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Abstract
Embryogenesis is characterized by dynamic chromatin remodeling and broad changes in chromosome architecture. These changes in chromatin organization are accompanied by transcriptional changes, which are crucial for the proper development of the embryo. Several independent mechanisms regulate this process of chromatin reorganization, including segregation of chromatin into heterochromatin and euchromatin, deposition of active and repressive histone modifications, and the formation of 3D chromatin domains such as TADs and LADs. These changes in chromatin structure are directly linked to developmental milestones such as the loss of developmental plasticity and acquisition of terminally differentiated cell identities. In this review we summarize these processes that underlie this chromatin reorganization and their impact on embryogenesis in the nematode C. elegans.
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Affiliation(s)
- Eshna Jash
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Györgyi Csankovszki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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de la Cruz-Ruiz P, Rodríguez-Palero MJ, Askjaer P, Artal-Sanz M. Tissue-specific chromatin-binding patterns of Caenorhabditis elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression. Genetics 2023; 224:iyad081. [PMID: 37119802 PMCID: PMC10324947 DOI: 10.1093/genetics/iyad081] [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: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
Heterochromatin is characterized by an enrichment of repetitive elements and low gene density and is often maintained in a repressed state across cell division and differentiation. The silencing is mainly regulated by repressive histone marks such as H3K9 and H3K27 methylated forms and the heterochromatin protein 1 (HP1) family. Here, we analyzed in a tissue-specific manner the binding profile of the two HP1 homologs in Caenorhabditis elegans, HPL-1 and HPL-2, at the L4 developmental stage. We identified the genome-wide binding profile of intestinal and hypodermal HPL-2 and intestinal HPL-1 and compared them with heterochromatin marks and other features. HPL-2 associated preferentially to the distal arms of autosomes and correlated positively with the methylated forms of H3K9 and H3K27. HPL-1 was also enriched in regions containing H3K9me3 and H3K27me3 but exhibited a more even distribution between autosome arms and centers. HPL-2 showed a differential tissue-specific enrichment for repetitive elements conversely with HPL-1, which exhibited a poor association. Finally, we found a significant intersection of genomic regions bound by the BLMP-1/PRDM1 transcription factor and intestinal HPL-1, suggesting a corepressive role during cell differentiation. Our study uncovers both shared and singular properties of conserved HP1 proteins, providing information about genomic binding preferences in relation to their role as heterochromatic markers.
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Affiliation(s)
- Patricia de la Cruz-Ruiz
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
| | - María Jesús Rodríguez-Palero
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Peter Askjaer
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
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Wang S, Meyer DH, Schumacher B. Inheritance of paternal DNA damage by histone-mediated repair restriction. Nature 2023; 613:365-374. [PMID: 36544019 PMCID: PMC9834056 DOI: 10.1038/s41586-022-05544-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
How paternal exposure to ionizing radiation affects genetic inheritance and disease risk in the offspring has been a long-standing question in radiation biology. In humans, nearly 80% of transmitted mutations arise in the paternal germline1, but the transgenerational effects of ionizing radiation exposure has remained controversial and the mechanisms are unknown. Here we show that in sex-separated Caenorhabditis elegans strains, paternal, but not maternal, exposure to ionizing radiation leads to transgenerational embryonic lethality. The offspring of irradiated males displayed various genome instability phenotypes, including DNA fragmentation, chromosomal rearrangement and aneuploidy. Paternal DNA double strand breaks were repaired by maternally provided error-prone polymerase theta-mediated end joining. Mechanistically, we show that depletion of an orthologue of human histone H1.0, HIS-24, or the heterochromatin protein HPL-1, could significantly reverse the transgenerational embryonic lethality. Removal of HIS-24 or HPL-1 reduced histone 3 lysine 9 dimethylation and enabled error-free homologous recombination repair in the germline of the F1 generation from ionizing radiation-treated P0 males, consequently improving the viability of the F2 generation. This work establishes the mechanistic underpinnings of the heritable consequences of paternal radiation exposure on the health of offspring, which may lead to congenital disorders and cancer in humans.
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Affiliation(s)
- Siyao Wang
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - David H Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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Li J, Chen Y, Zhang G, Ruan W, Shan S, Lai X, Yang D, Yu Z. Integration of behavioural tests and transcriptome sequencing of C. elegans reveals how the nematode responds to peanut shell biochar amendment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:136024. [PMID: 31972909 DOI: 10.1016/j.scitotenv.2019.136024] [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: 09/07/2019] [Revised: 11/05/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Biochars have drawn wide attention as adsorbents, carbon sequesters and soil re-mediators. However, these substances are ambiguous regarding their effects on the motility, phenotypic changes and potential adaptative mechanisms of soil organisms. This study investigated how peanut shell biochar (PBC) affects the C. elegans model via a one-choice selection test and RNA-seq analysis. The results showed that C. elegans were able to select either PBC or a water control, and a clear preference for PBC was observed after 48 h of exposure, with the chemotaxis index (CI) reaching approximately 1.0. The nematode preferences for PBC vs sterile PBC/graphite were not significant, which demonstrated that initial microorganisms and appearances were not the reasons for the worms' selection, but the selection behaviour was instead determined by volatile odours. The treatments also showed that biochar amendment significantly decreased the body length, brood size and superoxide dismutase (SOD) activity of C. elegans to 960.20 ± 15.23 μm, 173.22 ± 4.56, 165.81 ± 3.82 U/mL SOD, respectively. Then, a possible molecular mechanism of PBC-induced developmental and reproductive effects on C. elegans was explored. Differential gene expression analysis was performed, and 1625 genes (1425 up- and 225 downregulated genes) were regulated in response to PBC treatment. The top 20 regulated genes were col genes (col-129; col-81; col-139; col-71), bli-6, perm-4 and his-24, which indicated that cuticle collagen synthesis, eggshell formation and/or heterochromatin in postembryonic growth may be disrupted following exposure to PBC. Therefore, our study suggested that quality standards be used to test nematode preferences and responses to biochar amendment, with the aim of safe application in soils, seedling substrates or fertilizers.
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Affiliation(s)
- Jie Li
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China.
| | - Yixuan Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China.
| | - Guilong Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China.
| | - Weibin Ruan
- College of Life Sciences, Nankai University, Tianjin 30071, China.
| | - Shaojie Shan
- College of Life Sciences, Nankai University, Tianjin 30071, China.
| | - Xin Lai
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China.
| | - Dianlin Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China.
| | - Zhiguo Yu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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Maremonti E, Eide DM, Oughton DH, Salbu B, Grammes F, Kassaye YA, Guédon R, Lecomte-Pradines C, Brede DA. Gamma radiation induces life stage-dependent reprotoxicity in Caenorhabditis elegans via impairment of spermatogenesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133835. [PMID: 31425988 DOI: 10.1016/j.scitotenv.2019.133835] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
The current study investigated life stage, tissue and cell dependent sensitivity to ionizing radiation of the nematode Caenorhabditis elegans. Results showed that irradiation of post mitotic L4 stage larvae induced no significant effects with respect to mortality, morbidity or reproduction at either acute dose ≤6 Gy (1500 mGy·h-1) or chronic exposure ≤15 Gy (≤100 mGy·h-1). In contrast, chronic exposure from the embryo to the L4-young adult stage caused a dose and dose-rate dependent reprotoxicity with 43% reduction in total brood size at 6.7 Gy (108 mGy·h-1). Systematic irradiation of the different developmental stages showed that the most sensitive life stage was L1 to young L4. Exposure during these stages was associated with dose-rate dependent genotoxic effects, resulting in a 1.8 to 2 fold increase in germ cell apoptosis in larvae subjected to 40 or 100 mGy·h-1, respectively. This was accompanied by a dose-rate dependent reduction in the number of spermatids, which was positively correlated to the reprotoxic effect (0.99, PCC). RNAseq analysis of nematodes irradiated from L1 to L4 stage revealed a significant enrichment of differentially expressed genes related to both male and hermaphrodite reproductive processes. Gene network analysis revealed effects related to down-regulation of genes required for spindle formation and sperm meiosis/maturation, including smz-1, smz-2 and htas-1. Furthermore, the expression of a subset of 28 set-17 regulated Major Sperm Proteins (MSP) required for spermatid production was correlated (R2 0.80) to the reduction in reproduction and the number of spermatids. Collectively these observations corroborate the impairment of spermatogenesis as the major cause of gamma radiation induced life-stage dependent reprotoxic effect. Furthermore, the progeny of irradiated nematodes showed significant embryonal DNA damage that was associated with persistent effect on somatic growth. Unexpectedly, these nematodes maintained much of their reproductive capacity in spite of the reduced growth.
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Affiliation(s)
- Erica Maremonti
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway.
| | - Dag M Eide
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway; Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Deborah H Oughton
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Brit Salbu
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Fabian Grammes
- Centre for Integrative Genetics (CIGENE), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Yetneberk A Kassaye
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Rémi Guédon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SERIS, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France
| | - Catherine Lecomte-Pradines
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SERIS, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France
| | - Dag Anders Brede
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
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Landes Highlights. Nucleus 2013. [PMCID: PMC3720742 DOI: 10.4161/nucl.24933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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