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Li F, Karimi N, Wang S, Pan T, Dong J, Wang X, Ma S, Shan Q, Liu C, Zhang Y, Li W, Feng G. mRNA isoform switches during mouse zygotic genome activation. Cell Prolif 2024; 57:e13655. [PMID: 38764347 PMCID: PMC11216927 DOI: 10.1111/cpr.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Fan Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Najmeh Karimi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Qingtong Shan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024; 25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [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: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. RESULTS By employing SLAM-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional activation events and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA-430 function, a key post transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression. CONCLUSION These insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. The findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.
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Affiliation(s)
- Danielson Baia Amaral
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Rhonda Egidy
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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Ray M, Conard AM, Urban J, Mahableshwarkar P, Aguilera J, Huang A, Vaidyanathan S, Larschan E. Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis. eLife 2023; 12:e87865. [PMID: 37466240 PMCID: PMC10400075 DOI: 10.7554/elife.87865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Sex-specific splicing is an essential process that regulates sex determination and drives sexual dimorphism. Yet, how early in development widespread sex-specific transcript diversity occurs was unknown because it had yet to be studied at the genome-wide level. We use the powerful Drosophila model to show that widespread sex-specific transcript diversity occurs early in development, concurrent with zygotic genome activation. We also present a new pipeline called time2Splice to quantify changes in alternative splicing over time. Furthermore, we determine that one of the consequences of losing an essential maternally deposited pioneer factor called CLAMP (chromatin-linked adapter for MSL proteins) is altered sex-specific splicing of genes involved in diverse biological processes that drive development. Overall, we show that sex-specific differences in transcript diversity exist even at the earliest stages of development..
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Affiliation(s)
- Mukulika Ray
- MCB department, Brown UniversityProvidenceUnited States
| | | | - Jennifer Urban
- Biology department, Johns Hopkins UniversityBaltimoreUnited States
| | - Pranav Mahableshwarkar
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
| | | | - Annie Huang
- MCB department, Brown UniversityProvidenceUnited States
| | - Smriti Vaidyanathan
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
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4
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Liu Y, Kong F, Wang W, Xin J, Zhang S, Chen J, Ming X, Wu X, Cui W, Wang H, Li W. Low estrogen level in aged mice leads to abnormal oogenesis affecting the quality of surrounded nucleolus-type immature oocytes. Reprod Fertil Dev 2022; 34:991-1001. [PMID: 36064201 DOI: 10.1071/rd22120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
CONTEXT With aging, various problems in the reproductive system emerge, especially in females. However, our understanding of reproductive aging in livestock and humans is limited. AIMS We aimed to investigate reproductive changes between young and aged mice. METHODS Eight- to ten-week-old female mice were used as the young group, and 10-month-old mice were studied as the aged group. Reproductive changes were investigated from physiological, histological, cytological, and epigenetic perspectives. KEY RESULTS The estrus cycle was shortened (P <0.0001), and the estradiol (E2) concentration was lower in aged mice (P <0.01), whereas the progesterone (P4) concentration did not differ between young and aged mice (P >0.05). The histological results revealed a lower number of antral follicles in the ovary and disordered epithelial tissue structures in the oviducts in aged mice. During oogenesis, the surrounded nucleolus (SN)-type oocytes in aged mice exhibited increased mitochondrial agglutination (P <0.05) and cellular apoptosis (P <0.01) as well as decreased H3K36 triple-methylation (P <0.001). Although many defects existed, the oocytes from aged mice could normally support cellular reprogramming after somatic cell nuclear transfer. CONCLUSIONS Our results indicate that the reduced levels of reproductive hormones in aged females lead to shorter estrus cycles and reduced follicular development, leading to abnormal oogenesis, particularly in SN-type immature oocytes. IMPLICATIONS These results provide new insight that enhance our understanding and improve the reproductive ability of aged females.
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Affiliation(s)
- Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China; and Department of Veterinary and Animal Sciences, Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA 01002, USA
| | - Feng Kong
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Wenying Wang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Jing Xin
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Shengnan Zhang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Ji Chen
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Xin Ming
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Xiaoqing Wu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Wei Cui
- Department of Veterinary and Animal Sciences, Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA 01002, USA
| | - Hongcheng Wang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China; and Linquan Modern Agricultural Technology Cooperation and Extension Service Center, the Anhui Agricultural University's Comprehensive Experimental Station in the Northwest of Anhui Province, Linquan, Anhui 236400, China
| | - Wenyong Li
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang 236037, China
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5
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Liu Z, Wang W, Li X, Zhao X, Zhao H, Yang W, Zuo Y, Cai L, Xing Y. Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish. Front Cell Dev Biol 2022; 10:879795. [PMID: 35874832 PMCID: PMC9304896 DOI: 10.3389/fcell.2022.879795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is pervasive in mammalian genomes and involved in embryo development, whereas research on crosstalk of alternative splicing and embryo development was largely restricted to mouse and human and the alternative splicing regulation during embryogenesis in zebrafish remained unclear. We constructed the alternative splicing atlas at 18 time-course stages covering maternal-to-zygotic transition, gastrulation, somitogenesis, pharyngula stages, and post-fertilization in zebrafish. The differential alternative splicing events between different developmental stages were detected. The results indicated that abundance alternative splicing and differential alternative splicing events are dynamically changed and remarkably abundant during the maternal-to-zygotic transition process. Based on gene expression profiles, we found splicing factors are expressed with specificity of developmental stage and largely expressed during the maternal-to-zygotic transition process. The better performance of cluster analysis was achieved based on the inclusion level of alternative splicing. The biological function analysis uncovered the important roles of alternative splicing during embryogenesis. The identification of isoform switches of alternative splicing provided a new insight into mining the regulated mechanism of transcript isoforms, which always is hidden by gene expression. In conclusion, we inferred that alternative splicing activation is synchronized with zygotic genome activation and discovered that alternative splicing is coupled with transcription during embryo development in zebrafish. We also unveiled that the temporal expression dynamics of splicing factors during embryo development, especially co-orthologous splicing factors. Furthermore, we proposed that the inclusion level of alternative splicing events can be employed for cluster analysis as a novel parameter. This work will provide a deeper insight into the regulation of alternative splicing during embryogenesis in zebrafish.
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Affiliation(s)
- Zhe Liu
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Wei Wang
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xinru Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, China
| | - Xiujuan Zhao
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hongyu Zhao
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Wuritu Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Hohhot Science and Technology Bureau, Hohhot, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, China
| | - Lu Cai
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
- *Correspondence: Yongqiang Xing,
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6
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Ma P, Liu X, Xu Z, Liu H, Ding X, Huang Z, Shi C, Liang L, Xu L, Li X, Li G, He Y, Ding Z, Chai C, Wang H, Qiu J, Zhu J, Wang X, Ding P, Zhou S, Yuan Y, Wu W, Wan C, Yan Y, Zhou Y, Zhou QJ, Wang GD, Zhang Q, Xu X, Li G, Zhang S, Mao B, Chen D. Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution. Cell Rep 2022; 39:110979. [PMID: 35732129 DOI: 10.1016/j.celrep.2022.110979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/21/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022] Open
Abstract
Vertebrate evolution was accompanied by two rounds of whole-genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single-cell sequencing has been widely used to construct the developmental cell atlas of several representative species of vertebrates (human, mouse, zebrafish, and frog) and tunicates (sea squirts). Here, we perform single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated, we constructed a developmental tree for amphioxus cell fate commitment and lineage specification and characterize the underlying key regulators and genetic regulatory networks. The data are publicly available on the online platform AmphioxusAtlas.
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Affiliation(s)
- Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xingyan Liu
- Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing 100190, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaoxu Xu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huimin Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China
| | - Xiangning Ding
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Huang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China; Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China
| | - Langchao Liang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaolu Li
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Guimei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuqi He
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Zhaoli Ding
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Chaochao Chai
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoyu Wang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaying Qiu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Peiwen Ding
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wendi Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Cen Wan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Yanan Yan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Yitao Zhou
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Qi-Jun Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qiujin Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China.
| | - Shihua Zhang
- Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing 100190, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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7
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Yoshizawa-Sugata N, Yamazaki S, Mita-Yoshida K, Ono T, Nishito Y, Masai H. Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation. J Biol Chem 2021; 297:101367. [PMID: 34736895 PMCID: PMC8686075 DOI: 10.1016/j.jbc.2021.101367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/21/2022] Open
Abstract
Rif1 regulates DNA replication timing and double-strand break repair, and its depletion induces transcriptional bursting of two-cell (2C) zygote-specific genes in mouse ES cells. However, how Rif1 regulates zygotic transcription is unclear. We show here that Rif1 depletion promotes the formation of a unique Zscan4 enhancer structure harboring both histone H3 lysine 27 acetylation (H3K27ac) and moderate levels of silencing chromatin mark H3K9me3. Curiously, another enhancer mark H3K4me1 is missing, whereas DNA methylation is still maintained in the structure, which spreads across gene bodies and neighboring regions within the Zscan4 gene cluster. We also found by function analyses of Rif1 domains in ES cells that ectopic expression of Rif1 lacking N-terminal domain results in upregulation of 2C transcripts. This appears to be caused by dominant negative inhibition of endogenous Rif1 protein localization at the nuclear periphery through formation of hetero-oligomers between the N-terminally truncated and endogenous forms. Strikingly, in murine 2C embryos, most of Rif1-derived polypeptides are expressed as truncated forms in soluble nuclear or cytosolic fraction and are likely nonfunctional. Toward the morula stage, the full-length form of Rif1 gradually increased. Our results suggest that the absence of the functional full-length Rif1 due to its instability or alternative splicing and potential inactivation of Rif1 through dominant inhibition by N-terminally truncated Rif1 polypeptides may be involved in 2C-specific transcription program.
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Key Words
- 2c, two-cell (embryo)
- 4-oht, 4-hydroxytamoxifen
- dox, doxycycline
- erv, endogenous retrovirus
- es, embryonic stem
- hpf, hours post fertilization
- idr, intrinsic disordered region
- ivf, in vitro fertilization
- kd, knockdown
- ko, knockout
- rt, room temperature
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Affiliation(s)
| | - Satoshi Yamazaki
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kaoru Mita-Yoshida
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tomio Ono
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yasumasa Nishito
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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8
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Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol 2021; 22:34. [PMID: 33446241 PMCID: PMC7807719 DOI: 10.1186/s13059-020-02245-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms. RESULTS Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription. CONCLUSIONS The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
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Affiliation(s)
- Minghao Chia
- The Francis Crick Institute, London, UK
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Cai Li
- The Francis Crick Institute, London, UK
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicente Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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Huang W, Zheng S, Wang X, Cai Z, Xiao J, Liu C, Wu K. A transcriptomics-based analysis of toxicity mechanisms of zebrafish embryos and larvae following parental Bisphenol A exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111165. [PMID: 32836160 DOI: 10.1016/j.ecoenv.2020.111165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/19/2020] [Accepted: 08/09/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Bisphenol A (BPA) is a well-known xenobiotic endocrine disrupting chemical, with estrogenic activity and many other potential biological effects. Although multiple toxicities have been reported for BPA, molecular mechanisms underlying the transgenerational toxic effects of BPA are still underestimated. METHODS Parental F0 fish were exposed to 1.0 μM BPA or control (0.1% DMSO, v/v) for 7 days. Eggs (F1) were collected and kept in control medium until 4.5 or 120 h post fertilization (hpf). RNA sequencing (RNA-seq) was conducted on embryos and larvae, to discover differentially expressed genes (DEGs), and then KEGG pathway, GO enrichment and GSEA were performed to interpret functional ontology. Histopathology was performed to explore the morphological and structural alterations in liver tissues of zebrafish larvae (120 hpf) after parental BPA exposure. RESULTS Parental BPA exposure induced global transcriptomic changes in zebrafish embryos and larvae. For embryos, epigenetic regulation genes were decidedly affected, highlighted epigenotoxicity might involve in the transgenerational effects during embryogenesis and early development. By further investigation on its delayed effects, our RNA-Seq data of larvae suggested ROS metabolic process, apoptosis, p53 and MAPK signaling pathway were concentrated, indicating defensive cellular processes still involved in protecting against BPA toxicity. Furthermore, parental BPA-treated larvae manifested hepatic injury by histopathological analysis. CONCLUSIONS Parental BPA exposure led to global transcriptomic changes involved in epigenetic regulation, oxidative stress, apoptosis and DNA damage of offspring. These findings advanced the field of the parental-mediated subsequent generational toxic effects of BPA.
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Affiliation(s)
- Wenlong Huang
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Shukai Zheng
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Xin Wang
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Zemin Cai
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Jiefeng Xiao
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Caixia Liu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Kusheng Wu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, 515041, Guangdong, China.
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10
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Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development 2019; 146:146/11/dev161471. [PMID: 31189646 DOI: 10.1242/dev.161471] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of animal embryos is initially directed by maternal gene products. Then, during the maternal-to-zygotic transition (MZT), developmental control is handed to the zygotic genome. Extensive research in both vertebrate and invertebrate model organisms has revealed that the MZT can be subdivided into two phases, during which very different modes of gene regulation are implemented: initially, regulation is exclusively post-transcriptional and post-translational, following which gradual activation of the zygotic genome leads to predominance of transcriptional regulation. These changes in the gene expression program of embryos are precisely controlled and highly interconnected. Here, we review current understanding of the mechanisms that underlie handover of developmental control during the MZT.
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Affiliation(s)
- Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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11
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Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish ( Danio rerio). G3-GENES GENOMES GENETICS 2019; 9:1831-1838. [PMID: 30872328 PMCID: PMC6553537 DOI: 10.1534/g3.119.200997] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Understanding early gene expression in zebrafish embryos is a prerequisite for developmental biology research. In this study, 1,629,447 polymerase reads were obtained from the unfertilized eggs of zebrafish via full-length transcriptome sequencing using the PacBio RS II platform first. Then, 102,920 unique isoforms were obtained by correction, clustering and comparison with the zebrafish genome. 12,782 genes in the genome were captured, accounting for 39.71% of the all annotated genes. Approximately 62.27% of the 12,782 genes have been alternatively spliced. GO and KEGG annotations revealed that the unfertilized eggs primarily stored genes that participate in RNA processing and nuclear protein complex composition. According to this PacBio data that aligned with the genome, 3,970 fusion genes, 819 ncRNAs, and 84 new transcripts were predicted. Illumina RNA-seq and RT-qPCR detection found that the expression of two new transcripts, PB.5289.1 and PB.10209.1, were significantly up-regulated at the 2-cell stage and down-regulated rapidly thereafter, suggesting their involvement in minor ZGA during early embryonic development. This study indicated that the unfertilized eggs of zebrafish may have retained genes directly related to cell division and development to initiate the subsequent development in a limited space and time. On the other hand, NTRs or new transcriptome regions in the genome were discovered, which provided new clues regarding ZGA of MZT during early embryonic development in fish.
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12
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Froussios K, Mourão K, Simpson G, Barton G, Schurch N. Relative Abundance of Transcripts ( RATs): Identifying differential isoform abundance from RNA-seq. F1000Res 2019; 8:213. [PMID: 30906538 PMCID: PMC6426083 DOI: 10.12688/f1000research.17916.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/16/2022] Open
Abstract
The biological importance of changes in RNA expression is reflected by the wide variety of tools available to characterise these changes from RNA-seq data. Several tools exist for detecting differential transcript isoform usage (DTU) from aligned or assembled RNA-seq data, but few exist for DTU detection from alignment-free RNA-seq quantifications. We present the RATs, an R package that identifies DTU transcriptome-wide directly from transcript abundance estimates. RATs is unique in applying bootstrapping to estimate the reliability of detected DTU events and shows good performance at all replication levels (median false positive fraction < 0.05). We compare RATs to two existing DTU tools, DRIM-Seq & SUPPA2, using two publicly available simulated RNA-seq datasets and a published human RNA-seq dataset, in which 248 genes have been previously identified as displaying significant DTU. RATs with default threshold values on the simulated Human data has a sensitivity of 0.55, a Matthews correlation coefficient of 0.71 and a false discovery rate (FDR) of 0.04, outperforming both other tools. Applying the same thresholds for SUPPA2 results in a higher sensitivity (0.61) but poorer FDR performance (0.33). RATs and DRIM-seq use different methods for measuring DTU effect-sizes complicating the comparison of results between these tools, however, for a likelihood-ratio threshold of 30, DRIM-Seq has similar FDR performance to RATs (0.06), but worse sensitivity (0.47). These differences persist for the simulated drosophila dataset. On the published human RNA-seq dataset the greatest agreement between the tools tested is 53%, observed between RATs and SUPPA2. The bootstrapping quality filter in RATs is responsible for removing the majority of DTU events called by SUPPA2 that are not reported by RATs. All methods, including the previously published qRT-PCR of three of the 248 detected DTU events, were found to be sensitive to annotation differences between Ensembl v60 and v87.
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Affiliation(s)
- Kimon Froussios
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Kira Mourão
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Gordon Simpson
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,The James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK
| | - Geoff Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Nicholas Schurch
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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13
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Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis. Cell 2019; 172:910-923.e16. [PMID: 29474919 DOI: 10.1016/j.cell.2018.01.035] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022]
Abstract
To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous genome-wide measurements of mRNA, translation, and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti-correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases, or over 8% of all measured genes, involves temporally regulated switching between production of a canonical, translatable transcript and a 5' extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether or not an mRNA is induced but rather on the type of transcript produced.
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14
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Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
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15
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One-two punch mechanism of gene repression: a fresh perspective on gene regulation. Curr Genet 2017; 64:581-588. [PMID: 29218463 PMCID: PMC5948300 DOI: 10.1007/s00294-017-0793-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 02/04/2023]
Abstract
Cellular differentiation depends on temporally controlled waves of gene activation and inactivation that ultimately transform one cell type into another. It is well established that transcription factor cascades coordinate the timely activation of gene expression clusters during development. In comparison, much less is understood about how gene repression events are coordinated with the transcription factor-driven waves of gene activation and how this repression is achieved at a mechanistic level. Using budding yeast as a model, we recently discovered a new gene regulatory event, whereby a central meiotic transcription factor induces the expression of an mRNA isoform to repress gene expression through an integrated transcriptional and translational mechanism. This new model could explain how gene activation and inactivation waves can be temporally coordinated. In this review, we discuss our findings and their potential implications.
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16
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Chia M, Tresenrider A, Chen J, Spedale G, Jorgensen V, Ünal E, van Werven FJ. Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter. eLife 2017; 6:e27420. [PMID: 28906248 PMCID: PMC5655139 DOI: 10.7554/elife.27420] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022] Open
Abstract
Cell differentiation programs require dynamic regulation of gene expression. During meiotic prophase in Saccharomyces cerevisiae, expression of the kinetochore complex subunit Ndc80 is downregulated by a 5' extended long undecoded NDC80 transcript isoform. Here we demonstrate a transcriptional interference mechanism that is responsible for inhibiting expression of the coding NDC80 mRNA isoform. Transcription from a distal NDC80 promoter directs Set1-dependent histone H3K4 dimethylation and Set2-dependent H3K36 trimethylation to establish a repressive chromatin state in the downstream canonical NDC80 promoter. As a consequence, NDC80 expression is repressed during meiotic prophase. The transcriptional mechanism described here is rapidly reversible, adaptable to fine-tune gene expression, and relies on Set2 and the Set3 histone deacetylase complex. Thus, expression of a 5' extended mRNA isoform causes transcriptional interference at the downstream promoter. We demonstrate that this is an effective mechanism to promote dynamic changes in gene expression during cell differentiation.
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Affiliation(s)
| | - Amy Tresenrider
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Jingxun Chen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | | | - Victoria Jorgensen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Elçin Ünal
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
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17
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Hurem S, Martín LM, Brede DA, Skjerve E, Nourizadeh-Lillabadi R, Lind OC, Christensen T, Berg V, Teien HC, Salbu B, Oughton DH, Aleström P, Lyche JL. Dose-dependent effects of gamma radiation on the early zebrafish development and gene expression. PLoS One 2017; 12:e0179259. [PMID: 28628668 PMCID: PMC5476279 DOI: 10.1371/journal.pone.0179259] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/27/2017] [Indexed: 01/07/2023] Open
Abstract
Ionizing radiation from natural sources or anthropogenic activity has the potential to cause oxidative stress or genetic damage in living organisms, through the ionization and excitation of molecules and the subsequent production of free radicals and reactive oxygen species (ROS). The present work focuses on radiation-induced biological effects using the zebrafish (Danio rerio) vertebrate model. Changes in developmental traits and gene expression in zebrafish were assessed after continuous external gamma irradiation (0.4, 3.9, 15 and 38 mGy/h) with corresponding controls, starting at 2.5 hours post fertilization (hpf) and lasting through embryogenesis and the early larval stage. The lowest dose rate corresponded to recommended benchmarks at which adverse effects are not expected to occur in aquatic ecosystems (2-10 mGy/day). The survival observed at 96 hours post fertilization (hpf) in the 38 mGy/h group was significantly lower, while other groups showed no significant difference compared to controls. The total hatching was significantly lower from controls in the 15 mGy/h group and a delay in hatching onset in the 0.4 mGy/h group was observed. The deformity frequency was significantly increased by prolonged exposure duration at dose rates ≥ 0.4 mGy/h. Molecular responses analyzed by RNA-seq at gastrulation (5.5 hpf transcriptome) indicate that the radiation induced adverse effects occurred during the earliest stages of development. A dose-response relationship was found in the numbers of differentially regulated genes in exposure groups compared to controls at a total dose as low as 1.62 mGy. Ingenuity Pathway Analysis identified retinoic acid receptor activation, apoptosis, and glutathione mediated detoxification signaling as the most affected pathways in the lower dose rate (0.54 mGy/h), while eif2 and mTOR, i.e., involved in the modulation of angiogenesis, were most affected in higher dose rates (5.4 and 10.9 mGy/h). By comparing gene expression data, myc was found to be the most significant upstream regulator, followed by tp53, TNF, hnf4a, TGFb1 and cebpa, while crabp2b and vegfab were identified as most frequent downstream target genes. These genes are associated with various developmental processes. The present findings show that continuous gamma irradiation (≥ 0.54 mGy/h) during early gastrula causes gene expression changes that are linked to developmental defects in zebrafish embryos.
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Affiliation(s)
- Selma Hurem
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
| | - Leonardo Martín Martín
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
- University of Camagüey Ignacio Agramonte y Loynaz (UC), Faculty of Agropecuary Sciences, Camagüey, Cuba
| | - Dag Anders Brede
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Environmental Sciences and Natural Resource Management, 1433 Ås, Norway
| | - Eystein Skjerve
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
| | - Rasoul Nourizadeh-Lillabadi
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
| | - Ole Christian Lind
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Environmental Sciences and Natural Resource Management, 1433 Ås, Norway
| | - Terje Christensen
- Norwegian Radiation Protection Authority (NRPA), CERAD CoE, Østerås, Norway
| | - Vidar Berg
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
| | - Hans-Christian Teien
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Environmental Sciences and Natural Resource Management, 1433 Ås, Norway
| | - Brit Salbu
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Environmental Sciences and Natural Resource Management, 1433 Ås, Norway
| | - Deborah Helen Oughton
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Environmental Sciences and Natural Resource Management, 1433 Ås, Norway
| | - Peter Aleström
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
| | - Jan Ludvig Lyche
- Norwegian University of Life Sciences (NMBU), CERAD CoE, Faculty of Veterinary Medicine and Biosciences, Oslo, Norway
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18
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Miccoli A, Dalla Valle L, Carnevali O. The maternal control in the embryonic development of zebrafish. Gen Comp Endocrinol 2017; 245:55-68. [PMID: 27013380 DOI: 10.1016/j.ygcen.2016.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Accepted: 03/19/2016] [Indexed: 12/13/2022]
Abstract
The maternal control directing the very first hours of life is of pivotal importance for ensuring proper development to the growing embryo. Thanks to the finely regulated inheritance of maternal factors including mRNAs and proteins produced during oogenesis and stored into the mature oocyte, the embryo is sustained throughout the so-called maternal-to-zygotic transition, a period in development characterized by a species-specific length in time, during which critical biological changes regarding cell cycle and zygotic transcriptional activation occur. In order not to provoke any kind of persistent damage, the process must be delicately balanced. Surprisingly, our knowledge as to the possible effects of beneficial bacteria regarding the modulation of the quality and/or quantity of both maternally-supplied and zygotically-transcribed mRNAs, is very limited. To date, only one group has investigated the consequences of the parentally-supplied Lactobacillus rhamnosus on the storage of mRNAs into mature oocytes, leading to an altered maternal control process in the F1 generation. Particular attention was called on the monitoring of several biomarkers involved in autophagy, apoptosis and axis patterning, while data on miRNA generation and pluripotency maintenance are herein presented for the first time, and can assist in laying the ground for further investigations in this field. In this review, the reader is supplied with the current knowledge on the above-mentioned biological process, first by drawing the general background and then by emphasizing the most important findings that have highlighted their focal role in normal animal development.
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Affiliation(s)
- Andrea Miccoli
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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19
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Rauwerda H, Pagano JFB, de Leeuw WC, Ensink W, Nehrdich U, de Jong M, Jonker M, Spaink HP, Breit TM. Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. BMC Genomics 2017; 18:287. [PMID: 28399811 PMCID: PMC5387192 DOI: 10.1186/s12864-017-3672-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/29/2017] [Indexed: 02/08/2023] Open
Abstract
Background Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways. Results In the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from. Conclusion Our unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3672-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Johanna F B Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim C de Leeuw
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrike Nehrdich
- Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.,Present address: GenomeScan B.V., Plesmanlaan, Leiden, The Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Herman P Spaink
- Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Timo M Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands. .,Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands. .,MAD/AB&RB, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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20
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Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing. PLoS One 2016; 11:e0160197. [PMID: 27462902 PMCID: PMC4962977 DOI: 10.1371/journal.pone.0160197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 07/17/2016] [Indexed: 11/28/2022] Open
Abstract
Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function.
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21
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Wragg J, Müller F. Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos. ADVANCES IN GENETICS 2016; 95:161-94. [PMID: 27503357 DOI: 10.1016/bs.adgen.2016.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Embryo development commences with the fusion of two terminally differentiated haploid gametes into the totipotent fertilized egg, which through a series of major cellular and molecular transitions generate a pluripotent cell mass. The activation of the zygotic genome occurs during the so-called maternal to zygotic transition and prepares the embryo for zygotic takeover from maternal factors, in the control of the development of cellular lineages during differentiation. Recent advances in next generation sequencing technologies have allowed the dissection of the genomic and epigenomic processes mediating this transition. These processes include reorganization of the chromatin structure to a transcriptionally permissive state, changes in composition and function of structural and regulatory DNA-binding proteins, and changeover of the transcriptome as it is overhauled from that deposited by the mother in the oocyte to a zygotically transcribed complement. Zygotic genome activation in zebrafish occurs 10 cell cycles after fertilization and provides an ideal experimental platform for elucidating the temporal sequence and dynamics of establishment of a transcriptionally active chromatin state and helps in identifying the determinants of transcription activation at polymerase II transcribed gene promoters. The relatively large number of pluripotent cells generated by the fast cell divisions before zygotic transcription provides sufficient biomass for next generation sequencing technology approaches to establish the temporal dynamics of events and suggest causative relationship between them. However, genomic and genetic technologies need to be improved further to capture the earliest events in development, where cell number is a limiting factor. These technologies need to be complemented with precise, inducible genetic interference studies using the latest genome editing tools to reveal the function of candidate determinants and to confirm the predictions made by classic embryological tools and genome-wide assays. In this review we summarize recent advances in the characterization of epigenetic regulation, transcription control, and gene promoter function during zygotic genome activation and how they fit with old models for the mechanisms of the maternal to zygotic transition. This review will focus on the zebrafish embryo but draw comparisons with other vertebrate model systems and refer to invertebrate models where informative.
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Affiliation(s)
- J Wragg
- University of Birmingham, Birmingham, United Kingdom
| | - F Müller
- University of Birmingham, Birmingham, United Kingdom
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22
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Dai Z, Xiong Y, Dai X. DNA signals at isoform promoters. Sci Rep 2016; 6:28977. [PMID: 27353836 PMCID: PMC4926256 DOI: 10.1038/srep28977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/08/2016] [Indexed: 11/14/2022] Open
Abstract
Transcriptional heterogeneity is extensive in the genome, and most genes express variable transcript isoforms. However, whether variable transcript isoforms of one gene are regulated by common promoter elements remain to be elucidated. Here, we investigated whether isoform promoters of one gene have separated DNA signals for transcription and translation initiation. We found that TATA box and nucleosome-disfavored DNA sequences are prevalent in distinct transcript isoform promoters of one gene. These DNA signals are conserved among species. Transcript isoform has a RNA-determined unstructured region around its start site. We found that these DNA/RNA features facilitate isoform transcription and translation. These results suggest a DNA-encoded mechanism by which transcript isoform is generated.
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Affiliation(s)
- Zhiming Dai
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou 510006, China.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China.,SYSU-CMU Shunde International Joint Research Institute, Shunde, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
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23
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Abstract
Reversible covalent histone modifications are known to influence spatiotemporal patterns of gene transcription during development. Here I review recent advances in the development and use of methods to analyze the distribution and functions of histone modifications in zebrafish chromatin. I discuss the roles of dynamic histone modification patterns at the promoters and enhancers of genes during the process of zygotic gene activation at blastula stages and the interplay between the molecular machinery responsible for histone modifications, chromatin remodeling and DNA methylation. Interactions are also described between developmentally regulated enhancer sequences and modified histones. A detailed method for chromatin immunoprecipitation using antibodies is provided, and I describe the use of high-throughput whole genome sequencing technology to generate DNA sequence data from chromatin immunoprecipitates. I also discuss computational approaches to integrating DNA sequence data obtained from chromatin immunoprecipitates with annotated reference genome sequences, transcriptome and methylome sequence data, transcription factor binding motif databases, and gene ontologies and describe the types of software tools currently available for visualizing the results.
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Affiliation(s)
- V T Cunliffe
- University of Sheffield, Sheffield, United Kingdom.
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24
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Rauwerda H, Wackers P, Pagano JFB, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM. Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS One 2016; 11:e0147151. [PMID: 26799215 PMCID: PMC4723340 DOI: 10.1371/journal.pone.0147151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/28/2015] [Indexed: 12/19/2022] Open
Abstract
Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature.
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Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Wackers
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Johanna F. B. Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Rob Dekker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Ulrike Nehrdich
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Herman P. Spaink
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Timo M. Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
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25
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Prindull G. Potential Gene Interactions in the Cell Cycles of Gametes, Zygotes, Embryonic Stem Cells and the Development of Cancer. Front Oncol 2015; 5:200. [PMID: 26442212 PMCID: PMC4585297 DOI: 10.3389/fonc.2015.00200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This review is to explore whether potential gene interactions in the cell cycles of gametes, zygotes, and embryonic stem (ES) cells are associated with the development of cancer. METHODS MEDPILOT at the Central Library of the University of Cologne, Germany (Zentralbibliothek Köln) that covers 5,800 international medical journals and 4,300 E-journals was used to collect data. The initial searches were done in December 2012 and additional searches in October 2013-May 2015. The search terms included "cancer development," "gene interaction," and "ES cells," and the time period was between 1998 and 2015. A total of 147 articles in English language only were included in this review. RESULTS Transgenerational gene translation is implemented in the zygote through interactions of epigenetic isoforms of transcription factors (TFs) from parental gametes, predominantly during the first two zygote cleavages. Pluripotent transcription factors may provide interacting links with mutated genes during zygote-to-ES cell switches. Translation of post-transcriptional carcinogenic genes is implemented by abnormally spliced, tumor-specific isoforms of gene-encoded mRNA/non-coding RNA variants of TFs employing de novo gene synthesis and neofunctionalization. Post-translationally, mutated genes are preserved in pre-neoplastic ES cell subpopulations that can give rise to overt cancer stem cells. Thus, TFs operate as cell/disease-specific epigenetic messengers triggering clinical expression of neoplasms. CONCLUSION Potential gene interactions in the cell cycle of gametes, zygotes, and ES cells may play some roles in the development of cancer.
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Affiliation(s)
- Gregor Prindull
- Medical Faculty, University of Göttingen , Göttingen , Germany
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26
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Deml B, Reis LM, Muheisen S, Bick D, Semina EV. EFTUD2 deficiency in vertebrates: Identification of a novel human mutation and generation of a zebrafish model. ACTA ACUST UNITED AC 2015; 103:630-40. [PMID: 26118977 DOI: 10.1002/bdra.23397] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/30/2015] [Accepted: 05/26/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Congenital microphthalmia and coloboma are severe developmental defects that are frequently associated with additional systemic anomalies and display a high level of genetic heterogeneity. METHODS To identify the pathogenic variant in a patient with microphthalmia, coloboma, retinal dystrophy, microcephaly, and other features, whole exome sequencing analysis of the patient and parental samples was undertaken. To further explore the identified variant/gene, expression and functional studies in zebrafish were performed. RESULTS Whole exome sequencing revealed a de novo variant, c.473_474delGA, p.(Arg158Lysfs*4), in EFTUD2 which encodes a component of the spliceosome complex. Dominant mutations in EFTUD2 cause Mandibulofacial Dysostosis, Guion-Almeida type, which does not involve microphthalmia, coloboma, or retinal dystrophy; analysis of genes known to cause these ocular phenotypes identified several variants of unknown significance but no causal alleles in the affected patient. Zebrafish eftud2 demonstrated high sequence conservation with the human gene and broad embryonic expression. TALEN-mediated disruption was employed to generate a c.378_385 del, p.(Ser127Aspfs*23) truncation mutation in eftud2. Homozygous mutants displayed a reduced head size, small eye, curved body, and early embryonic lethality. Apoptosis assays demonstrated a striking increase in terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL)-positive cells in the developing brain, eye, spinal cord, and other tissues starting at 30 hours postfertilization. CONCLUSION This study reports a novel mutation in EFTUD2 in a Mandibulofacial Dysostosis, Guion-Almeida type patient with unusual ocular features and the generation of a first animal model of eftud2 deficiency. The severe embryonic phenotype observed in eftud2 mutants indicates an important conserved role during development of diverse tissues in vertebrates.
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Affiliation(s)
- Brett Deml
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - David Bick
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
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27
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Abstract
Over the past decade, high-throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non-coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the process of translation rather than the resulting peptides that serves a function. Here, we review annotation studies in zebrafish to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein-encoding mRNAs to potentially non-functional peptide-producing RNAs to non-coding RNAs. As highlighted by the discovery of the novel signaling peptide Apela/ELABELA/Toddler, accurate annotations can give rise to exciting opportunities to identify the functions of previously uncharacterized transcripts.
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Affiliation(s)
- Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
| | - Eivind Valen
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
| | - Alexander F. Schier
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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28
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Lee MT, Bonneau AR, Giraldez AJ. Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol 2014; 30:581-613. [PMID: 25150012 DOI: 10.1146/annurev-cellbio-100913-013027] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Embryogenesis depends on a highly coordinated cascade of genetically encoded events. In animals, maternal factors contributed by the egg cytoplasm initially control development, whereas the zygotic nuclear genome is quiescent. Subsequently, the genome is activated, embryonic gene products are mobilized, and maternal factors are cleared. This transfer of developmental control is called the maternal-to-zygotic transition (MZT). In this review, we discuss recent advances toward understanding the scope, timing, and mechanisms that underlie zygotic genome activation at the MZT in animals. We describe high-throughput techniques to measure the embryonic transcriptome and explore how regulation of the cell cycle, chromatin, and transcription factors together elicits specific patterns of embryonic gene expression. Finally, we illustrate the interplay between zygotic transcription and maternal clearance and show how these two activities combine to reprogram two terminally differentiated gametes into a totipotent embryo.
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Affiliation(s)
- Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520; ,
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29
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Maussion G, Yang J, Suderman M, Diallo A, Nagy C, Arnovitz M, Mechawar N, Turecki G. Functional DNA methylation in a transcript specific 3'UTR region of TrkB associates with suicide. Epigenetics 2014; 9:1061-70. [PMID: 24802768 DOI: 10.4161/epi.29068] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previous studies indicate that a subgroup of suicide completers has low cortical brain expression levels of TrkB-T1, a TrkB gene transcript that is highly expressed in astrocytes. Epigenetic modifications, including methylation changes in the TrkB promoter, partially explain TrkB-T1 low expression levels in brain tissue from suicide completers. The aim of this study was to investigate whether methylation changes in other regions of the TrkB gene could also contribute to the significant downregulation of the TrkB-T1 transcript observed in the brain of suicide completers. Methylation levels were assessed on BA8/9 from suicide completers expressing low TrkB-T1 transcript levels and controls, using custom-made Agilent arrays tiling the whole TrkB gene. After statistical correction for multiple testing, five probes located in the TrkB-T1 3'UTR region were found hypermethylated in the frontal cortex of suicide completers. These results were validated for four CpGs spanning a 150 bp sequence by cloning and Sanger sequencing bisulfite treated DNA. We found a significant correlation between the methylation level at these four CpGs and TrkB-T1 expression in BA8/9. Site-specific hypermethylation on this 3'UTR sequence induced decreased luciferase activity in reporter gene cell assays. Site-specific differential methylation in the TrkB-T1 3'UTR region associates with functional changes in TrkB-T1 expression and may play a significant role in the important decrease of cortical TrkB-T1 expression observed among suicide completers.
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Affiliation(s)
- Gilles Maussion
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
| | - Jennie Yang
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
| | - Matthew Suderman
- Departments of Pharmacology and Therapeutics; McGill University; Montreal, QC Canada
| | - Alpha Diallo
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
| | - Corina Nagy
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
| | - Mitchell Arnovitz
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
| | - Naguib Mechawar
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies; Douglas Hospital Research Institute; McGill University; Montreal, QC Canada
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30
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Aanes H, Collas P, Aleström P. Transcriptome dynamics and diversity in the early zebrafish embryo. Brief Funct Genomics 2013; 13:95-105. [PMID: 24335756 DOI: 10.1093/bfgp/elt049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent years advances in high-throughput sequencing have improved our understanding of how transcripts regulate early vertebrate development. Here, we review the transcriptome dynamics and diversity during early stages of zebrafish embryogenesis. Transcriptome dynamics is characterized by different patterns of mRNA degradation, activation of dormant transcripts and onset of transcription. Several studies have shown a striking diversity of both coding and non-coding transcripts. However, in the aftermath of this immense increase in data, functional studies of both protein-coding and non-coding transcripts are lagging behind. We anticipate that the forthcoming years will see studies relying on different high-throughput sequencing technologies and genomic tools developed for zebrafish embryos to further pin down yet un-annotated transcript-function relationships.
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Affiliation(s)
- Håvard Aanes
- BasAM, Norwegian School of Veterinary Science, Dep., 0033 Oslo, Norway.
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