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Yu Y, Wang X, Fox J, Yu R, Thakre P, McCauley B, Nikoloutsos N, Yu Y, Li Q, Hastings PJ, Dang W, Chen K, Ira G. Yeast EndoG prevents genome instability by degrading extranuclear DNA species. Nat Commun 2024; 15:7653. [PMID: 39227600 PMCID: PMC11372161 DOI: 10.1038/s41467-024-52147-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
In metazoans mitochondrial DNA (mtDNA) or retrotransposon cDNA released to cytoplasm are degraded by nucleases to prevent sterile inflammation. It remains unknown whether degradation of these DNA also prevents nuclear genome instability. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. In non-dividing stationary phase cells, Pol4-mediated non-homologous end-joining increases, resulting in frequent insertions of 1-3 nucleotides, and insertions of mtDNA (NUMTs) or retrotransposon cDNA. Yeast EndoG (Nuc1) nuclease limits insertion of cDNA and transfer of very long mtDNA ( >10 kb) to the nucleus, where it forms unstable circles, while promoting the formation of short NUMTs (~45-200 bp). Nuc1 also regulates transfer of extranuclear DNA to nucleus in aging or meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating extranuclear DNA preserve genome stability.
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Affiliation(s)
- Yang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Xin Wang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, USA
| | - Jordan Fox
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Pilendra Thakre
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Brenna McCauley
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Nicolas Nikoloutsos
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX, USA
| | - Yang Yu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, USA
| | - Qian Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, USA.
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
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2
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Martin R, Espinoza CY, Large CRL, Rosswork J, Van Bruinisse C, Miller AW, Sanchez JC, Miller M, Paskvan S, Alvino GM, Dunham MJ, Raghuraman MK, Brewer BJ. Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA. PLoS Genet 2024; 20:e1010850. [PMID: 38175823 PMCID: PMC10766183 DOI: 10.1371/journal.pgen.1010850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 01/06/2024] Open
Abstract
Inherited and germ-line de novo copy number variants (CNVs) are increasingly found to be correlated with human developmental and cancerous phenotypes. Several models for template switching during replication have been proposed to explain the generation of these gross chromosomal rearrangements. We proposed a model of template switching (ODIRA-origin dependent inverted repeat amplification) in which simultaneous ligation of the leading and lagging strands at diverging replication forks could generate segmental inverted triplications through an extrachromosomal inverted circular intermediate. Here, we created a genetic assay using split-ura3 cassettes to trap the proposed inverted intermediate. However, instead of recovering circular inverted intermediates, we found inverted linear chromosomal fragments ending in native telomeres-suggesting that a template switch had occurred at the centromere-proximal fork of a replication bubble. As telomeric inverted hairpin fragments can also be created through double strand breaks we tested whether replication errors or repair of double stranded DNA breaks were the most likely initiating event. The results from CRISPR/Cas9 cleavage experiments and growth in the replication inhibitor hydroxyurea indicate that it is a replication error, not a double stranded break that creates the inverted junctions. Since inverted amplicons of the SUL1 gene occur during long-term growth in sulfate-limited chemostats, we sequenced evolved populations to look for evidence of linear intermediates formed by an error in replication. All of the data are compatible with a two-step version of the ODIRA model in which sequential template switching at short inverted repeats between the leading and lagging strands at a replication fork, followed by integration via homologous recombination, generates inverted interstitial triplications.
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Affiliation(s)
- Rebecca Martin
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Claudia Y. Espinoza
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christopher R. L. Large
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua Rosswork
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Cole Van Bruinisse
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Aaron W. Miller
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joseph C. Sanchez
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Madison Miller
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samantha Paskvan
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gina M. Alvino
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bonita J. Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Yu Y, Wang X, Fox J, Yu R, Thakre P, McCauley B, Nikoloutsos N, Li Q, Hastings PJ, Dang W, Chen K, Ira G. Yeast EndoG prevents genome instability by degrading cytoplasmic DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571550. [PMID: 38168242 PMCID: PMC10760121 DOI: 10.1101/2023.12.13.571550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease. Cytoplasmic nucleases degrade these DNA species to limit inflammation. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. Nu clear mt DNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (∼45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.
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Morton EA, Hall AN, Cuperus JT, Queitsch C. Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Genetics 2023; 224:iyad039. [PMID: 36919976 PMCID: PMC10474940 DOI: 10.1093/genetics/iyad039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.
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Affiliation(s)
| | - Ashley N Hall
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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5
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Kwan EX, Alvino GM, Lynch KL, Levan PF, Amemiya HM, Wang XS, Johnson SA, Sanchez JC, Miller MA, Croy M, Lee SB, Naushab M, Bedalov A, Cuperus JT, Brewer BJ, Queitsch C, Raghuraman MK. Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast. Cell Rep 2023; 42:112161. [PMID: 36842087 PMCID: PMC10142053 DOI: 10.1016/j.celrep.2023.112161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Timely completion of genome replication is a prerequisite for mitosis, genome integrity, and cell survival. A challenge to this timely completion comes from the need to replicate the hundreds of untranscribed copies of rDNA that organisms maintain in addition to the copies required for ribosome biogenesis. Replication of these rDNA arrays is relegated to late S phase despite their large size, repetitive nature, and essentiality. Here, we show that, in Saccharomyces cerevisiae, reducing the number of rDNA repeats leads to early rDNA replication, which results in delaying replication elsewhere in the genome. Moreover, cells with early-replicating rDNA arrays and delayed genome-wide replication aberrantly release the mitotic phosphatase Cdc14 from the nucleolus and enter anaphase prematurely. We propose that rDNA copy number determines the replication time of the rDNA locus and that the release of Cdc14 upon completion of rDNA replication is a signal for cell cycle progression.
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Affiliation(s)
- Elizabeth X Kwan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gina M Alvino
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kelsey L Lynch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Paula F Levan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Haley M Amemiya
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Xiaobin S Wang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sarah A Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph C Sanchez
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Madison A Miller
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Mackenzie Croy
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Seung-Been Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Maria Naushab
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Bonita J Brewer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - M K Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Abstract
Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.
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7
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Mitochondrial form, function and signalling in aging. Biochem J 2017; 473:3421-3449. [PMID: 27729586 DOI: 10.1042/bcj20160451] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 02/07/2023]
Abstract
Aging is often accompanied by a decline in mitochondrial mass and function in different tissues. Additionally, cell resistance to stress is frequently found to be prevented by higher mitochondrial respiratory capacity. These correlations strongly suggest mitochondria are key players in aging and senescence, acting by regulating energy homeostasis, redox balance and signalling pathways central in these processes. However, mitochondria display a wide array of functions and signalling properties, and the roles of these different characteristics are still widely unexplored. Furthermore, differences in mitochondrial properties and responses between tissues and cell types, and how these affect whole body metabolism are also still poorly understood. This review uncovers aspects of mitochondrial biology that have an impact upon aging in model organisms and selected mammalian cells and tissues.
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Molina-Serrano D, Schiza V, Demosthenous C, Stavrou E, Oppelt J, Kyriakou D, Liu W, Zisser G, Bergler H, Dang W, Kirmizis A. Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity. EMBO Rep 2016; 17:1829-1843. [PMID: 27799288 PMCID: PMC5167350 DOI: 10.15252/embr.201642540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/07/2023] Open
Abstract
Changes in histone modifications are an attractive model through which environmental signals, such as diet, could be integrated in the cell for regulating its lifespan. However, evidence linking dietary interventions with specific alterations in histone modifications that subsequently affect lifespan remains elusive. We show here that deletion of histone N‐alpha‐terminal acetyltransferase Nat4 and loss of its associated H4 N‐terminal acetylation (N‐acH4) extend yeast replicative lifespan. Notably, nat4Δ‐induced longevity is epistatic to the effects of calorie restriction (CR). Consistent with this, (i) Nat4 expression is downregulated and the levels of N‐acH4 within chromatin are reduced upon CR, (ii) constitutive expression of Nat4 and maintenance of N‐acH4 levels reduces the extension of lifespan mediated by CR, and (iii) transcriptome analysis indicates that nat4Δ largely mimics the effects of CR, especially in the induction of stress‐response genes. We further show that nicotinamidase Pnc1, which is typically upregulated under CR, is required for nat4Δ‐mediated longevity. Collectively, these findings establish histone N‐acH4 as a regulator of cellular lifespan that links CR to increased stress resistance and longevity.
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Affiliation(s)
| | - Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Wei Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Gertrude Zisser
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Helmut Bergler
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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