOI: 10.3390/nu14153012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 12/26/2022] Open
Abstract
No organism can avoid the process of aging, which is often accompanied by chronic disease. The process of biological aging is driven by a series of interrelated mechanisms through different signal pathways, including oxidative stress, inflammatory states, autophagy and others. In addition, the intestinal microbiota play a key role in regulating oxidative stress of microglia, maintaining homeostasis of microglia and alleviating age-related diseases. Tea polyphenols can effectively regulate the composition of the intestinal microbiota. In recent years, the potential anti-aging benefits of tea polyphenols have attracted increasing attention because they can inhibit neuroinflammation and prevent degenerative effects in the brain. The interaction between human neurological function and the gut microbiota suggests that intervention with tea polyphenols is a possible way to alleviate brain-aging. Studies have been undertaken into the possible mechanisms underpinning the preventative effect of tea polyphenols on brain-aging mediated by the intestinal microbiota. Tea polyphenols may be regarded as potential neuroprotective substances which can act with high efficiency and low toxicity.
Collapse
|
3
|
Chaux-Jukic F, O'Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 2021; 49:7571-7587. [PMID: 34165564 PMCID: PMC8287924 DOI: 10.1093/nar/gkab534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.
Collapse
Affiliation(s)
- Frédéric Chaux-Jukic
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Olivier Vallon
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| |
Collapse
|
4
|
Chaux-Jukic F, O'Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 2021. [PMID: 34165564 DOI: 10.1101/2021.01.29.428817)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.
Collapse
Affiliation(s)
- Frédéric Chaux-Jukic
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Olivier Vallon
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| |
Collapse
|
5
|
Kuklyte J, Fitzgerald J, Nelissen S, Wei H, Whelan A, Power A, Ahmad A, Miarka M, Gregson M, Maxwell M, Raji R, Lenihan J, Finn-Moloney E, Rafferty M, Cary M, Barale-Thomas E, O’Shea D. Evaluation of the Use of Single- and Multi-Magnification Convolutional Neural Networks for the Determination and Quantitation of Lesions in Nonclinical Pathology Studies. Toxicol Pathol 2021; 49:815-842. [PMID: 33618634 PMCID: PMC8091423 DOI: 10.1177/0192623320986423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Digital pathology platforms with integrated artificial intelligence have the potential to increase the efficiency of the nonclinical pathologist's workflow through screening and prioritizing slides with lesions and highlighting areas with specific lesions for review. Herein, we describe the comparison of various single- and multi-magnification convolutional neural network (CNN) architectures to accelerate the detection of lesions in tissues. Different models were evaluated for defining performance characteristics and efficiency in accurately identifying lesions in 5 key rat organs (liver, kidney, heart, lung, and brain). Cohorts for liver and kidney were collected from TG-GATEs open-source repository, and heart, lung, and brain from internally selected R&D studies. Annotations were performed, and models were trained on each of the available lesion classes in the available organs. Various class-consolidation approaches were evaluated from generalized lesion detection to individual lesion detections. The relationship between the amount of annotated lesions and the precision/accuracy of model performance is elucidated. The utility of multi-magnification CNN implementations in specific tissue subtypes is also demonstrated. The use of these CNN-based models offers users the ability to apply generalized lesion detection to whole-slide images, with the potential to generate novel quantitative data that would not be possible with conventional image analysis techniques.
Collapse
Affiliation(s)
| | | | | | - Haolin Wei
- Deciphex, Dublin City University, Dublin, Ireland
| | - Aoife Whelan
- Deciphex, Dublin City University, Dublin, Ireland
| | - Adam Power
- Deciphex, Dublin City University, Dublin, Ireland
| | - Ajaz Ahmad
- Deciphex, Dublin City University, Dublin, Ireland
| | | | - Mark Gregson
- Deciphex, Dublin City University, Dublin, Ireland
| | | | - Ruka Raji
- Deciphex, Dublin City University, Dublin, Ireland
| | | | | | | | - Maurice Cary
- Pathology Experts GmbH, Technologie Zentrum Witterswil, Witters, Switzerland
| | | | - Donal O’Shea
- Deciphex, Dublin City University, Dublin, Ireland
| |
Collapse
|
6
|
Kwapisz M, Morillon A. Subtelomeric Transcription and its Regulation. J Mol Biol 2020; 432:4199-4219. [PMID: 32035903 PMCID: PMC7374410 DOI: 10.1016/j.jmb.2020.01.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022]
Abstract
The subtelomeres, highly heterogeneous repeated sequences neighboring telomeres, are transcribed into coding and noncoding RNAs in a variety of organisms. Telomereproximal subtelomeric regions produce non-coding transcripts i.e., ARRET, αARRET, subTERRA, and TERRA, which function in telomere maintenance. The role and molecular mechanisms of the majority of subtelomeric transcripts remain unknown. This review depicts the current knowledge and puts into perspective the results obtained in different models from yeasts to humans.
Collapse
Affiliation(s)
- Marta Kwapisz
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France.
| |
Collapse
|
7
|
Henninger E, Teixeira MT. Telomere-driven mutational processes in yeast. Curr Opin Genet Dev 2020; 60:99-106. [DOI: 10.1016/j.gde.2020.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022]
|