1
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Zhao S, Wang C, Luo H, Li F, Wang Q, Xu J, Huang Z, Liu W, Zhang W. A role for Retinoblastoma 1 in hindbrain morphogenesis by regulating GBX family. J Genet Genomics 2024:S1673-8527(24)00061-4. [PMID: 38570112 DOI: 10.1016/j.jgg.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
The hindbrain, which develops from the anterior end of the neural tube expansion, can differentiate into the metencephalon and myelencephalon, with varying sizes and functions. The midbrain-hindbrain boundary (MHB) and hindbrain myelencephalon/ventral midline (HMVM) are known to be the source of the progenitors for the anterior hindbrain and myelencephalon, respectively. However, the molecular networks regulating hindbrain morphogenesis in these structures remain unclear. In this study, we show that retinoblastoma 1 (rb1) is highly expressed at the MHB and HMVM in zebrafish. Knocking out rb1 in mice and zebrafish results in an enlarged hindbrain due to hindbrain neuronal hyperproliferation. Further study reveals that Rb1 controls the hindbrain morphogenesis by suppressing the expression of Gbx1/Gbx2, essential transcription factors for hindbrain development, through its binding to E2f3/Hdac1, respectively. Interestingly, we find that Gbx1 and Gbx2 are expressed in different types of hindbrain neurons, suggesting distinct roles in hindbrain morphogenesis. In summary, our study clarifies the specific role of RB1 in hindbrain neural cell proliferation and morphogenesis by regulating the E2f3-Gbx1 axis and the Hdac1-Gbx2 axis. These findings provide a research paradigm for exploring the differential proliferation of neurons in various brain regions.
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Affiliation(s)
- Shuang Zhao
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Chen Wang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Haiping Luo
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Feifei Li
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Qiang Wang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jin Xu
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Zhibin Huang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Wei Liu
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Wenqing Zhang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China.
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2
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Jiao F, Zhao Y, Limbu SM, Kong L, Zhang D, Liu X, Yang S, Gui W, Rong H. Cyhexatin causes developmental toxic effects by disrupting endocrine system and inducing behavioral inhibition, apoptosis and DNA hypomethylation in zebrafish (Danio rerio) larvae. CHEMOSPHERE 2023; 339:139769. [PMID: 37562506 DOI: 10.1016/j.chemosphere.2023.139769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/16/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Cyhexatin (CYT), an organotin acaricide, is extensively utilized in developing countries to mitigate plant diseases caused by mites and minimize agricultural crop losses. However, the comprehensive mechanisms underlying the developmental stage of non-target organisms remain largely unexplored. In this study, zebrafish embryos were firstly exposed to CYT (0.06, 0.12, and 0.20 ng/mL, referred to as CYTL, CYTM, and CYTH, respectively) from 2 hpf (hours post fertilization) to 30 dpf (days post fertilization). No developmental toxicity was observed in the CYTL and CYTM groups, except for induced deformed phenotypes in the CYTM group at 120 hpf. However, exposure to CYTH resulted in significant reductions in spontaneous movement (24 hpf), heart rate (48 hpf), hatching rate (48 and 72 hpf), body weight (30 dpf), whole body length (30 dpf), and locomotion (30 dpf). Additionally, CYTH exposure induced morphological malformations, including spinal curvature, pericardial edema, and tail curvature in zebrafish larvae. Moreover, CYTH treatment induced apoptosis, increased reactive oxygen species (ROS) production, and resulted in significant reductions in free T3, cholesterol, estradiol, and testosterone levels in zebrafish larvae, while free T4 levels were increased. RNA-Seq analysis indicated that CYTH exposure led to significant alterations in the genome-wide gene expression profiles of zebrafish, particularly in the thyroid hormone and steroid biosynthesis signaling pathways, indicating endocrine disruption. Furthermore, CYTH exposure induced global DNA hypomethylation, reduced S-adenosylmethionine (SAM) levels and the SAM/S-adenosylhomocysteine (SAH) ratio, elevated SAH levels, and suppressed the mRNA expression of DNA methyltransferases (DNMTs) while also downregulating DNMT1 at both the gene and protein levels in zebrafish larvae. Overall, this study partially elucidated the developmental toxicity and endocrine disruption caused by CYT in zebrafish, providing evidence of the environmental hazards associated with this acaricide.
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Affiliation(s)
- Fang Jiao
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, PR China
| | - Yang Zhao
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310058, PR China
| | - Samwel Mchele Limbu
- Department of Aquaculture Technology, School of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, P. O. Box 60091, Dar es Salaam, Tanzania
| | - Lingfu Kong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, PR China
| | - Daitao Zhang
- Xiangyang Polytechnic, Xiangyang, 441050, PR China
| | - Xianghe Liu
- Xiangyang Polytechnic, Xiangyang, 441050, PR China
| | - Sha Yang
- Xiangyang Polytechnic, Xiangyang, 441050, PR China
| | - Wenjun Gui
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China.
| | - Hua Rong
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, PR China; Xiangyang Polytechnic, Xiangyang, 441050, PR China.
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3
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Eldem V, Zararsız G, Erkan M. Global expression pattern of genes containing positively selected sites in European anchovy (Engraulis encrasicolus L.) may shed light on teleost reproduction. PLoS One 2023; 18:e0289940. [PMID: 37566603 PMCID: PMC10420382 DOI: 10.1371/journal.pone.0289940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
European anchovy is a multiple-spawning and highly fecundate pelagic fish with high economic and ecological significance. Although fecundity is influenced by nutrition, temperature and weight of spawners, high reproductive capacity is related to molecular processes in the ovary. The ovary is an essential and complex reproductive organ composed of various somatic and germ cells, which interact to facilitate the development of the ovary and functional oocytes. Revealing the ovarian transcriptome profile of highly fecundate fishes provides insights into oocyte production in teleosts. Here we use a comprehensive tissue-specific RNA sequencing which yielded 102.3 billion clean bases to analyze the transcriptional profiles of the ovary compared with other organs (liver, kidney, ovary, testis, fin, cauda and gill) and juvenile tissues of European anchovy. We conducted a comparative transcriptome and positive selection analysis of seven teleost species with varying fecundity rates to identify genes potentially involved in oogenesis and oocyte development. Of the 2,272 single copies of orthologous genes found, up to 535 genes were under positive selection in European anchovy and these genes are associated with a wide spectrum of cellular and molecular functions, with enrichments such as RNA methylation and modification, ribosome biogenesis, DNA repair, cell cycle processing and peptide/amide biosynthesis. Of the 535 positively selected genes, 55 were upregulated, and 45 were downregulated in the ovary, most of which were related to RNA and DNA transferase, developmental transcription factors, protein kinases and replication factors. Overall, our analysis of the transcriptome level in the ovarian tissue of a teleost will provide further insights into molecular processes and deepen our genetic understanding of egg production in highly fecund fish.
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Affiliation(s)
- Vahap Eldem
- Faculty of Sciences, Department of Biology, Istanbul University, Istanbul, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
| | - Melike Erkan
- Faculty of Sciences, Department of Biology, Istanbul University, Istanbul, Turkey
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4
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Sun Q, Lu H, Zhang W, Du Y, Liang Q, Zhang Y, Wu J, Zhong M. RNF106 aggravates esophageal squamous cell carcinoma progression through LATS2/YAP axis. Arch Biochem Biophys 2023; 742:109640. [PMID: 37207933 DOI: 10.1016/j.abb.2023.109640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/21/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal solid tumors in China, with the 5-year overall survival rate less than 20%. Although the carcinogenic process of ESCC is still not clear, recent studies using whole genomic profiling revealed that dysregulation of Hippo signaling pathway might play important roles in ESCC progression. The ubiquitin-like with PHD and RING finger domain 1 (RNF106) was a modifier of DNA methylation and histone ubiquitination. In this study, we evaluate the oncogenic function of RNF106 in ESCC both in vitro and in vivo. Wound healing and transwell data showed that RNF106 was required for ESCC cell migration and invasion. RNF106 depletion dramatically restrained Hippo signaling targeted gene expression. The bioinformatics analysis displayed that RNF106 was increased in ESCC tumor tissues and related with poor survival in ESCC patients. Mechanistic studies demonstrated that RNF106 was associated with LATS2 and facilitate LATS2 K48-linked ubiquitination and degradation, which subsequently inhibited YAP phosphorylation and promoted YAP oncogenic function in ESCC. Taken together, our study revealed a novel link between RNF106 and Hippo signaling in ESCC, suggesting that RNF106 could be a promising target for ESCC therapy.
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Affiliation(s)
- Qifeng Sun
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Hongda Lu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Wenjie Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Yang Du
- Department of Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Qian Liang
- Department of Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Yehui Zhang
- Department of Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Jing Wu
- Department of Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, China.
| | - Mingwei Zhong
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, China.
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5
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Sadler KC. Epigenetics across the evolutionary tree: New paradigms from non-model animals. Bioessays 2023; 45:e2200036. [PMID: 36403219 DOI: 10.1002/bies.202200036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude of epigenomic mechanisms utilized across the evolutionary tree. Now, comparative epigenomics is a rapidly growing field that is uncovering mechanistic aspects of epigenetic modifications and chromatin organization in non-model invertebrates, ranging from octopus to sponges. This review puts recent discoveries in the epigenetics of non-model invertebrates in historical context, and describes new insight into the patterning and functions of DNA methylation and other highly conserved epigenetic modifications.
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Affiliation(s)
- Kirsten C Sadler
- Program in Biology, New York University, Abu Dhabi, United Arab Emirates
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6
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Wang N, Yang Q, Wang J, Shi R, Li M, Gao J, Xu W, Yang Y, Chen Y, Chen S. Integration of Transcriptome and Methylome Highlights the Roles of Cell Cycle and Hippo Signaling Pathway in Flatfish Sexual Size Dimorphism. Front Cell Dev Biol 2021; 9:743722. [PMID: 34926443 PMCID: PMC8675331 DOI: 10.3389/fcell.2021.743722] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/14/2023] Open
Abstract
Sexual size dimorphism (SSD) is the difference in segments or body size between sexes prevalent in various species. Understanding the genetic architecture of SSD has remained a significant challenge owing to the complexity of growth mechanisms and the sexual influences among species. The Chinese tongue sole (Cynoglossus semilaevis), which exhibits a female-biased SSD and sex reversal from female to pseudomale, is an ideal model for exploring SSD mechanism at the molecular level. The present study aimed to integrate transcriptome and methylome analysis to unravel the genetic and epigenetic changes in female, male, and pseudomale C. semilaevis. The somatotropic and reproductive tissues (brain, liver, gonad, and muscle) transcriptomes were characterized by RNA-seq technology. Transcriptomic analysis unravelled numerous differentially expressed genes (DEGs) involved in cell growth and death-related pathways. The gonad and muscle methylomes were further employed for screening differentially methylated genes (DMGs). Relatively higher DNA methylation levels were observed in the male and pseudomale individuals. In detail, hypermethylation of the chromosome W was pronounced in the pseudomale group than in the female group. Furthermore, weighted gene co-expression network analysis showed that turquoise and brown modules positively and negatively correlated with the female-biased SSD, respectively. A combined analysis of the module genes and DMGs revealed the female-biased mRNA transcripts and hypomethylated levels in the upstream and downstream regions across the cell cycle-related genes. Moreover, the male and pseudomale-biased gene expression in the hippo signaling pathway were positively correlated with their hypermethylation levels in the gene body. These findings implied that the activation of the cell cycle and the inhibition of the hippo signaling pathway were implicated in C. semilaevis female-biased SSD. In addition, the dynamic expression pattern of the epigenetic regulatory factors, including dnmt1, dnmt3a, dnmt3b, and uhrf1, among the different sexes correspond with their distinct DNA methylation levels. Herein, we provide valuable clues for understanding female-biased SSD in C. semilaevis.
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Affiliation(s)
- Na Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Qian Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jialin Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Rui Shi
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming Li
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jin Gao
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenteng Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yingming Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yadong Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
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7
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Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1. Genes (Basel) 2021; 12:genes12071081. [PMID: 34356097 PMCID: PMC8304062 DOI: 10.3390/genes12071081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
Acquisition of cellular fate during development is initiated and maintained by well-coordinated patterns of gene expression that are dictated by the epigenetic landscape and genome organization in the nucleus. While the epigenetic marks that mediate developmental gene expression patterns during organogenesis have been well studied, less is known about how epigenetic marks influence nuclear organization during development. This study examines the relationship between nuclear structure, chromatin accessibility, DNA methylation, and gene expression during hepatic outgrowth in zebrafish larvae. We investigate the relationship between these features using mutants that lack DNA methylation. Hepatocyte nuclear morphology was established coincident with hepatocyte differentiation at 80 h post-fertilization (hpf), and nuclear shape and size continued to change until the conclusion of outgrowth and morphogenesis at 120 hpf. Integrating ATAC-Seq analysis with DNA methylation profiling of zebrafish livers at 120 hpf showed that closed and highly methylated chromatin occupies most transposable elements and that open chromatin correlated with gene expression. DNA hypomethylation, due to mutation of genes encoding ubiquitin-like, containing PHD and RING Finger Domains 1 (uhrf1) and DNA methyltransferase (dnmt1), did not block hepatocyte differentiation, but had dramatic effects on nuclear organization. Hepatocytes in uhrf1 mutants have large, deformed nuclei with multiple nucleoli, downregulation of nucleolar genes, and a complete lack of the nuclear lamina. Loss of lamin B2 staining was phenocopied by dnmt1 mutation. Together, these data show that hepatocyte nuclear morphogenesis coincides with organ morphogenesis and outgrowth, and that DNA methylation directs chromatin organization, and, in turn, hepatocyte nuclear shape and size during liver development.
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8
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Mancini M, Magnani E, Macchi F, Bonapace IM. The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity. Nucleic Acids Res 2021; 49:6053-6068. [PMID: 33939809 PMCID: PMC8216287 DOI: 10.1093/nar/gkab293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
During S phase, the cooperation between the macromolecular complexes regulating DNA synthesis, epigenetic information maintenance and DNA repair is advantageous for cells, as they can rapidly detect DNA damage and initiate the DNA damage response (DDR). UHRF1 is a fundamental epigenetic regulator; its ability to coordinate DNA methylation and histone code is unique across proteomes of different species. Recently, UHRF1’s role in DNA damage repair has been explored and recognized to be as important as its role in maintaining the epigenome. UHRF1 is a sensor for interstrand crosslinks and a determinant for the switch towards homologous recombination in the repair of double-strand breaks; its loss results in enhanced sensitivity to DNA damage. These functions are finely regulated by specific post-translational modifications and are mediated by the SRA domain, which binds to damaged DNA, and the RING domain. Here, we review recent studies on the role of UHRF1 in DDR focusing on how it recognizes DNA damage and cooperates with other proteins in its repair. We then discuss how UHRF1’s epigenetic abilities in reading and writing histone modifications, or its interactions with ncRNAs, could interlace with its role in DDR.
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Affiliation(s)
- Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA 21052, Italy
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, United Arab Emirates
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA 21052, Italy
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9
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Zhang C, Macchi F, Magnani E, Sadler KC. Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver. Nat Commun 2021; 12:4110. [PMID: 34226551 PMCID: PMC8257577 DOI: 10.1038/s41467-021-24466-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/10/2021] [Indexed: 02/06/2023] Open
Abstract
We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.
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Affiliation(s)
- Chi Zhang
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elena Magnani
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C. Sadler
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
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10
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Magnani E, Macchi F, Madakashira BP, Zhang C, Alaydaroos F, Sadler KC. uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements. Front Immunol 2021; 12:627926. [PMID: 33854502 PMCID: PMC8039153 DOI: 10.3389/fimmu.2021.627926] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Activation of transposable elements (TEs) can cause cellular damage. Cytoplasmic nucleic acid sensing pathways evolved to detect pathogens, but can also serve to cull cells with inappropriate TE activation as TEs can be viral mimetics. Epigenetic silencing of TEs is mediated in part by DNA methylation, but it is not clear if TE activation or the immune system contribute to the cellular damage caused by loss of DNA methylation. Here, we provide mechanistic insight into the observation of an activated interferon response in the liver of zebrafish larvae with deletion in critical components of the DNA methylation machinery, uhrf1 and dnmt1. We focus on dissecting the relationship between DNA methylation, TE activation and induction of an immune response through cytoplasmic DNA and double stranded RNA sensing pathways and identify tnfa as a mediator of cell death in the liver of these mutants. Integrated RNAseq and methylome analysis identified LTR transposons as the most upregulated in these mutants and also the most methylated in control larvae, indicating a direct role of DNA methylation in suppressing this TE subclass. RNAseq analysis from these same samples revealed expression signatures of a type-I interferon response and of tnfa activation, mimicking the pattern of gene expression in virally infected cells. CRISPR/Cas9 mediated depletion of the cellular antiviral sensors sting and mavs reduced expression of interferon response genes and tnfa depletion dramatically reduced cell death in uhrf1 mutant livers. This suggests that the antiviral response induced by DNA hypomethylation and TE activation in the liver is mediated by the signaling pathways activated by both cytoplasmic double stranded RNA and DNA and that tnfa mediates cell death as a potential mechanism to eliminate these damaged cells.
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Affiliation(s)
- Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Fatima Alaydaroos
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C Sadler
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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11
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El Fersioui Y, Pinton G, Allaman-Pillet N, Schorderet DF. Hmx1 regulates urfh1 expression in the craniofacial region in zebrafish. PLoS One 2021; 16:e0245239. [PMID: 33465110 PMCID: PMC7815118 DOI: 10.1371/journal.pone.0245239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/24/2020] [Indexed: 11/19/2022] Open
Abstract
H6 family homeobox 1 (HMX1) regulates multiple aspects of craniofacial development as it is widely expressed in the eye, peripheral ganglia and branchial arches. Mutations in HMX1 are linked to an ocular defect termed Oculo-auricular syndrome of Schorderet-Munier-Franceschetti (MIM #612109). We identified UHRF1 as a target of HMX1 during development. UHRF1 and its partner proteins actively regulate chromatin modifications and cellular proliferation. Luciferase assays and in situ hybridization analyses showed that HMX1 exerts a transcriptional inhibitory effect on UHRF1 and a modification of its expression pattern. Overexpression of hmx1 in hsp70-hmx1 zebrafish increased uhrf1 expression in the cranial region, while mutations in the hmx1 dimerization domains reduced uhrf1 expression. Moreover, the expression level of uhrf1 and its partner dnmt1 was increased in the eye field in response to hmx1 overexpression. These results indicate that hmx1 regulates uhrf1 expression and, potentially through regulating the expression of factors involved in DNA methylation, contribute to the development of the craniofacial region of zebrafish.
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Affiliation(s)
- Younes El Fersioui
- IRO – Institute for Research in Ophthalmology, Sion, Switzerland
- * E-mail: (YEF); (DFS)
| | - Gaëtan Pinton
- IRO – Institute for Research in Ophthalmology, Sion, Switzerland
| | | | - Daniel F. Schorderet
- IRO – Institute for Research in Ophthalmology, Sion, Switzerland
- Faculty of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail: (YEF); (DFS)
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12
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Reardon ES, Shukla V, Xi S, Gara SK, Liu Y, Straughan D, Zhang M, Hong JA, Payabyab EC, Kumari A, Richards WG, De Rienzo A, Hassan R, Miettinen M, Xi L, Raffeld M, Uechi LT, Li X, Wang R, Chen H, Hoang CD, Bueno R, Schrump DS. UHRF1 Is a Novel Druggable Epigenetic Target in Malignant Pleural Mesothelioma. J Thorac Oncol 2021; 16:89-103. [PMID: 32927122 PMCID: PMC7775915 DOI: 10.1016/j.jtho.2020.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Ubiquitin-like with plant homeodomain and ring finger domains 1 (UHRF1) encodes a master regulator of DNA methylation that has emerged as an epigenetic driver in human cancers. To date, no studies have evaluated UHRF1 expression in malignant pleural mesothelioma (MPM). This study was undertaken to explore the therapeutic potential of targeting UHRF1 in MPM. METHODS Microarray, real-time quantitative reverse transcription-polymerase chain reaction, immunoblot, and immunohistochemistry techniques were used to evaluate UHRF1 expression in normal mesothelial cells (NMCs) cultured with or without asbestos, MPM lines, normal pleura, and primary MPM specimens. The impact of UHRF1 expression on MPM patient survival was evaluated using two independent databases. RNA-sequencing, proliferation, invasion, and colony formation assays, and murine xenograft experiments were performed to evaluate gene expression and growth of MPM cells after biochemical or pharmacologic inhibition of UHRF1 expression. RESULTS UHRF1 expression was significantly higher in MPM lines and specimens relative to NMC and normal pleura. Asbestos induced UHRF1 expression in NMC. The overexpression of UHRF1 was associated with decreased overall survival in patients with MPM. UHRF1 knockdown reversed genomewide DNA hypomethylation, and inhibited proliferation, invasion, and clonogenicity of MPM cells, and growth of MPM xenografts. These effects were phenocopied by the repurposed chemotherapeutic agent, mithramycin. Biochemical or pharmacologic up-regulation of p53 significantly reduced UHRF1 expression in MPM cells. RNA-sequencing experiments exhibited the pleiotropic effects of UHRF1 down-regulation and identified novel, clinically relevant biomarkers of UHRF1 expression in MPM. CONCLUSIONS UHRF1 is an epigenetic driver in MPM. These findings support the efforts to target UHRF1 expression or activity for mesothelioma therapy.
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Affiliation(s)
- Emily S Reardon
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Vivek Shukla
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sichuan Xi
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sudheer K Gara
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yi Liu
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Straughan
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mary Zhang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Julie A Hong
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eden C Payabyab
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Anju Kumari
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - William G Richards
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Assunta De Rienzo
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Raffit Hassan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Markku Miettinen
- Laboratory of Pathology; National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Liqiang Xi
- Laboratory of Pathology; National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark Raffeld
- Laboratory of Pathology; National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa T Uechi
- Microarray Core Facility, University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Xinmin Li
- Microarray Core Facility, University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Ruihong Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Haobin Chen
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Chuong D Hoang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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13
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Akdogan-Ozdilek B, Duval KL, Goll MG. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model. F1000Res 2020; 9. [PMID: 32528656 PMCID: PMC7262572 DOI: 10.12688/f1000research.21809.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.
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Affiliation(s)
| | | | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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14
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Sun X, Cui Y, Feng H, Liu H, Liu X. TGF-β signaling controls Foxp3 methylation and T reg cell differentiation by modulating Uhrf1 activity. J Exp Med 2019; 216:2819-2837. [PMID: 31515281 PMCID: PMC6888975 DOI: 10.1084/jem.20190550] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/28/2019] [Accepted: 08/28/2019] [Indexed: 01/02/2023] Open
Abstract
Regulatory T (T reg) cells are required for the maintenance of immune homeostasis. Both TGF-β signaling and epigenetic modifications are important for Foxp3 induction, but how TGF-β signaling participates in the epigenetic regulation of Foxp3 remains largely unknown. Here we showed that T cell-specific ablation of Uhrf1 resulted in T reg-biased differentiation in TCR-stimulated naive T cells in the absence of TGF-β signaling, and these Foxp3+ T cells had a suppressive function. Adoptive transfer of Uhrf1 -/- naive T cells could significantly suppress colitis due to increased iT reg cell generation. Mechanistically, Uhrf1 was induced upon TCR stimulation and participated in the maintenance of DNA methylation patterns of T reg cell-specific genes during cell division, while it was phosphorylated upon TGF-β stimulation and sequestered outside the nucleus, and ultimately underwent proteasome-dependent degradation. Collectively, our study reveals a novel epigenetic mechanism of TGF-β-mediated iT reg cell differentiation by modulating Uhrf1 activity and suggests that Uhrf1 may be a potential therapeutic target in inflammatory diseases for generating stable iT reg cells.
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Affiliation(s)
- Xiang Sun
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Cui
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Haiyun Feng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Haifeng Liu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaolong Liu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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15
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Wang S, Zhang C, Hasson D, Desai A, SenBanerjee S, Magnani E, Ukomadu C, Lujambio A, Bernstein E, Sadler KC. Epigenetic Compensation Promotes Liver Regeneration. Dev Cell 2019; 50:43-56.e6. [PMID: 31231040 PMCID: PMC6615735 DOI: 10.1016/j.devcel.2019.05.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Two major functions of the epigenome are to regulate gene expression and to suppress transposons. It is unclear how these functions are balanced during physiological challenges requiring tissue regeneration, where exquisite coordination of gene expression is essential. Transcriptomic analysis of seven time points following partial hepatectomy identified the epigenetic regulator UHRF1, which is essential for DNA methylation, as dynamically expressed during liver regeneration in mice. UHRF1 deletion in hepatocytes (Uhrf1HepKO) caused genome-wide DNA hypomethylation but, surprisingly, had no measurable effect on gene or transposon expression or liver homeostasis. Partial hepatectomy of Uhrf1HepKO livers resulted in early and sustained activation of proregenerative genes and enhanced liver regeneration. This was attributed to redistribution of H3K27me3 from promoters to transposons, effectively silencing them and, consequently, alleviating repression of liver regeneration genes, priming them for expression in Uhrf1HepKO livers. Thus, epigenetic compensation safeguards the genome against transposon activation, indirectly affecting gene regulation.
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Affiliation(s)
- Shuang Wang
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anal Desai
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sucharita SenBanerjee
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; College of Arts and Sciences, Wentworth Institute of Technology, 504 Parker St., Boston, MA 02115, USA
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Chinweike Ukomadu
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kirsten C Sadler
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates.
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16
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High resolution annotation of zebrafish transcriptome using long-read sequencing. Genome Res 2018; 28:1415-1425. [PMID: 30061115 PMCID: PMC6120630 DOI: 10.1101/gr.223586.117] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
Abstract
With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short-read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2539 high-confidence novel transcripts that originated from previously unannotated loci and 1835 high-confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology, and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and noncoding RNAs, isoform switching occurrences, and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8-kb transcript spanning multiple mir-430 elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.
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17
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Chen C, Zhai S, Zhang L, Chen J, Long X, Qin J, Li J, Huo R, Wang X. Uhrf1 regulates germinal center B cell expansion and affinity maturation to control viral infection. J Exp Med 2018; 215:1437-1448. [PMID: 29618490 PMCID: PMC5940267 DOI: 10.1084/jem.20171815] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/07/2017] [Accepted: 03/01/2018] [Indexed: 12/12/2022] Open
Abstract
The production of high-affinity antibody is essential for pathogen clearance. Antibody affinity is increased through germinal center (GC) affinity maturation, which relies on BCR somatic hypermutation (SHM) followed by antigen-based selection. GC B cell proliferation is essentially involved in these processes; it provides enough templates for SHM and also serves as a critical mechanism of positive selection. In this study, we show that expression of epigenetic regulator ubiquitin-like with PHD and RING finger domains 1 (Uhrf1) was markedly up-regulated by c-Myc-AP4 in GC B cells, and it was required for GC response. Uhrf1 regulates cell proliferation-associated genes including cdkn1a, slfn1, and slfn2 by DNA methylation, and its deficiency inhibited the GC B cell cycle at G1-S phase. Subsequently, GC B cell SHM and affinity maturation were impaired, and Uhrf1 GC B knockout mice were unable to control chronic virus infection. Collectively, our data suggest that Uhrf1 regulates GC B cell proliferation and affinity maturation, and its expression in GC B cells is required for virus clearance.
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Affiliation(s)
- Chao Chen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Sulan Zhai
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Le Zhang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Jingjing Chen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuehui Long
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Jun Qin
- Key Laboratory of Stem Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianhua Li
- Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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18
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Jessop P, Ruzov A, Gering M. Developmental Functions of the Dynamic DNA Methylome and Hydroxymethylome in the Mouse and Zebrafish: Similarities and Differences. Front Cell Dev Biol 2018; 6:27. [PMID: 29616219 PMCID: PMC5869911 DOI: 10.3389/fcell.2018.00027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/05/2018] [Indexed: 12/25/2022] Open
Abstract
5-methylcytosine (5mC) is the best understood DNA modification and is generally believed to be associated with repression of gene expression. Over the last decade, sequentially oxidized forms of 5mC (oxi-mCs) have been discovered within the genomes of vertebrates. Their discovery was accompanied by that of the ten-eleven translocation (TET) methylcytosine dioxygenases, the enzymes that catalyze the formation of the oxi-mCs. Although a number of studies performed on different vertebrate models and embryonic stem cells demonstrated that both TET enzymes and oxi-mCs are likely to be important for several developmental processes it is currently unclear whether their developmental roles are conserved among vertebrates. Here, we summarize recent developments in this field suggesting that biological roles of TETs/oxi-mCs may significantly differ between mice and zebrafish. Thus, although the role of TET proteins in late organogenesis has been documented for both these systems; unlike in mice the enzymatic oxidation of 5mC does not seem to be involved in zygotic reprogramming or gastrulation in zebrafish. Our analysis may provide an insight into the general principles of epigenetic regulation of animal development and cellular differentiation.
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Affiliation(s)
- Peter Jessop
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Alexey Ruzov
- Division of Cancer and Stem Cells, Centre for Biomolecular Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin Gering
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
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19
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Madakashira B, Corbett L, Zhang C, Paoli P, Casement JW, Mann J, Sadler KC, Mann DA. Variant Histone H2afv reprograms DNA methylation during early zebrafish development. Epigenetics 2017; 12:811-824. [PMID: 29099280 PMCID: PMC5739095 DOI: 10.1080/15592294.2017.1359382] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are 2 waves of global DNA demethylation and re-methylation: the first occurs before gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that, in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage, and peaks during mid-somitogenesis; by 24 hours post -fertilization, total DNA methylation levels return to those detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
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Affiliation(s)
- Bhavani Madakashira
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates
| | - Laura Corbett
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - Chi Zhang
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates
| | - Pier Paoli
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - John W Casement
- c Bioinformatics Support Unit, Faculty of Medical Sciences , Newcastle University , Newcastle Upon Tyne , NE24HH
| | - Jelena Mann
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - Kirsten C Sadler
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates.,d Department of Medicine/Division of Liver Diseases, Department of Developmental and Regenerative Biology , Icahn School of Medicine at Mount Sinai , New York , New York
| | - Derek A Mann
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
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20
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Ye J, Zhang Y, Liang W, Huang J, Wang L, Zhong X. UHRF1 is an Independent Prognostic Factor and a Potential Therapeutic Target of Esophageal Squamous Cell Carcinoma. J Cancer 2017; 8:4027-4039. [PMID: 29187878 PMCID: PMC5706005 DOI: 10.7150/jca.21256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
Abstract
Purpose: Ubiquitin-like with plant homeodomain and ring-finger domains 1 (UHRF1) plays an essential role in DNA methylation, and the overexpression of UHRF1 is associated with poor prognosis in various cancers. Esophageal squamous cell carcinoma (ESCC) accounts for approximately 90% of esophageal cancer cases in China, but the five-year survival rate for patients is less than 10% due to limited clinical approaches for early diagnosis and treatment. The present research aimed to investigate the expression of UHRF1 in ESCC and its biological role in ESCC development. Methods: UHRF1 expression in ESCC and normal esophageal tissues was examined using immunohistochemical staining, followed by analysis of the correlation between UHRF1 expression and clinical features. In addition, the effects of lentivirus-mediated RNA interference of UHRF1 on global DNA methylation, cell proliferation, cell cycle progression and apoptosis and were investigated in ESCC cells. Results: UHRF1 was overexpressed in ESCC tissues and was an independent prognostic factor for ESCC patients. In ESCC cells, knockdown of UHRF1 caused global DNA hypomethylation, inhibited cell proliferation and induced apoptosis. Furthermore, UHRF1 depletion induced cell cycle arrest at the G2/M phase, accompanied by activation of Wee1 and DNA damage response pathway. Conclusions: Our findings identify UHRF1 as a promising prognostic marker for ESCC and suggest that UHRF1 may be a potential therapy target for ESCC patients with elevated UHRF1 expression.
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Affiliation(s)
- Jiecheng Ye
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Yong Zhang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiye Liang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Jianxian Huang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lihui Wang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Xueyun Zhong
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
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21
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Ashraf W, Ibrahim A, Alhosin M, Zaayter L, Ouararhni K, Papin C, Ahmad T, Hamiche A, Mély Y, Bronner C, Mousli M. The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer. Oncotarget 2017; 8:51946-51962. [PMID: 28881702 PMCID: PMC5584303 DOI: 10.18632/oncotarget.17393] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/02/2017] [Indexed: 12/12/2022] Open
Abstract
Cancer is one of the deadliest diseases in the world causing record number of mortalities in both developed and undeveloped countries. Despite a lot of advances and breakthroughs in the field of oncology still, it is very hard to diagnose and treat the cancers at early stages. Here in this review we analyze the potential of Ubiquitin-like containing PHD and Ring Finger domain 1 (UHRF1) as a universal biomarker for cancers. UHRF1 is an important epigenetic regulator maintaining DNA methylation and histone code in the cell. It is highly expressed in a variety of cancers and is a well-known oncogene that can disrupt the epigenetic code and override the senescence machinery. Many studies have validated UHRF1 as a powerful diagnostic and prognostic tool to differentially diagnose cancer, predict the therapeutic response and assess the risk of tumor progression and recurrence. Highly sensitive, non-invasive and cost effective approaches are therefore needed to assess the level of UHRF1 in patients, which can be deployed in diagnostic laboratories to detect cancer and monitor disease progression.
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Affiliation(s)
- Waseem Ashraf
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Abdulkhaleg Ibrahim
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, King Fahd Centre for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Liliyana Zaayter
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Christophe Papin
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Tanveer Ahmad
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Yves Mély
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Marc Mousli
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
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Integrative Characterization of Toxic Response of Zebra Fish (Danio rerio) to Deltamethrin Based on AChE Activity and Behavior Strength. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7309184. [PMID: 27999812 PMCID: PMC5141558 DOI: 10.1155/2016/7309184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/13/2016] [Accepted: 10/26/2016] [Indexed: 01/31/2023]
Abstract
In order to characterize the toxic response of zebra fish (Danio rerio) to Deltamethrin (DM), behavior strength (BS) and muscle AChE activity of zebra fish were investigated. The results showed that the average values of both BS and AChE activity showed a similarly decreased tendency as DM concentration increased, which confirmed the dose-effect relationship, and high and low levels of AChE and BS partly matched low and high levels of exposure concentrations in self-organizing map. These indicated that AChE and BS had slight different aspects of toxicity although overall trend was similar. Behavior activity suggested a possibility of reviving circadian rhythm in test organisms after exposure to the chemical in lower concentration (0.1 TU). This type of rhythm disappeared in higher concentrations (1.0 TU and 2.0 TU). Time series trend analysis of BS and AChE showed an evident time delayed effect of AChE, and a 2 h AChE inhibition delay with higher correlation coefficients (r) in different treatments was observed. It was confirmed that muscle AChE inhibition of zebra fish is a factor for swimming behavior change, though there was a 2 h delay, and other factors should be investigated to illustrate the detailed behavior response mechanism.
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