1
|
Huang J, Jiang Z, Ruan Z, Sheng H, Liu S, Dong X, Su X, Feng L, Li Y, Xu H, Chen J, Xia H, Li T, Li J, Xu L, Lou J. Cr (VI)-induced ribosomal DNA copy number variation is associated with semen quality impairment: Evidence from human to animal study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116700. [PMID: 38981392 DOI: 10.1016/j.ecoenv.2024.116700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVES This study aimed to analyze the possible role of rDNA copy number variation in the association between hexavalent chromium [Cr (VI)] exposure and semen quality in semen donors and further confirm this association in mice. METHODS In this cross-sectional study, whole blood and semen samples were collected from 155 semen donors in the Zhejiang Human Sperm Bank from January 1st to April 31st, 2021. Adult C57BL/6 J male mice were treated with different doses of Cr (VI) (0, 10, or 15 mg/kg b.w./day). Semen quality, including semen volume, total spermatozoa count, sperm concentration, progressive motility, and total motility, were analyzed according to the WHO laboratory manual. Cr concentration was detected using inductively coupled plasma mass spectrometry. The rDNA copy number was measured using qPCR. RESULTS In semen donors, whole blood Cr concentration was negatively associated with semen concentration and total sperm counts. Semen 5 S and 45 S rDNA copy numbers were negatively associated with whole blood Cr concentration and whole blood 5.8 S rDNA copy number was negatively associated with semen Cr concentration. In mice, Cr (VI) damaged testicular tissue, decreased semen quality, and caused rDNA copy number variation. Semen quality was related to the rDNA copy number in whole blood, testicular tissue, and semen samples in mice. CONCLUSION Cr (VI) was associated with decreased semen quality in semen donors and mice. Our findings suggest an in-depth analysis of the role of the rDNA copy number variation in the Cr (VI)-induced impairment of semen quality.
Collapse
Affiliation(s)
- Jing Huang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Zhaoqiang Jiang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Zheng Ruan
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Huiqiang Sheng
- Zhejiang Mater Child and Reproductive Health Center, Hangzhou, Zhejiang Province, China
| | - Shuang Liu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Xiaowen Dong
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Xin Su
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Yongxin Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Huadong Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Hailing Xia
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Tao Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Jiaping Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Ling Xu
- Zhejiang Mater Child and Reproductive Health Center, Hangzhou, Zhejiang Province, China.
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China; School of Medicine, and The First Affiliated Hospital, Huzhou University, Huzhou, Zhejiang Province, China.
| |
Collapse
|
2
|
Kindelay SM, Maggert KA. Insights into ribosomal DNA dominance and magnification through characterization of isogenic deletion alleles. Genetics 2024; 227:iyae063. [PMID: 38797870 DOI: 10.1093/genetics/iyae063] [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: 03/12/2024] [Accepted: 04/02/2024] [Indexed: 05/29/2024] Open
Abstract
The major loci for the large primary ribosomal RNA (rRNA) genes (35S rRNAs) exist as hundreds to thousands of tandem repeats in all organisms and dozens to hundreds in Drosophila. The highly repetitive nature of the ribosomal DNA (rDNA) makes it intrinsically unstable, and many conditions arise from the reduction in or magnification of copy number, but the conditions under which it does so remain unknown. By targeted DNA damage to the rDNA of the Y chromosome, we created and investigated a series of rDNA alleles. We found that complete loss of rDNA leads to lethality after the completion of embryogenesis, blocking larval molting and metamorphosis. We find that the resident retrotransposons-R1 and R2-are regulated by active rDNA such that reduction in copy number derepresses these elements. Their expression is highest during the early first instar, when loss of rDNA is lethal. Regulation of R1 and R2 may be related to their structural arrangement within the rDNA, as we find they are clustered in the flanks of the nucleolus organizing region (NOR; the cytological appearance of the rDNA). We assessed the complex nucleolar dominance relationship between X- and Y-linked rDNA using a histone H3.3-GFP reporter construct and incorporation at the NOR and found that dominance is controlled by rDNA copy number as at high multiplicity the Y-linked array is dominant, but at low multiplicity the X-linked array becomes derepressed. Finally, we found that multiple conditions that disrupt nucleolar dominance lead to increased rDNA magnification, suggesting that the phenomena of dominance and magnification are related, and a single mechanism may underlie and unify these two longstanding observations in Drosophila.
Collapse
Affiliation(s)
- Selina M Kindelay
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
| | - Keith A Maggert
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| |
Collapse
|
3
|
Lau NC, Macias VM. Transposon and Transgene Tribulations in Mosquitoes: A Perspective of piRNA Proportions. DNA 2024; 4:104-128. [PMID: 39076684 PMCID: PMC11286205 DOI: 10.3390/dna4020006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Mosquitoes, like Drosophila, are dipterans, the order of "true flies" characterized by a single set of two wings. Drosophila are prime model organisms for biomedical research, while mosquito researchers struggle to establish robust molecular biology in these that are arguably the most dangerous vectors of human pathogens. Both insects utilize the RNA interference (RNAi) pathway to generate small RNAs to silence transposons and viruses, yet details are emerging that several RNAi features are unique to each insect family, such as how culicine mosquitoes have evolved extreme genomic feature differences connected to their unique RNAi features. A major technical difference in the molecular genetic studies of these insects is that generating stable transgenic animals are routine in Drosophila but still variable in stability in mosquitoes, despite genomic DNA-editing advances. By comparing and contrasting the differences in the RNAi pathways of Drosophila and mosquitoes, in this review we propose a hypothesis that transgene DNAs are possibly more intensely targeted by mosquito RNAi pathways and chromatin regulatory pathways than in Drosophila. We review the latest findings on mosquito RNAi pathways, which are still much less well understood than in Drosophila, and we speculate that deeper study into how mosquitoes modulate transposons and viruses with Piwi-interacting RNAs (piRNAs) will yield clues to improving transgene DNA expression stability in transgenic mosquitoes.
Collapse
Affiliation(s)
- Nelson C. Lau
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- Genome Science Institute and National Emerging Infectious Disease Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
| | - Vanessa M. Macias
- Department of Biology, University of North Texas, Denton, TX 76205, USA
- Advanced Environmental Research Institute, University of North Texas, Denton, TX 76205, USA
| |
Collapse
|
4
|
Watase GJ, Yamashita YM. RNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila. PLoS Genet 2024; 20:e1011136. [PMID: 38758955 PMCID: PMC11139327 DOI: 10.1371/journal.pgen.1011136] [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: 01/11/2024] [Revised: 05/30/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
Ribosomal DNA (rDNA), which encodes ribosomal RNA, is an essential but unstable genomic element due to its tandemly repeated nature. rDNA's repetitive nature causes spontaneous intrachromatid recombination, leading to copy number (CN) reduction, which must be counteracted by a mechanism that recovers CN to sustain cells' viability. Akin to telomere maintenance, rDNA maintenance is particularly important in cell types that proliferate for an extended time period, most notably in the germline that passes the genome through generations. In Drosophila, the process of rDNA CN recovery, known as 'rDNA magnification', has been studied extensively. rDNA magnification is mediated by unequal sister chromatid exchange (USCE), which generates a sister chromatid that gains the rDNA CN by stealing copies from its sister. However, much remains elusive regarding how germ cells sense rDNA CN to decide when to initiate magnification, and how germ cells balance between the need to generate DNA double-strand breaks (DSBs) to trigger USCE vs. avoiding harmful DSBs. Recently, we identified an rDNA-binding Zinc-finger protein Indra as a factor required for rDNA magnification, however, the underlying mechanism of action remains unknown. Here we show that Indra is a negative regulator of rDNA magnification, balancing the need of rDNA magnification and repression of dangerous DSBs. Mechanistically, we show that Indra is a repressor of RNA polymerase II (Pol II)-dependent transcription of rDNA: Under low rDNA CN conditions, Indra protein amount is downregulated, leading to Pol II-mediated transcription of rDNA. This results in the expression of rDNA-specific retrotransposon, R2, which we have shown to facilitate rDNA magnification via generation of DBSs at rDNA. We propose that differential use of Pol I and Pol II plays a critical role in regulating rDNA CN expansion only when it is necessary.
Collapse
Affiliation(s)
- George J. Watase
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto-shi, Kumamoto, JAPAN
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Yukiko M. Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| |
Collapse
|
5
|
Murai T, Yanagi S, Hori Y, Kobayashi T. Replication fork blocking deficiency leads to a reduction of rDNA copy number in budding yeast. iScience 2024; 27:109120. [PMID: 38384843 PMCID: PMC10879690 DOI: 10.1016/j.isci.2024.109120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/27/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The ribosomal RNA genes are encoded as hundreds of tandem repeats, known as the rDNA, in eukaryotes. Maintaining these copies seems to be necessary, but copy number changes in an active manner have been reported in only frogs, flies, Neurospora, and yeast. In the best-studied system, yeast, a protein (Fob1) binds to the rDNA and unidirectionally blocks the replication fork. This block stimulates rDNA double-strand breaks (DSBs) leading to recombination and copy number change. To date, copy number maintenance and concerted evolution mediated by rDNA repeat turnover were the proposed benefits of Fob1-dependent replication fork arrest. In this study, we tested whether Fob1 provides these benefits and found that rDNA copy number decreases when FOB1 is deleted, suggesting that Fob1 is important for recovery from low copy number. We suppose that replication fork stalling at rDNA is necessary for recovering from rDNA copy number loss in other species as well.
Collapse
Affiliation(s)
- Taichi Murai
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuichi Yanagi
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yutaro Hori
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|
6
|
Nelson JO, Slicko A, Raz AA, Yamashita YM. Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582629. [PMID: 38464041 PMCID: PMC10925281 DOI: 10.1101/2024.02.28.582629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Preserving a large number of essential yet highly unstable ribosomal DNA (rDNA) repeats is critical for the germline to perpetuate the genome through generations. Spontaneous rDNA loss must be countered by rDNA copy number (CN) expansion. Germline rDNA CN expansion is best understood in Drosophila melanogaster, which relies on unequal sister chromatid exchange (USCE) initiated by DNA breaks at rDNA. The rDNA-specific retrotransposon R2 responsible for USCE-inducing DNA breaks is typically expressed only when rDNA CN is low to minimize the danger of DNA breaks; however, the underlying mechanism of R2 regulation remains unclear. Here we identify the insulin receptor (InR) as a major repressor of R2 expression, limiting unnecessary R2 activity. Through single-cell RNA sequencing we find that male germline stem cells (GSCs), the major cell type that undergoes rDNA CN expansion, have reduced InR expression when rDNA CN is low. Reduced InR activity in turn leads to R2 expression and CN expansion. We further find that dietary manipulation alters R2 expression and rDNA CN expansion activity. This work reveals that the insulin pathway integrates rDNA CN surveying with environmental sensing, revealing a potential mechanism by which diet exerts heritable changes to genomic content.
Collapse
Affiliation(s)
- Jonathan O Nelson
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY
- Whitehead Institute for Biomedical Research, Cambridge, MA
- Howard Hughes Medical Institute, Cambridge, MA
| | - Alyssa Slicko
- Whitehead Institute for Biomedical Research, Cambridge, MA
- Howard Hughes Medical Institute, Cambridge, MA
| | - Amelie A Raz
- Whitehead Institute for Biomedical Research, Cambridge, MA
- Howard Hughes Medical Institute, Cambridge, MA
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA
- Howard Hughes Medical Institute, Cambridge, MA
- Department of Biology, MIT, Cambridge, MA
| |
Collapse
|
7
|
Yamashita YM. Asymmetric Stem Cell Division and Germline Immortality. Annu Rev Genet 2023; 57:181-199. [PMID: 37552892 DOI: 10.1146/annurev-genet-022123-040039] [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] [Indexed: 08/10/2023]
Abstract
Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms supporting the germline's remarkable ability to continue in this eternal cycle, termed germline immortality. Even unicellular organisms age at a cellular level, demonstrating that cellular aging is inevitable. Extensive studies in yeast have established the framework of how asymmetric cell division and gametogenesis may contribute to the resetting of cellular age. This review examines the mechanisms of germline immortality-how germline cells reset the aging of cells-drawing a parallel between yeast and multicellular organisms.
Collapse
Affiliation(s)
- Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| |
Collapse
|
8
|
Nelson JO, Kumon T, Yamashita YM. rDNA magnification is a unique feature of germline stem cells. Proc Natl Acad Sci U S A 2023; 120:e2314440120. [PMID: 37967216 PMCID: PMC10666004 DOI: 10.1073/pnas.2314440120] [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: 08/21/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023] Open
Abstract
Ribosomal DNA (rDNA) encodes ribosomal RNA and exists as tandem repeats of hundreds of copies in the eukaryotic genome to meet the high demand of ribosome biogenesis. Tandemly repeated DNA elements are inherently unstable; thus, mechanisms must exist to maintain rDNA copy number (CN), in particular in the germline that continues through generations. A phenomenon called rDNA magnification was discovered over 50 y ago in Drosophila as a process that recovers the rDNA CN on chromosomes that harbor minimal CN. Our recent studies indicated that rDNA magnification is the mechanism to maintain rDNA CN under physiological conditions to counteract spontaneous CN loss that occurs during aging. Our previous studies that explored the mechanism of rDNA magnification implied that asymmetric division of germline stem cells (GSCs) may be particularly suited to achieve rDNA magnification. However, it remains elusive whether GSCs are the unique cell type that undergoes rDNA magnification or differentiating germ cells are also capable of magnification. In this study, we provide empirical evidence that suggests that rDNA magnification operates uniquely in GSCs, but not in differentiating germ cells. We further provide computer simulation that suggests that rDNA magnification is only achievable through asymmetric GSC divisions. We propose that despite known plasticity and transcriptomic similarity between GSCs and differentiating germ cells, GSCs' unique ability to divide asymmetrically serves a critical role of maintaining rDNA CN through generations, supporting germline immortality.
Collapse
Affiliation(s)
- Jonathan O Nelson
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Chevy Chase, MD 20815
| | - Tomohiro Kumon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Chevy Chase, MD 20815
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Chevy Chase, MD 20815
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| |
Collapse
|
9
|
Gleason RJ, Chen X. Epigenetic dynamics during germline development: insights from Drosophila and C. elegans. Curr Opin Genet Dev 2023; 78:102017. [PMID: 36549194 PMCID: PMC10100592 DOI: 10.1016/j.gde.2022.102017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/08/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
Gametogenesis produces the only cell type within a metazoan that contributes both genetic and epigenetic information to the offspring. Extensive epigenetic dynamics are required to express or repress gene expression in a precise spatiotemporal manner. On the other hand, early embryos must be extensively reprogrammed as they begin a new life cycle, involving intergenerational epigenetic inheritance. Seminal work in both Drosophila and C. elegans has elucidated the role of various regulators of epigenetic inheritance, including (1) histones, (2) histone-modifying enzymes, and (3) small RNA-dependent epigenetic regulation in the maintenance of germline identity. This review highlights recent discoveries of epigenetic regulation during the stepwise changes of transcription and chromatin structure that takes place during germline stem cell self-renewal, maintenance of germline identity, and intergenerational epigenetic inheritance. Findings from these two species provide precedence and opportunity to extend relevant studies to vertebrates.
Collapse
Affiliation(s)
- Ryan J. Gleason
- Department of Biology, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Xin Chen
- HHMI, Department of Biology, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| |
Collapse
|