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Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 DOI: 10.1016/j.celrep.2023.113664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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Guevara E, Gopalan S, Massey DJ, Adegboyega M, Zhou W, Solis A, Anaya AD, Churchill SE, Feldblum J, Lawler RR. Getting it right: Teaching undergraduate biology to undermine racial essentialism. Biol Methods Protoc 2023; 8:bpad032. [PMID: 38023347 PMCID: PMC10674104 DOI: 10.1093/biomethods/bpad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students' racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students' racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and the misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographical distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students' endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.
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Affiliation(s)
- Elaine Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Dashiell J Massey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Mayowa Adegboyega
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Wen Zhou
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
- Department of Evolutionary Anthropology, Duke Kunshan University, Kunshan, Jiangsu 215316, China
| | - Alma Solis
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Alisha D Anaya
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Steven E Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Joseph Feldblum
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, United States
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Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. bioRxiv 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
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Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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Palmerola KL, Amrane S, De Los Angeles A, Xu S, Wang N, de Pinho J, Zuccaro MV, Taglialatela A, Massey DJ, Turocy J, Robles A, Subbiah A, Prosser B, Lobo R, Ciccia A, Koren A, Baslan T, Egli D. Replication stress impairs chromosome segregation and preimplantation development in human embryos. Cell 2022; 185:2988-3007.e20. [PMID: 35858625 DOI: 10.1016/j.cell.2022.06.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Human cleavage-stage embryos frequently acquire chromosomal aneuploidies during mitosis due to unknown mechanisms. Here, we show that S phase at the 1-cell stage shows replication fork stalling, low fork speed, and DNA synthesis extending into G2 phase. DNA damage foci consistent with collapsed replication forks, DSBs, and incomplete replication form in G2 in an ATR- and MRE11-dependent manner, followed by spontaneous chromosome breakage and segmental aneuploidies. Entry into mitosis with incomplete replication results in chromosome breakage, whole and segmental chromosome errors, micronucleation, chromosome fragmentation, and poor embryo quality. Sites of spontaneous chromosome breakage are concordant with sites of DNA synthesis in G2 phase, locating to gene-poor regions with long neural genes, which are transcriptionally silent at this stage of development. Thus, DNA replication stress in mammalian preimplantation embryos predisposes gene-poor regions to fragility, and in particular in the human embryo, to the formation of aneuploidies, impairing developmental potential.
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Affiliation(s)
- Katherine L Palmerola
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Selma Amrane
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alejandro De Los Angeles
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Shuangyi Xu
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA; Masters of Biotechnology Program, Columbia University, New York, NY 10027, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Joao de Pinho
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jenna Turocy
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alex Robles
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Anisa Subbiah
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Bob Prosser
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Rogerio Lobo
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA; Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA.
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Massey DJ, Koren A. Telomere-to-telomere human DNA replication timing profiles. Sci Rep 2022; 12:9560. [PMID: 35688856 PMCID: PMC9187705 DOI: 10.1038/s41598-022-13638-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
The spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first nearly-gapless telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.
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Affiliation(s)
- Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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Yaacov A, Vardi O, Blumenfeld B, Greenberg A, Massey DJ, Koren A, Adar S, Simon I, Rosenberg S. Cancer Mutational Processes Vary in Their Association with Replication Timing and Chromatin Accessibility. Cancer Res 2021; 81:6106-6116. [PMID: 34702725 DOI: 10.1158/0008-5472.can-21-2039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Cancer somatic mutations are the product of multiple mutational and repair processes, both of which are tightly associated with DNA replication. Distinctive patterns of somatic mutation accumulation, termed mutational signatures, are indicative of processes sustained within tumors. However, the association of various mutational processes with replication timing (RT) remains an open question. In this study, we systematically analyzed the mutational landscape of 2,787 tumors from 32 tumor types separately for early and late replicating regions using sequence context normalization and chromatin data to account for sequence and chromatin accessibility differences. To account for sequence differences between various genomic regions, an artificial genome-based approach was developed to expand the signature analyses to doublet base substitutions and small insertions and deletions. The association of mutational processes and RT was signature specific: Some signatures were associated with early or late replication (such as SBS7b and SBS7a, respectively), and others had no association. Most associations existed even after normalizing for genome accessibility. A focused mutational signature identification approach was also developed that uses RT information to improve signature identification; this approach found that SBS16, which is biased toward early replication, is strongly associated with better survival rates in liver cancer. Overall, this novel and comprehensive approach provides a better understanding of the etiology of mutational signatures, which may lead to improved cancer prevention, diagnosis, and treatment. SIGNIFICANCE: Many mutational processes associate with early or late replication timing regions independently of chromatin accessibility, enabling development of a focused identification approach to improve mutational signature detection.
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Affiliation(s)
- Adar Yaacov
- The Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.,The Wohl Institute for Translational Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.,Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oriya Vardi
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avraham Greenberg
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Shai Rosenberg
- The Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel. .,The Wohl Institute for Translational Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Koren A, Massey DJ, Bracci AN. TIGER: inferring DNA replication timing from whole-genome sequence data. Bioinformatics 2021; 37:4001-4005. [PMID: 33704387 PMCID: PMC8913259 DOI: 10.1093/bioinformatics/btab166] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. RESULTS We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. AVAILABILITY AND IMPLEMENTATION TIGER is available at https://github.com/TheKorenLab/TIGER. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14850 USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14850 USA
| | - Alexa N Bracci
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14850 USA
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Abstract
Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding the mechanisms and cellular consequences of DNA replication timing. Several methods, such as quantification of nucleotide analog incorporation and DNA copy number analyses, can accurately reconstruct the genomic replication timing profiles of various species and cell types. More recent developments have expanded the DNA replication genomic toolkit to assays that directly measure the activity of replication origins, while single-cell replication timing assays are beginning to reveal a new level of replication timing regulation. The combination of these methods, applied on a genomic scale and in multiple biological systems, promises to resolve many open questions and lead to a holistic understanding of how eukaryotic cells replicate their genomes accurately and efficiently.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A. Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. Genes (Basel) 2019; 10:genes10040269. [PMID: 30987063 PMCID: PMC6523654 DOI: 10.3390/genes10040269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Centromeres serve a critical function in preserving genome integrity across sequential cell divisions, by mediating symmetric chromosome segregation. The repetitive, heterochromatic nature of centromeres is thought to be inhibitory to DNA replication, but has also led to their underrepresentation in human reference genome assemblies. Consequently, centromeres have been excluded from genomic replication timing analyses, leaving their time of replication unresolved. However, the most recent human reference genome, hg38, included models of centromere sequences. To establish the experimental requirements for achieving replication timing profiles for centromeres, we sequenced G1- and S-phase cells from five human cell lines, and aligned the sequence reads to hg38. We were able to infer DNA replication timing profiles for the centromeres in each of the five cell lines, which showed that centromere replication occurs in mid-to-late S phase. Furthermore, we found that replication timing was more variable between cell lines in the centromere regions than expected, given the distribution of variation in replication timing genome-wide. These results suggest the potential of these, and future, sequence models to enable high-resolution studies of replication in centromeres and other heterochromatic regions.
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Affiliation(s)
- Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Dongsung Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Kayla E Brooks
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Delabaere L, Ertl HA, Massey DJ, Hofley CM, Sohail F, Bienenstock EJ, Sebastian H, Chiolo I, LaRocque JR. Aging impairs double-strand break repair by homologous recombination in Drosophila germ cells. Aging Cell 2017; 16:320-328. [PMID: 28000382 PMCID: PMC5334535 DOI: 10.1111/acel.12556] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 12/23/2022] Open
Abstract
Aging is characterized by genome instability, which contributes to cancer formation and cell lethality leading to organismal decline. The high levels of DNA double-strand breaks (DSBs) observed in old cells and premature aging syndromes are likely a primary source of genome instability, but the underlying cause of their formation is still unclear. DSBs might result from higher levels of damage or repair defects emerging with advancing age, but repair pathways in old organisms are still poorly understood. Here, we show that premeiotic germline cells of young and old flies have distinct differences in their ability to repair DSBs by the error-free pathway homologous recombination (HR). Repair of DSBs induced by either ionizing radiation (IR) or the endonuclease I-SceI is markedly defective in older flies. This correlates with a remarkable reduction in HR repair measured with the DR-white DSB repair reporter assay. Strikingly, most of this repair defect is already present at 8 days of age. Finally, HR defects correlate with increased expression of early HR components and increased recruitment of Rad51 to damage in older organisms. Thus, we propose that the defect in the HR pathway for germ cells in older flies occurs following Rad51 recruitment. These data reveal that DSB repair defects arise early in the aging process and suggest that HR deficiencies are a leading cause of genome instability in germ cells of older animals.
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Affiliation(s)
- Laetitia Delabaere
- Molecular and Computational Biology Department; University of Southern California; Los Angeles CA 90089 USA
| | - Henry A. Ertl
- Department of Human Science; Georgetown University Medical Center; Washington DC 20057 USA
| | - Dashiell J. Massey
- Department of Human Science; Georgetown University Medical Center; Washington DC 20057 USA
| | - Carolyn M. Hofley
- Department of Human Science; Georgetown University Medical Center; Washington DC 20057 USA
| | - Faraz Sohail
- Department of Human Science; Georgetown University Medical Center; Washington DC 20057 USA
| | - Elisa J. Bienenstock
- Department of Human Science; Georgetown University Medical Center; Washington DC 20057 USA
- College of Public Service & Community Solutions; Arizona State University; Phoenix AZ 85004 USA
| | - Hans Sebastian
- Molecular and Computational Biology Department; University of Southern California; Los Angeles CA 90089 USA
| | - Irene Chiolo
- Molecular and Computational Biology Department; University of Southern California; Los Angeles CA 90089 USA
| | - Jeannine R. LaRocque
- Department of Human Science; Georgetown University Medical Center; Washington DC 20057 USA
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