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Karttunen K, Patel D, Sahu B. Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer. Bioessays 2024; 46:e2400059. [PMID: 39073128 DOI: 10.1002/bies.202400059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
Transposable elements (TEs) have emerged as important factors in establishing the cell type-specific gene regulatory networks and evolutionary novelty of embryonic and placental development. Recently, studies on the role of TEs and their dysregulation in cancers have shed light on the transcriptional, transpositional, and regulatory activity of TEs, revealing that the activation of developmental transcriptional programs by TEs may have a role in the dedifferentiation of cancer cells to the progenitor-like cell states. This essay reviews the recent evidence of the cis-regulatory TEs (henceforth crTE) in normal development and malignancy as well as the key transcription factors and regulatory pathways that are implicated in both cell states, and presents existing gaps remaining to be studied, limitations of current technologies, and therapeutic possibilities.
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Affiliation(s)
- Konsta Karttunen
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Divyesh Patel
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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2
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Guan T, Guo J, Lin R, Liu J, Luo R, Zhang Z, Pei D, Liu J. Single-cell analysis of preimplantation embryonic development in guinea pigs. BMC Genomics 2024; 25:911. [PMID: 39350018 PMCID: PMC11440810 DOI: 10.1186/s12864-024-10815-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Guinea pigs exhibit numerous physiological similarities to humans, yet the details of their preimplantation embryonic development remain largely unexplored. RESULTS To address this, we conducted single-cell sequencing on the transcriptomes of cells isolated from the zygote stage through preimplantation stages in guinea pigs. This study identified seven distinct cell types within guinea pig preimplantation embryos and pinpointed the timing of zygotic gene activation (ZGA). Trajectory analysis revealed a bifurcation into two lineage-specific branches, accompanied by alterations in specific pathways, including oxidative phosphorylation and vascular endothelial growth factor (VEGF). Additionally, co-expressed gene network analysis highlighted the most enriched functional modules for the epiblast (EPI), primitive endoderm (PrE), and inner cell mass (ICM). Finally, we compared the similarities and differences between human and guinea pig epiblasts (EPIs). CONCLUSION This study systematically constructs a cell atlas of guinea pig preimplantation embryonic development, offering fresh insights into mammalian embryonic development and providing alternative experimental models for studying human embryonic development.
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Affiliation(s)
- Tongxing Guan
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jing Guo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Runxia Lin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jinpeng Liu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Science, Beijing, 100049, People's Republic of China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Rongping Luo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhen Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Duanqing Pei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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3
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González-Rojas A, Valencia-Narbona M. Neurodevelopmental Disruptions in Children of Preeclamptic Mothers: Pathophysiological Mechanisms and Consequences. Int J Mol Sci 2024; 25:3632. [PMID: 38612445 PMCID: PMC11012011 DOI: 10.3390/ijms25073632] [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: 01/24/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Preeclampsia (PE) is a multisystem disorder characterized by elevated blood pressure in the mother, typically occurring after 20 weeks of gestation and posing risks to both maternal and fetal health. PE causes placental changes that can affect the fetus, particularly neurodevelopment. Its key pathophysiological mechanisms encompass hypoxia, vascular and angiogenic dysregulation, inflammation, neuronal and glial alterations, and disruptions in neuronal signaling. Animal models indicate that PE is correlated with neurodevelopmental alterations and cognitive dysfunctions in offspring and in humans, an association between PE and conditions such as cerebral palsy, autism spectrum disorder, attention deficit hyperactivity disorder, and sexual dimorphism has been observed. Considering the relevance for mothers and children, we conducted a narrative literature review to describe the relationships between the pathophysiological mechanisms behind neurodevelopmental alterations in the offspring of PE mothers, along with their potential consequences. Furthermore, we emphasize aspects pertinent to the prevention/treatment of PE in pregnant mothers and alterations observed in their offspring. The present narrative review offers a current, complete, and exhaustive analysis of (i) the pathophysiological mechanisms that can affect neurodevelopment in the children of PE mothers, (ii) the relationship between PE and neurological alterations in offspring, and (iii) the prevention/treatment of PE.
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Affiliation(s)
- Andrea González-Rojas
- Laboratorio de Neurociencias Aplicadas, Escuela de Kinesiología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2950, Valparaíso 2340025, Chile;
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Neyroud AS, Rolland AD, Lecuyer G, Evrard B, Alary N, Dejucq-Rainsford N, Bujan L, Ravel C, Chalmel F. Sperm DNA methylation dynamics after chemotherapy: a longitudinal study of a patient with testicular germ cell tumor treatment. Andrology 2024; 12:396-409. [PMID: 37354024 DOI: 10.1111/andr.13485] [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: 01/10/2023] [Revised: 05/26/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND An important issue for young men affected by testicular germ cell tumor (TGCT) is how TGCT and its treatment will affect, transiently or permanently, their future reproductive health. Previous studies have reported that xenobiotics can induce changes on human sperm epigenome and have the potential to promote epigenetic alterations in the offspring. OBJECTIVES Here, we report the first longitudinal DNA methylation profiling of frozen sperm from a TGCT patient before and up to 2 years after a bleomycin, etoposide, and cisplatin (BEP) chemotherapy. MATERIALS AND METHODS A TGCT was diagnosed in a 30-year-old patient. A cryopreservation of spermatozoa was proposed before adjuvant BEP treatment. Semen samples were collected before and after chemotherapy at 6, 9, 12, and 24 months. The DNA methylation status was determined by RRBS to detect DNA differentially methylated regions (DMRs). RESULTS The analysis revealed that among the 74 DMRs showing modified methylation status 6 months after therapy, 17 remained altered 24 months after treatment. We next associated DMRs with differentially methylated genes (DMGs), which were subsequently intersected with loci known to be important or expressed during early development. DISCUSSION AND CONCLUSION The consequences of the cancer treatment on the sperm epigenome during the recovery periods are topical issues of increasing significance as epigenetic modifications to the paternal genome may have deleterious effects on the offspring. The altered methylated status of these DMGs important for early development might modify their expression pattern and thus affect their function during key stages of embryogenesis, potentially leading to developmental disorders or miscarriages.
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Affiliation(s)
- Anne-Sophie Neyroud
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
- CHU de Rennes, Département de Gynécologie Obstétrique Reproduction-CECOS, Rennes, France
| | - Antoine Dominique Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Gwendoline Lecuyer
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Nathan Alary
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Nathalie Dejucq-Rainsford
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Louis Bujan
- Développement Embryonnaire, Fertilité, Environnement (DEFE), UMR Inserm 1203 Université Toulouse 3 et Montpellier, Toulouse, France
- CECOS, Groupe d'activité de médecine de la reproduction, Hôpital Paule de Viguier, CHU Toulouse, Toulouse, France
| | - Célia Ravel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
- CHU de Rennes, Département de Gynécologie Obstétrique Reproduction-CECOS, Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
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5
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Wu Q, Zhou Z, Yan Z, Connel M, Garzo G, Yeo A, Zhang W, Su HI, Zhong S. A temporal extracellular transcriptome atlas of human pre-implantation development. CELL GENOMICS 2024; 4:100464. [PMID: 38216281 PMCID: PMC10794780 DOI: 10.1016/j.xgen.2023.100464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/09/2023] [Accepted: 11/19/2023] [Indexed: 01/14/2024]
Abstract
Non-invasively evaluating gene expression products in human pre-implantation embryos remains a significant challenge. Here, we develop a non-invasive method for comprehensive characterization of the extracellular RNAs (exRNAs) in a single droplet of spent media that was used to culture human in vitro fertilization embryos. We generate the temporal extracellular transcriptome atlas (TETA) of human pre-implantation development. TETA consists of 245 exRNA sequencing datasets for five developmental stages. These data reveal approximately 4,000 exRNAs at each stage. The exRNAs of the developmentally arrested embryos are enriched with the genes involved in negative regulation of the cell cycle, revealing an exRNA signature of developmental arrest. Furthermore, a machine-learning model can approximate the morphology-based rating of embryo quality based on the exRNA levels. These data reveal the widespread presence of coding gene-derived exRNAs at every stage of human pre-implantation development, and these exRNAs provide rich information on the physiology of the embryo.
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Affiliation(s)
- Qiuyang Wu
- Shu Chien-Gene Ley Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zixu Zhou
- Genemo, Inc., San Diego, CA 92130, USA
| | - Zhangming Yan
- Shu Chien-Gene Ley Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan Connel
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - Gabriel Garzo
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - Analisa Yeo
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - Wei Zhang
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - H Irene Su
- Reproductive Partners San Diego, La Jolla, CA 92037, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Sheng Zhong
- Shu Chien-Gene Ley Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Genemo, Inc., San Diego, CA 92130, USA.
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6
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Yu T, Zhang C, Song W, Zhao X, Cheng Y, Liu J, Su J. Single-cell RNA-seq and single-cell bisulfite-sequencing reveal insights into yak preimplantation embryogenesis. J Biol Chem 2024; 300:105562. [PMID: 38097189 PMCID: PMC10821408 DOI: 10.1016/j.jbc.2023.105562] [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: 03/24/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/13/2024] Open
Abstract
Extensive epigenetic reprogramming occurs during preimplantation embryonic development. However, the impact of DNA methylation in plateau yak preimplantation embryos and how epigenetic reprogramming contributes to transcriptional regulatory networks are unclear. In this study, we quantified gene expression and DNA methylation in oocytes and a series of yak embryos at different developmental stages and at single-cell resolution using single-cell bisulfite-sequencing and RNA-seq. We characterized embryonic genome activation and maternal transcript degradation and mapped epigenetic reprogramming events critical for embryonic development. Through cross-species transcriptome analysis, we identified 31 conserved maternal hub genes and 39 conserved zygotic hub genes, including SIN3A, PRC1, HDAC1/2, and HSPD1. Notably, by combining single-cell DNA methylation and transcriptome analysis, we identified 43 candidate methylation driver genes, such as AURKA, NUSAP1, CENPF, and PLK1, that may be associated with embryonic development. Finally, using functional approaches, we further determined that the epigenetic modifications associated with the histone deacetylases HDAC1/2 are essential for embryonic development and that the deubiquitinating enzyme USP7 may affect embryonic development by regulating DNA methylation. Our data represent an extensive resource on the transcriptional dynamics of yak embryonic development and DNA methylation remodeling, and provide new insights into strategies for the conservation of germplasm resources, as well as a better understanding of mammalian early embryonic development that can be applied to investigate the causes of early developmental disorders.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengtu Zhang
- Academician Zhang Yong Innovation Center, Xining Animal Disease Control Center, Xining, Qinghai, China
| | - Weijia Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyao Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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7
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Guo Y, Li TD, Modzelewski AJ, Siomi H. Retrotransposon renaissance in early embryos. Trends Genet 2024; 40:39-51. [PMID: 37949723 DOI: 10.1016/j.tig.2023.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Despite being the predominant genetic elements in mammalian genomes, retrotransposons were often dismissed as genomic parasites with ambiguous biological significance. However, recent studies reveal their functional involvement in early embryogenesis, encompassing crucial processes such as zygotic genome activation (ZGA) and cell fate decision. This review underscores the paradigm shift in our understanding of retrotransposon roles during early preimplantation development, as well as their rich functional reservoir that is exploited by the host to provide cis-regulatory elements, noncoding RNAs, and functional proteins. The rapid advancement in long-read sequencing, low input multiomics profiling, advanced in vitro systems, and precise gene editing techniques encourages further dissection of retrotransposon functions that were once obscured by the intricacies of their genomic footprints.
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ten D Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Andrew J Modzelewski
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA.
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo 160-8582, Japan.
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8
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Knoblochova L, Duricek T, Vaskovicova M, Zorzompokou C, Rayova D, Ferencova I, Baran V, Schultz RM, Hoffmann ER, Drutovic D. CHK1-CDC25A-CDK1 regulate cell cycle progression and protect genome integrity in early mouse embryos. EMBO Rep 2023; 24:e56530. [PMID: 37694680 PMCID: PMC10561370 DOI: 10.15252/embr.202256530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated and transcriptionally quiescent cells into early cleavage-stage blastomeres that are transcriptionally active and totipotent. This developmental transition is accompanied by cell cycle adaptation, such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in two-cell stage mouse embryos. Finally, Chk1 depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.
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Affiliation(s)
- Lucie Knoblochova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomas Duricek
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Michaela Vaskovicova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Chrysoula Zorzompokou
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Diana Rayova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Ivana Ferencova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Vladimir Baran
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of SciencesKosiceSlovakia
| | - Richard M Schultz
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
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Zhang Z, Shi Q, Zhu X, Jin L, Lang L, Lyu S, Xin X, Huang Y, Yu X, Li Z, Chen S, Xu Z, Zhang W, Wang E. Identification and Functional Analysis of Transcriptome Profiles, Long Non-Coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing. Genes (Basel) 2023; 14:1145. [PMID: 37372325 DOI: 10.3390/genes14061145] [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: 04/03/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development has not been studied. Here, we carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS) of cells from sheep from the oocyte to the blastocyst developmental stages. We found between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis.
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Affiliation(s)
- Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Xiaoting Zhu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Lei Jin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Limin Lang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Xiaoling Xin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiang Yu
- Henan Animal Health Supervision Institute, Zhengzhou 450003, China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China
| | - Sujuan Chen
- Synthetic Biology Engineering Lab of Henan Province, School of Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, China
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Wei Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
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10
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Uzbekov R, Singina GN, Shedova EN, Banliat C, Avidor-Reiss T, Uzbekova S. Centrosome Formation in the Bovine Early Embryo. Cells 2023; 12:1335. [PMID: 37174735 PMCID: PMC10177215 DOI: 10.3390/cells12091335] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
Centrosome formation during early development in mice and rats occurs due to the appearance of centrioles de novo. In contrast, in humans and other non-rodent mammals, centrioles are thought to be derived from spermatozoa. Ultrastructural study of zygotes and early embryos of cattle at full series of ultrathin sections show that the proximal centriole of the spermatozoon disappears by the end of the first cleavage division. Centrioles appear in two to four cell embryos in fertilized oocytes and in parthenogenetic embryos. Centriole formation includes the appearance of atypical centrioles with randomly arranged triplets and centrioles with microtubule triplets of various lengths. After the third cleavage, four centriolar cylinders appear for the first time in the blastomeres while each embryo still has two atypical centrioles. Our results showed that the mechanisms of centriole formation in different groups of mammals are universal, differing only in the stage of development in which they occur.
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Affiliation(s)
- Rustem Uzbekov
- Laboratory of Cell Biology and Electron Microscopy, Faculty of Medicine, University of Tours, 37032 Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia
| | - Galina N. Singina
- Laboratory of Experimental Embryology, L.K. Ernst Federal Research Center for Animal Husbandry, Moscow Region, 142132 Podolsk, Russia
| | - Ekaterina N. Shedova
- Laboratory of Experimental Embryology, L.K. Ernst Federal Research Center for Animal Husbandry, Moscow Region, 142132 Podolsk, Russia
| | - Charles Banliat
- Ecole Supérieure d’agricultures (ESA), Unité de Recherche sur les Systèmes D’élevage (URSE), 55 rue Rabelais BP, 30748 Angers, France
| | - Tomer Avidor-Reiss
- Department of Biological Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Svetlana Uzbekova
- UMR Physiologie de la Reproduction et des Comportements (PRC), INRAE, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France
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11
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Niu H, Lei A, Tian H, Yao W, Liu Y, Li C, An X, Chen X, Zhang Z, Wu J, Yang M, Huang J, Cheng F, Zhao J, Hua J, Liu S, Luo J. Scd1 Deficiency in Early Embryos Affects Blastocyst ICM Formation through RPs-Mdm2-p53 Pathway. Int J Mol Sci 2023; 24:ijms24021750. [PMID: 36675264 PMCID: PMC9864350 DOI: 10.3390/ijms24021750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Embryos contain a large number of lipid droplets, and lipid metabolism is gradually activated during embryonic development to provide energy. However, the regulatory mechanisms remain to be investigated. Stearoyl-CoA desaturase 1 (Scd1) is a fatty acid desaturase gene that is mainly involved in intracellular monounsaturated fatty acid production, which takes part in many physiological processes. Analysis of transcripts at key stages of embryo development revealed that Scd1 was important and expressed at an increased level during the cleavage and blastocyst stages. Knockout Scd1 gene by CRISPR/Cas9 from zygotes revealed a decrease in lipid droplets (LDs) and damage in the inner cell mass (ICM) formation of blastocyst. Comparative analysis of normal and knockout embryo transcripts showed a suppression of ribosome protein (RPs) genes, leading to the arrest of ribosome biogenesis at the 2-cell stage. Notably, the P53-related pathway was further activated at the blastocyst stage, which eventually caused embryonic development arrest and apoptosis. In summary, Scd1 helps in providing energy for embryonic development by regulating intra-embryonic lipid droplet formation. Moreover, deficiency activates the RPs-Mdm2-P53 pathway due to ribosomal stress and ultimately leads to embryonic development arrest. The present results suggested that Scd1 gene is essential to maintain healthy development of embryos by regulating energy support.
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Affiliation(s)
- Huimin Niu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Anmin Lei
- Shaanxi Stem Cell Engineering and Technology Research Center, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Huibin Tian
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weiwei Yao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ying Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuetong An
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoying Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhifei Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiao Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Min Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiangtao Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fei Cheng
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jinlian Hua
- Shaanxi Stem Cell Engineering and Technology Research Center, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shimin Liu
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6018, Australia
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Correspondence:
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12
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Zhai Y, Yu H, An X, Zhang Z, Zhang M, Zhang S, Li Q, Li Z. Profiling the transcriptomic signatures and identifying the patterns of zygotic genome activation - a comparative analysis between early porcine embryos and their counterparts in other three mammalian species. BMC Genomics 2022; 23:772. [PMID: 36434523 PMCID: PMC9700911 DOI: 10.1186/s12864-022-09015-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The transcriptional changes around zygotic genome activation (ZGA) in preimplantation embryos are critical for studying mechanisms of embryonic developmental arrest and searching for key transcription factors. However, studies on the transcription profile of porcine ZGA are limited. RESULTS In this study, we performed RNA sequencing in porcine in vivo developed (IVV) and somatic cell nuclear transfer (SCNT) embryo at different stages and compared the transcriptional activity of porcine embryos with mouse, bovine and human embryos. The results showed that the transcriptome map of the early porcine embryos was significantly changed at the 4-cell stage, and 5821 differentially expressed genes (DEGs) in SCNT embryos failed to be reprogrammed or activated during ZGA, which mainly enrichment to metabolic pathways. c-MYC was identified as the highest expressed transcription factor during ZGA. By treating with 10,058-F4, an inhibitor of c-MYC, the cleavage rate (38.33 ± 3.4%) and blastocyst rate (23.33 ± 4.3%) of porcine embryos were significantly lower than those of the control group (50.82 ± 2.7% and 34.43 ± 1.9%). Cross-species analysis of transcriptome during ZGA showed that pigs and bovines had the highest similarity coefficient in biological processes. KEGG pathway analysis indicated that there were 10 co-shared pathways in the four species. CONCLUSIONS Our results reveal that embryos with impaired developmental competence may be arrested at an early stage of development. c-MYC helps promote ZGA and preimplantation embryonic development in pigs. Pigs and bovines have the highest coefficient of similarity in biological processes during ZGA. This study provides an important reference for further studying the reprogramming regulatory mechanism of porcine embryos during ZGA.
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Affiliation(s)
- Yanhui Zhai
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Hao Yu
- grid.64924.3d0000 0004 1760 5735College of Animal Science, Jilin University, Changchun, 130062 Jilin China
| | - Xinglan An
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Zhiren Zhang
- grid.452930.90000 0004 1757 8087Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, 519000 Guangdong China
| | - Meng Zhang
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Sheng Zhang
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Qi Li
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Ziyi Li
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
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13
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Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z. High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development 2022; 149:280468. [PMID: 36227586 PMCID: PMC9687001 DOI: 10.1242/dev.200819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
High-resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome and the polysome- and non-polysome-bound RNA profiles of bovine oocytes (germinal vesicle and metaphase II stages) and early embryos at the two-cell, eight-cell, morula and blastocyst stages, and revealed four modes of translational selectivity: (1) selective translation of non-abundant mRNAs; (2) active, but modest translation of a selection of highly expressed mRNAs; (3) translationally suppressed abundant to moderately abundant mRNAs; and (4) mRNAs associated specifically with monosomes. A strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes was found throughout bovine embryonic development. Notably, genes involved in mitochondrial function were prioritized for translation. We found that translation largely reflected transcription in oocytes and two-cell embryos, but observed a marked shift in the translational control in eight-cell embryos that was associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become more synchronized in morulae and blastocysts. Taken together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.
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Affiliation(s)
- Linkai Zhu
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557-0352, USA
| | - Rajan Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Dvoran
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - R Michael Roberts
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
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14
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Palmerola KL, Amrane S, De Los Angeles A, Xu S, Wang N, de Pinho J, Zuccaro MV, Taglialatela A, Massey DJ, Turocy J, Robles A, Subbiah A, Prosser B, Lobo R, Ciccia A, Koren A, Baslan T, Egli D. Replication stress impairs chromosome segregation and preimplantation development in human embryos. Cell 2022; 185:2988-3007.e20. [PMID: 35858625 DOI: 10.1016/j.cell.2022.06.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Human cleavage-stage embryos frequently acquire chromosomal aneuploidies during mitosis due to unknown mechanisms. Here, we show that S phase at the 1-cell stage shows replication fork stalling, low fork speed, and DNA synthesis extending into G2 phase. DNA damage foci consistent with collapsed replication forks, DSBs, and incomplete replication form in G2 in an ATR- and MRE11-dependent manner, followed by spontaneous chromosome breakage and segmental aneuploidies. Entry into mitosis with incomplete replication results in chromosome breakage, whole and segmental chromosome errors, micronucleation, chromosome fragmentation, and poor embryo quality. Sites of spontaneous chromosome breakage are concordant with sites of DNA synthesis in G2 phase, locating to gene-poor regions with long neural genes, which are transcriptionally silent at this stage of development. Thus, DNA replication stress in mammalian preimplantation embryos predisposes gene-poor regions to fragility, and in particular in the human embryo, to the formation of aneuploidies, impairing developmental potential.
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Affiliation(s)
- Katherine L Palmerola
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Selma Amrane
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alejandro De Los Angeles
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Shuangyi Xu
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA; Masters of Biotechnology Program, Columbia University, New York, NY 10027, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Joao de Pinho
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jenna Turocy
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alex Robles
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Anisa Subbiah
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Bob Prosser
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Rogerio Lobo
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA; Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA.
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15
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Wyatt CDR, Pernaute B, Gohr A, Miret-Cuesta M, Goyeneche L, Rovira Q, Salzer MC, Boke E, Bogdanovic O, Bonnal S, Irimia M. A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation. SCIENCE ADVANCES 2022; 8:eabn4935. [PMID: 35417229 PMCID: PMC9007516 DOI: 10.1126/sciadv.abn4935] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Transition from maternal to embryonic transcriptional control is crucial for embryogenesis. However, alternative splicing regulation during this process remains understudied. Using transcriptomic data from human, mouse, and cow preimplantation development, we show that the stage of zygotic genome activation (ZGA) exhibits the highest levels of exon skipping diversity reported for any cell or tissue type. Much of this exon skipping is temporary, leads to disruptive noncanonical isoforms, and occurs in genes enriched for DNA damage response in the three species. Two core spliceosomal components, Snrpb and Snrpd2, regulate these patterns. These genes have low maternal expression at ZGA and increase sharply thereafter. Microinjection of Snrpb/d2 messenger RNA into mouse zygotes reduces the levels of exon skipping at ZGA and leads to increased p53-mediated DNA damage response. We propose that mammalian embryos undergo an evolutionarily conserved, developmentally programmed splicing failure at ZGA that contributes to the attenuation of cellular responses to DNA damage.
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Affiliation(s)
- Christopher D. R. Wyatt
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Barbara Pernaute
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - André Gohr
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Miret-Cuesta
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lucia Goyeneche
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Quirze Rovira
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marion C. Salzer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elvan Boke
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
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16
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Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Res 2021; 32:189-202. [PMID: 34965939 PMCID: PMC8744685 DOI: 10.1101/gr.275761.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.
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Affiliation(s)
- Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Neil Michel Longo Pendy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,École Doctorale Régional (EDR) en Infectiologie Tropicale d'Afrique Centrale, BP 876, Franceville, Gabon
| | - Sandrine E Nsango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, BP 2701, Douala, Cameroun
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Diego Ayala
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université Montpellier, CNRS, IRD, 64501 Montpellier, France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
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17
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Kotlyar M, Pastrello C, Ahmed Z, Chee J, Varyova Z, Jurisica I. IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. Nucleic Acids Res 2021; 50:D640-D647. [PMID: 34755877 PMCID: PMC8728267 DOI: 10.1093/nar/gkab1034] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/13/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
Improved bioassays have significantly increased the rate of identifying new protein-protein interactions (PPIs), and the number of detected human PPIs has greatly exceeded early estimates of human interactome size. These new PPIs provide a more complete view of disease mechanisms but precise understanding of how PPIs affect phenotype remains a challenge. It requires knowledge of PPI context (e.g. tissues, subcellular localizations), and functional roles, especially within pathways and protein complexes. The previous IID release focused on PPI context, providing networks with comprehensive tissue, disease, cellular localization, and druggability annotations. The current update adds developmental stages to the available contexts, and provides a way of assigning context to PPIs that could not be previously annotated due to insufficient data or incompatibility with available context categories (e.g. interactions between membrane and cytoplasmic proteins). This update also annotates PPIs with conservation across species, directionality in pathways, membership in large complexes, interaction stability (i.e. stable or transient), and mutation effects. Enrichment analysis is now available for all annotations, and includes multiple options; for example, context annotations can be analyzed with respect to PPIs or network proteins. In addition to tabular view or download, IID provides online network visualization. This update is available at http://ophid.utoronto.ca/iid.
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Affiliation(s)
- Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Justin Chee
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Zofia Varyova
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON M5S 1A4, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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18
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Su G, Wang L, Gao G, Wu S, Yang L, Wu M, Liu X, Yang M, Wei Z, Bai C, Li G. C23 gene regulates the nucleolin structure and biosynthesis of ribosomes in bovine intraspecific and interspecific somatic cell nuclear transfer embryos. FASEB J 2021; 35:e21993. [PMID: 34670005 DOI: 10.1096/fj.202100737rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/15/2021] [Accepted: 10/01/2021] [Indexed: 01/07/2023]
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram differentiated somatic cells to produce individual animals, thus having advantages in animal breeding and chromatin reprogramming. Interspecies SCNT (iSCNT) provides extreme cases of reprogramming failure that can be used to understand the basic biological mechanism of genome reprogramming. It is important to understand the possible mechanisms for the failure of zygotic genome activation (ZGA) in iSCNT embryos in order to improve the efficiency of SCNT embryos. In the present study, we compared the development of bovine-bovine (B-B), ovine-ovine (O-O) SCNT, and ovine-bovine (O-B) iSCNT embryos and found that a developmental block existed in the 8-cell stage in O-B iSCNT embryos. RNA sequencing and q-PCR analysis revealed that the large ribosomal subunit genes (RPL) or the small ribosomal subunit genes (RPS) were expressed at lower levels in the O-B iSCNT embryos. The nucleolin (C23) gene that regulates the ribosomal subunit generation was transcribed at a lower level during embryonic development in O-B iSCNT embryos. In addition, the nucleolin exhibited a clear circular-ring structure in B-B 8-cell stage embryos, whereas this was shell-like or dot-like in the O-B embryos. Furthermore, overexpression of C23 could increase the blastocyst rate of both SCNT and iSCNT embryos and partly rectify the ring-like nucleolin structure and the expression of ribosomal subunit related genes were upregulation, while knockdown of C23 increased the shell-like nucleolin-structure in B-B cloned embryos and downregulated the expression of ribosomal subunit related genes. These results implied that abnormal C23 and ribosome subunit gene expression would lead to the developmental block of iSCNT embryos and ZGA failure. Overexpression of the C23 gene could partly improve the blastocyst development and facilitate the nucleolin structure in bovine preimplantation SCNT embryos.
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Affiliation(s)
- Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Lina Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Guangqi Gao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
| | - Shanshan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Meiling Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xuefei Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Miaomiao Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Zhuying Wei
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
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19
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Aboussahoud WS, Smith H, Stevens A, Wangsaputra I, Hunter HR, Kimber SJ, Seif MW, Brison DR. The expression and activity of Toll-like receptors in the preimplantation human embryo suggest a new role for innate immunity. Hum Reprod 2021; 36:2661-2675. [PMID: 34517414 PMCID: PMC8450873 DOI: 10.1093/humrep/deab188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
STUDY QUESTION Is the innate immunity system active in early human embryo development? SUMMARY ANSWER The pattern recognition receptors and innate immunity Toll-like receptor (TLR) genes are widely expressed in preimplantation human embryos and the pathway appears to be active in response to TLR ligands. WHAT IS KNOWN ALREADY Early human embryos are highly sensitive to their local environment, however relatively little is known about how embryos detect and respond to specific environmental cues. While the maternal immune response is known to be key to the establishment of pregnancy at implantation, the ability of human embryos to detect and signal the presence of pathogens is unknown. STUDY DESIGN, SIZE, DURATION Expression of TLR family and related genes in human embryos was assessed by analysis of published transcriptome data (n = 40). Day 5 (D-5) human embryos (n = 25) were cultured in the presence of known TLR ligands and gene expression and cytokine production measured compared to controls. PARTICIPANTS/MATERIALS, SETTING, METHODS Human embryos surplus to treatment requirements were donated with informed consent from several ART centres. Embryos were cultured to Day 6 (D-6) in the presence of the TLR3 and TLR5 ligands Poly (I: C) and flagellin, with gene expression measured by quantitative PCR and cytokine release into medium measured using cytometric bead arrays. MAIN RESULTS AND THE ROLE OF CHANCE TLR and related genes, including downstream signalling molecules, were expressed variably at all human embryo developmental stages. Results showed the strongest expression in the blastocyst for TLRs 9 and 5, and throughout development for TLRs 9, 5, 2, 6 and 7. Stimulation of Day 5 blastocysts with TLR3 and TLR5 ligands Poly (I: C) and flagellin produced changes in mRNA expression levels of TLR genes, including the hyaluronan-mediated motility receptor (HMMR), TLR5, TLR7, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and monocyte chemoattractant Protein-1 (MCP-1) (P < 0.05, P < 0.001 compared to unstimulated controls), and release into culture medium of cytokines and chemokines, notably IL8 (P = 0.00005 and 0.01277 for flagellin and Poly (I: C), respectively). LIMITATIONS, REASONS FOR CAUTION This was a descriptive and experimental study which suggests that the TLR system is active in human embryos and capable of function, but does not confirm any particular role. Although we identified embryonic transcripts for a range of TLR genes, the expression patterns were not always consistent across published studies and expression levels of some genes were low, leaving open the possibility that these were expressed from the maternal rather than embryonic genome. WIDER IMPLICATIONS OF THE FINDINGS This is the first report of the expression and activity of a number of components of the innate immunity TLR system in human embryos. Understanding the role of TLRs during preimplantation human development may be important to reveal immunological mechanisms and potential clinical markers of embryo quality and pregnancy initiation during natural conception and in ART. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by the Ministry of Higher Education, The State of Libya, the UK Medical Research Council, and the NIHR Local Comprehensive Research Network and NIHR Manchester Clinical Research Facility and the European Union's Horizon 2020 Research and Innovation Programmes under the Marie Skłodowska-Curie Grant Agreement No. 812660 (DohART-NET). In accordance with H2020 rules, no new human embryos were sacrificed for research activities performed from the EU funding, which concerned only in silico analyses of recorded time-lapse and transcriptomics datasets. None of the authors has any conflict of interest to declare. TRIAL REGISTRATION NUMBER n/a.
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Affiliation(s)
- Wedad S Aboussahoud
- Division of Developmental Biology and Medicine, Maternal and Fetal Health Research Centre, School of Medical Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
- Maternal and Fetal Health Research Centre, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Helen Smith
- Division of Developmental Biology and Medicine, Maternal and Fetal Health Research Centre, School of Medical Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Adam Stevens
- Division of Developmental Biology and Medicine, Maternal and Fetal Health Research Centre, School of Medical Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
- Maternal and Fetal Health Research Centre, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Ivan Wangsaputra
- Division of Developmental Biology and Medicine, Maternal and Fetal Health Research Centre, School of Medical Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
- Maternal and Fetal Health Research Centre, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Helen R Hunter
- Department of Reproductive Medicine, Old St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Mourad W Seif
- Division of Developmental Biology and Medicine, Maternal and Fetal Health Research Centre, School of Medical Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
- Department of Reproductive Medicine, Old St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Daniel R Brison
- Department of Reproductive Medicine, Old St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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20
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Hermant C, Torres-Padilla ME. TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 2021; 35:22-39. [PMID: 33397727 PMCID: PMC7778262 DOI: 10.1101/gad.344473.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Hermant and Torres-Padilla summarize and discuss the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific transposable element families or subfamilies. Transposable elements (TEs) are genetic elements capable of changing position within the genome. Although their mobilization can constitute a threat to genome integrity, nearly half of modern mammalian genomes are composed of remnants of TE insertions. The first critical step for a successful transposition cycle is the generation of a full-length transcript. TEs have evolved cis-regulatory elements enabling them to recruit host-encoded factors driving their own, selfish transcription. TEs are generally transcriptionally silenced in somatic cells, and the mechanisms underlying their repression have been extensively studied. However, during germline formation, preimplantation development, and tumorigenesis, specific TE families are highly expressed. Understanding the molecular players at stake in these contexts is of utmost importance to establish the mechanisms regulating TEs, as well as the importance of their transcription to the biology of the host. Here, we review the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific TE families or subfamilies. We discuss the diversity of TE regulatory elements within mammalian genomes and highlight the importance of TE mobilization in the dispersal of transcription factor-binding sites over the course of evolution.
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Affiliation(s)
- Clara Hermant
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany.,Faculty of Biology, Ludwig-Maximilians Universität München, D-82152 Planegg-Martinsried, Germany
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21
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Kong CS, Ordoñez AA, Turner S, Tremaine T, Muter J, Lucas ES, Salisbury E, Vassena R, Tiscornia G, Fouladi-Nashta AA, Hartshorne G, Brosens JJ, Brighton PJ. Embryo biosensing by uterine natural killer cells determines endometrial fate decisions at implantation. FASEB J 2021; 35:e21336. [PMID: 33749894 PMCID: PMC8251835 DOI: 10.1096/fj.202002217r] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Decidualizing endometrial stromal cells (EnSC) critically determine the maternal response to an implanting conceptus, triggering either menstruation-like disposal of low-fitness embryos or creating an environment that promotes further development. However, the mechanism that couples maternal recognition of low-quality embryos to tissue breakdown remains poorly understood. Recently, we demonstrated that successful transition of the cycling endometrium to a pregnancy state requires selective elimination of pro-inflammatory senescent decidual cells by activated uterine natural killer (uNK) cells. Here we report that uNK cells express CD44, the canonical hyaluronan (HA) receptor, and demonstrate that high molecular weight HA (HMWHA) inhibits uNK cell-mediated killing of senescent decidual cells. In contrast, low molecular weight HA (LMWHA) did not attenuate uNK cell activity in co-culture experiments. Killing of senescent decidual cells by uNK cells was also inhibited upon exposure to medium conditioned by IVF embryos that failed to implant, but not successful embryos. Embryo-mediated inhibition of uNK cell activity was reversed by recombinant hyaluronidase 2 (HYAL2), which hydrolyses HMWHA. We further report a correlation between the levels of HYAL2 secretion by human blastocysts, morphological scores, and implantation potential. Taken together, the data suggest a pivotal role for uNK cells in embryo biosensing and endometrial fate decisions at implantation.
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Affiliation(s)
- Chow-Seng Kong
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Sarah Turner
- Centre for Reproductive Medicine, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - Tina Tremaine
- Comparative Biomedical Sciences, The Royal Veterinary College, University of London, Hatfield, UK
| | - Joanne Muter
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK.,Tommy's National Centre for Miscarriage Research, University Hospitals Coventry & Warwickshire NHS Trust, Coventry, UK
| | - Emma S Lucas
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK
| | - Emma Salisbury
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK
| | | | | | - Ali A Fouladi-Nashta
- Comparative Biomedical Sciences, The Royal Veterinary College, University of London, Hatfield, UK
| | - Geraldine Hartshorne
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK.,Centre for Reproductive Medicine, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - Jan J Brosens
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK.,Tommy's National Centre for Miscarriage Research, University Hospitals Coventry & Warwickshire NHS Trust, Coventry, UK
| | - Paul J Brighton
- Centre for Early Life, Warwick Medical School, University of Warwick, Coventry, UK
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22
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Mohanty A, Mohanty SK, Rout S, Pani C. Liquid Biopsy, the hype vs. hope in molecular and clinical oncology. Semin Oncol 2021; 48:259-267. [PMID: 34384614 DOI: 10.1053/j.seminoncol.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/28/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
The molecular landscape of tumors has been traditionally established using a biopsy or resection specimens. These modalities result in sampling bias that offer only a single snapshot of tumor heterogeneity. Over the last decade intensive research towards alleviating such a bias and obtaining an integral yet accurate portrait of the tumors, evolved to the use of established molecular and genetic analysis using blood and several other body fluids, such as urine, saliva, and pleural effusions as liquid biopsies. Genomic profiling of the circulating markers including circulating cell-free tumor DNA (ctDNA), circulating tumor cells (CTCs) or even RNA, proteins, and lipids constituting exosomes, have facilitated the diligent monitoring of response to treatment, allowed one to follow the emergence of drug resistance, and enumerate minimal residual disease. The prevalence of tumor educated platelets (TEPs) and our understanding of how tumor cells influence platelets are beginning to unearth TEPs as a potentially dynamic component of liquid biopsies. Here, we review the biology, methodology, approaches, and clinical applications of biomarkers used to assess liquid biopsies. The current review addresses recent technological advances and different forms of liquid biopsy along with upcoming challenges and how they can be integrated to get the best possible tumor-derived genetic information that can be leveraged to more precise therapies for patient as liquid biopsies become increasingly routine in clinical practice.
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Affiliation(s)
- Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India.
| | - Sambit K Mohanty
- Advanced Medical Research Institute, Bhubaneswar, Odisha, India; CORE Diagnostics, Gurgaon, Haryana, India
| | - Sipra Rout
- Christian Medical College, Vellore, Tamil Nadu, India
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23
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Bode D, Cull AH, Rubio-Lara JA, Kent DG. Exploiting Single-Cell Tools in Gene and Cell Therapy. Front Immunol 2021; 12:702636. [PMID: 34322133 PMCID: PMC8312222 DOI: 10.3389/fimmu.2021.702636] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Single-cell molecular tools have been developed at an incredible pace over the last five years as sequencing costs continue to drop and numerous molecular assays have been coupled to sequencing readouts. This rapid period of technological development has facilitated the delineation of individual molecular characteristics including the genome, transcriptome, epigenome, and proteome of individual cells, leading to an unprecedented resolution of the molecular networks governing complex biological systems. The immense power of single-cell molecular screens has been particularly highlighted through work in systems where cellular heterogeneity is a key feature, such as stem cell biology, immunology, and tumor cell biology. Single-cell-omics technologies have already contributed to the identification of novel disease biomarkers, cellular subsets, therapeutic targets and diagnostics, many of which would have been undetectable by bulk sequencing approaches. More recently, efforts to integrate single-cell multi-omics with single cell functional output and/or physical location have been challenging but have led to substantial advances. Perhaps most excitingly, there are emerging opportunities to reach beyond the description of static cellular states with recent advances in modulation of cells through CRISPR technology, in particular with the development of base editors which greatly raises the prospect of cell and gene therapies. In this review, we provide a brief overview of emerging single-cell technologies and discuss current developments in integrating single-cell molecular screens and performing single-cell multi-omics for clinical applications. We also discuss how single-cell molecular assays can be usefully combined with functional data to unpick the mechanism of cellular decision-making. Finally, we reflect upon the introduction of spatial transcriptomics and proteomics, its complementary role with single-cell RNA sequencing (scRNA-seq) and potential application in cellular and gene therapy.
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Affiliation(s)
- Daniel Bode
- Wellcome Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Alyssa H. Cull
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
| | - Juan A. Rubio-Lara
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
| | - David G. Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
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24
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Zhang W, Li S, Li K, Li LI, Yin P, Tong G. The role of protein arginine methyltransferase 7 in human developmentally arrested embryos cultured in vitro. Acta Biochim Biophys Sin (Shanghai) 2021; 53:925-932. [PMID: 34041522 DOI: 10.1093/abbs/gmab068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Human embryos of in vitro fertilization (IVF) are often susceptible to developmental arrest, which greatly reduces the efficiency of IVF treatment. In recent years, it has been found that protein arginine methyltransferase 7 (PRMT7) plays an important role in the process of early embryonic development. However, not much is known about the relationship between PRMT7 and developmentally arrested embryos. The role of PRMT7 in developmentally arrested embryos was thus investigated in this study. Discarded human embryos from IVF were collected for experimental materials. Quantitative real-time polymerase chain reaction (qRT-PCR) and confocal analyses were used to identify PRMT7 mRNA and protein levels in early embryos at different developmental stages, as well as changes in the methylation levels of H4R3me2s. Additionally, PRMT7 was knocked down in the developmentally arrested embryos to observe the further development of these embryos. Our results demonstrated that PRMT7 mRNA and protein levels in arrested embryos were significantly increased compared with those in control embryos; meanwhile, the methylation levels of H4R3me2s in arrested embryos were also increased significantly. Knockdown of PRMT7 could rescue partially developmentally arrested embryos, and even individual developmentally arrested embryos could develop into blastocysts. In conclusion, over-expression of PRMT7 disrupts the early embryo development process, leading to early embryos developmental arrest, but these developmentally arrested defects could be partially rescued by knockdown of the PRMT7 protein.
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Affiliation(s)
- Wuwen Zhang
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shifeng Li
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Li
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - L i Li
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ping Yin
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guoqing Tong
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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25
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Telonis AG, Rigoutsos I. The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content. BMC Biol 2021; 19:60. [PMID: 33765992 PMCID: PMC7995781 DOI: 10.1186/s12915-020-00928-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation stages examining the architectural properties and content of genes whose abundance changes significantly across developmental time points. Results Analysis of preimplantation embryos from human and mouse showed that short genes whose introns are enriched in Alu (human) and B (mouse) elements, respectively, have higher abundance in the blastocyst compared to the zygote. These highly expressed genes encode ribosomal proteins or metabolic enzymes. On the other hand, long genes whose introns are depleted in repetitive elements have lower abundance in the blastocyst and include genes from signaling pathways. Additionally, the sequences of the genes that are differentially expressed between the blastocyst and the zygote contain distinct collections of pyknon motifs that differ between up- and down-regulated genes. Further examination of the genes that participate in the stem cell-specific protein interaction network shows that their introns are short and enriched in Alu (human) and B (mouse) elements. As organogenesis progresses, in both human and mouse, we find that the primarily short and repeat-rich expressed genes make way for primarily longer, repeat-poor genes. With that in mind, we used a machine learning-based approach to identify gene signatures able to classify human adult tissues: we find that the most discriminatory genes comprising these signatures have long introns that are repeat-poor and include transcription factors and signaling-cascade genes. The introns of widely expressed genes across human tissues, on the other hand, are short and repeat-rich, and coincide with those with the highest expression at the blastocyst stage. Conclusions Protein-coding genes that are characteristic of each trajectory, i.e., proliferation/pluripotency or differentiation, exhibit antithetical biases in their intronic and exonic lengths and in their repetitive-element content. While the respective human and mouse gene signatures are functionally and evolutionarily conserved, their introns and exons are enriched or depleted in organism-specific repetitive elements. We posit that these organism-specific repetitive sequences found in exons and introns are used to effect the corresponding genes’ regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-020-00928-8.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, 1020 Locust Street, Suite M81, Philadelphia, PA, 19107, USA. .,Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, 1020 Locust Street, Suite M81, Philadelphia, PA, 19107, USA.
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26
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Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat Genet 2021; 53:354-366. [PMID: 33603233 PMCID: PMC8812996 DOI: 10.1038/s41588-021-00782-6] [Citation(s) in RCA: 262] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution chromatin immunoprecipitation (ChIP)-nexus binding profiles of pluripotency TFs. We develop interpretation tools to learn predictive motif representations and identify soft syntax rules for cooperative TF binding interactions. Strikingly, Nanog preferentially binds with helical periodicity, and TFs often cooperate in a directional manner, which we validate using clustered regularly interspaced short palindromic repeat (CRISPR)-induced point mutations. Our model represents a powerful general approach to uncover the motifs and syntax of cis-regulatory sequences in genomics data.
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Affiliation(s)
- Žiga Avsec
- Department of Informatics, Technical University of Munich, Garching, Germany,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany,Currently at DeepMind, London, UK
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Amr Alexandari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Khyati Dalal
- Stowers Institute for Medical Research, Kansas City, MO, USA,The University of Kansas Medical Center, Kansas City, KS, USA
| | - Robin Fropf
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Charles McAnany
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA,Department of Genetics, Stanford University, Stanford, CA, USA,correspondence: ,
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA,The University of Kansas Medical Center, Kansas City, KS, USA,correspondence: ,
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27
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Hu Y, Huang K, Zeng Q, Feng Y, Ke Q, An Q, Qin LJ, Cui Y, Guo Y, Zhao D, Peng Y, Tian D, Xia K, Chen Y, Ni B, Wang J, Zhu X, Wei L, Liu Y, Xiang P, Liu JY, Xue Z, Fan G. Single-cell analysis of nonhuman primate preimplantation development in comparison to humans and mice. Dev Dyn 2021; 250:974-985. [PMID: 33449399 DOI: 10.1002/dvdy.295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genetic programs underlying preimplantation development and early lineage segregation are highly conserved across mammals. It has been suggested that nonhuman primates would be better model organisms for human embryogenesis, but a limited number of studies have investigated the monkey preimplantation development. In this study, we collect single cells from cynomolgus monkey preimplantation embryos for transcriptome profiling and compare with single-cell RNA-seq data derived from human and mouse embryos. RESULTS By weighted gene-coexpression network analysis, we found that cynomolgus gene networks have greater conservation with human embryos including a greater number of conserved hub genes than that of mouse embryos. Consistently, we found that early ICM/TE lineage-segregating genes in monkeys exhibit greater similarity with human when compared to mouse, so are the genes in signaling pathways such as LRP1 and TCF7 involving in WNT pathway. Last, we tested the role of one conserved pre-EGA hub gene, SIN3A, using a morpholino knockdown of maternal RNA transcripts in monkey embryos followed by single-cell RNA-seq. We found that SIN3A knockdown disrupts the gene-silencing program during the embryonic genome activation transition and results in developmental delay of cynomolgus embryos. CONCLUSION Taken together, our study provided new insight into evolutionarily conserved and divergent transcriptome dynamics during mammalian preimplantation development.
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Affiliation(s)
- Youjin Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun-Ye-Sat University, Guangzhou, China.,Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Kevin Huang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Qiao Zeng
- State Key Laboratory of Reproductive Medicine, Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yun Feng
- Reproductive Medicine Center, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Qiong Ke
- Key Laboratory of Stem Cell Engineering Ministry of Education, Zhongshan College of Medicine, Sun-Ye-Sat University, Guangzhou, China
| | - Qin An
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Lian-Ju Qin
- State Key Laboratory of Reproductive Medicine, Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - YuGui Cui
- State Key Laboratory of Reproductive Medicine, Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Ying Guo
- The Second Affiliated Hospital, Xiangya School of Medicine, Central South University, Changsha, China
| | - Dicheng Zhao
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Peng
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, China
| | - Di Tian
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yong Chen
- Key Laboratory of Genetics and Birth Health of Hunan Province, Changsha, China
| | - Bin Ni
- Key Laboratory of Genetics and Birth Health of Hunan Province, Changsha, China
| | - Jinmei Wang
- Shanghai East Hospital, School of Life Sciences & Technology, Tongji University, Shanghai, China
| | - Xianmin Zhu
- Shanghai East Hospital, School of Life Sciences & Technology, Tongji University, Shanghai, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun-Ye-Sat University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun-Ye-Sat University, Guangzhou, China
| | - Peng Xiang
- Key Laboratory of Stem Cell Engineering Ministry of Education, Zhongshan College of Medicine, Sun-Ye-Sat University, Guangzhou, China
| | - Jia-Yin Liu
- State Key Laboratory of Reproductive Medicine, Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zhigang Xue
- Reproductive Medicine Center, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
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Hu C, Xu Q, Shen J, Wang Y. Clinical and Genetic Characteristics of Mitochondrial Encephalopathy Due to FOXRED1 Mutations: Two Chinese Case Reports and a Review of the Literature. Front Neurol 2021; 12:633397. [PMID: 33613441 PMCID: PMC7887287 DOI: 10.3389/fneur.2021.633397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/12/2021] [Indexed: 11/30/2022] Open
Abstract
Background: As one of the assembly factors of complex I in the mitochondrial respiratory chain, FOXRED1 plays an important role in mitochondrial function. However, only a few patients with mitochondrial encephalopathy due to FOXRED1 defects have been reported. Methods: Two Chinese patients with mitochondrial encephalopathy due to mutations in FOXRED1 were identified through trio whole-exome sequencing. The clinical presentation, laboratory data, brain imaging findings, and genetic results were collected and reviewed. All previously reported cases with FOXRED1-related mitochondrial encephalopathy were collected using a PubMed search, and their data were reviewed. Results: Two patients presented with severe neurodevelopmental delay, epilepsy, high lactic acid levels, and remarkable diffuse brain atrophy and polycystic encephalomalacia during early infancy. Trio whole-exome sequencing revealed compound heterozygous variants in both patients: one case harbored a c.606_607delAG frameshift variant and a c.1054C>T (p.R352W) variant. At the same time, the other carried a novel c.352C>T (p.Q118X) variant and a reported c.1054C>T (p.R352W) variant. To date, nine patients have been reported with FOXRED1 defects, including our two cases. The most common presentations were neurodevelopment delay (100%), epilepsy (80%), poor feeding (30%), and vision loss (20%). Multisystem involvement comprised cardiovascular dysfunction (30%), abnormal liver function (20%), and hypoglycemia (10%). The neuroimaging results ranged from normal to severe cerebral atrophy and polycystic encephalomalacia in early infancy. Eleven pathogenic variants in FOXRED1 have been reported, comprising six missense variants, two non-sense variants, two frameshift variants, and one splice variant; among these the c.1054C>T (p.R352W) and c.612_615dupAGTG (p.A206SfsX15) variants are more common. Conclusion:FOXRED1-related mitochondrial disorders have high clinical and genetic heterogeneity. Our study expanded the clinical and genetic spectrum of FOXRED1 defects. Early infantile onset and progressive encephalopathy are the most common clinical presentations, while the variants c.1054C>T (p.R352W) and c.612_615dupAGTG (p.A206SfsX15) may be critical founder mutations.
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Affiliation(s)
- Chaoping Hu
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
| | - Qiong Xu
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Shen
- Department of Radiology, Children's Hospital of Fudan University, Shanghai, China
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
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29
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Carreiro LE, Santos GSD, Luedke FE, Goissis MD. Cell differentiation events in pre-implantation mouse and bovine embryos. Anim Reprod 2021; 18:e20210054. [PMID: 35035540 PMCID: PMC8747937 DOI: 10.1590/1984-3143-ar2021-0054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
Early mammal embryogenesis starts with oocyte fertilization, giving rise to the zygote. The events that the newly formed zygote surpasses are crucial to the embryo developmental success. Shortly after activation of its genome, cells of the embryo segregate into the inner cell mass (ICM) or the trophectoderm (TE). The first will give rise to the embryo while the latter will become the placenta. This first segregation involves cellular and molecular processes that include cell polarity linked to intracellular pathway activation, which will regulate the transcription of trophectoderm-related genes. Then, cells of the ICM undergo the second event of mammalian cell differentiation, which consists of the separation between epiblast (EPI) and hypoblast or primitive endoderm (PrE). This second segregation involves paracrine signaling, leading to differential expression of key genes that will dictate the fate of the cell. Although these processes are described in detail in the mouse, recent studies suggest that the bovine embryo could also be an interesting model for early development, since there are differences to the mouse and similarities with early human embryogenesis. In this review, we gathered the main data available in the literature upon bovine and mouse early development events, suggesting that both models should be analyzed and studied in a complementary way, to better model early events occurring in human development.
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30
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Min B, Park JS, Jeong YS, Jeon K, Kang YK. Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos. Nucleic Acids Res 2020; 48:8431-8444. [PMID: 32667642 PMCID: PMC7470951 DOI: 10.1093/nar/gkaa584] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/10/2020] [Accepted: 07/03/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.
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Affiliation(s)
- Byungkuk Min
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Young Sun Jeong
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, South Korea
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31
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Kay VR, Rätsep MT, Figueiró-Filho EA, Croy BA. Preeclampsia may influence offspring neuroanatomy and cognitive function: a role for placental growth factor†. Biol Reprod 2020; 101:271-283. [PMID: 31175349 DOI: 10.1093/biolre/ioz095] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
Preeclampsia (PE) is a common pregnancy complication affecting 3-5% of women. Preeclampsia is diagnosed clinically as new-onset hypertension with associated end organ damage after 20 weeks of gestation. Despite being diagnosed as a maternal syndrome, fetal experience of PE is a developmental insult with lifelong cognitive consequences. These cognitive alterations are associated with distorted neuroanatomy and cerebrovasculature, including a higher risk of stroke. The pathophysiology of a PE pregnancy is complex, with many factors potentially able to affect fetal development. Deficient pro-angiogenic factor expression is one aspect that may impair fetal vascularization, alter brain structure, and affect future cognition. Of the pro-angiogenic growth factors, placental growth factor (PGF) is strongly linked to PE. Concentrations of PGF are inappropriately low in maternal blood both before and during a PE gestation. Fetal concentrations of PGF appear to mirror maternal circulating concentrations. Using Pgf-/- mice that may model effects of PE on offspring, we demonstrated altered central nervous system vascularization, neuroanatomy, and behavior. Overall, we propose that development of the fetal brain is impaired in PE, making the offspring of preeclamptic pregnancies a unique cohort with greater risk of altered cognition and cerebrovasculature. These individuals may benefit from early interventions, either pharmacological or environmental. The early neonatal period may be a promising window for intervention while the developing brain retains plasticity.
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Affiliation(s)
- Vanessa R Kay
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Matthew T Rätsep
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | | | - B Anne Croy
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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32
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Tetkova A, Susor A, Kubelka M, Nemcova L, Jansova D, Dvoran M, Del Llano E, Holubcova Z, Kalous J. Follicle-stimulating hormone administration affects amino acid metabolism in mammalian oocytes†. Biol Reprod 2020; 101:719-732. [PMID: 31290535 DOI: 10.1093/biolre/ioz117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022] Open
Abstract
Culture media used in assisted reproduction are commonly supplemented with gonadotropin hormones to support the nuclear and cytoplasmic maturation of in vitro matured oocytes. However, the effect of gonadotropins on protein synthesis in oocytes is yet to be fully understood. As published data have previously documented a positive in vitro effect of follicle-stimulating hormone (FSH) on cytoplasmic maturation, we exposed mouse denuded oocytes to FSH in order to evaluate the changes in global protein synthesis. We found that dose-dependent administration of FSH resulted in a decrease of methionine incorporation into de novo synthesized proteins in denuded mouse oocytes and oocytes cultured in cumulus-oocyte complexes. Similarly, FSH influenced methionine incorporation in additional mammalian species including human. Furthermore, we showed the expression of FSH-receptor protein in oocytes. We found that major translational regulators were not affected by FSH treatment; however, the amino acid uptake became impaired. We propose that the effect of FSH treatment on amino acid uptake is influenced by FSH receptor with the effect on oocyte metabolism and physiology.
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Affiliation(s)
- Anna Tetkova
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Andrej Susor
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Michal Kubelka
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Lucie Nemcova
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Denisa Jansova
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Michal Dvoran
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Edgar Del Llano
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Zuzana Holubcova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Reprofit International, Clinic of Reproductive Medicine, Brno, Czech Republic
| | - Jaroslav Kalous
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
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33
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Yin SY, Sun BM, Xu T, Liu X, Huo LJ, Zhang X, Zhou J, Miao YL. CHIR99021 and rpIL6 promote porcine parthenogenetic embryo development and blastocyst quality. Theriogenology 2020; 158:470-476. [PMID: 33049572 DOI: 10.1016/j.theriogenology.2020.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/09/2020] [Accepted: 08/08/2020] [Indexed: 12/20/2022]
Abstract
Signaling pathways and transcription factors are involved in porcine embryonic development. Here, we demonstrate that glycogen synthase kinase-3 (GSK3) inhibitor, CHIR99021 and recombinant porcine interleukin-6 (rpIL6) significantly promote porcine parthenogenetic blastocyst formation (49.23 ± 8.40% vs 32.34 ± 4.15%), with increased inner cell mass (ICM) cell numbers (7.72 ± 2.30 vs 4.28 ± 1.60) and higher expression of pluripotent genes, such as OCT4, SOX2 and NANOG. Furthermore, CHIR99021 and rpIL6 improve blastocyst quality with increased blastocyst hatching percentage (16.19 ± 1.96% vs 10.25 ± 1.12%) and subsequently porcine pluripotent stem cells (pPSCs) derivation efficiency. These results advance the understanding of porcine pre-implantation development and provide evidences in improving the blastocyst quality.
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Affiliation(s)
- Shu-Yuan Yin
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Bing-Min Sun
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Tian Xu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Li-Jun Huo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; National Demonstration Center for Experimental Veterinary Medicine Education (Huazhong Agricultural University), Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Jilong Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China.
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34
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Hübner JM, Müller T, Papageorgiou DN, Mauermann M, Krijgsveld J, Russell RB, Ellison DW, Pfister SM, Pajtler KW, Kool M. EZHIP/CXorf67 mimics K27M mutated oncohistones and functions as an intrinsic inhibitor of PRC2 function in aggressive posterior fossa ependymoma. Neuro Oncol 2020; 21:878-889. [PMID: 30923826 DOI: 10.1093/neuonc/noz058] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Posterior fossa A (PFA) ependymomas are one of 9 molecular groups of ependymoma. PFA tumors are mainly diagnosed in infants and young children, show a poor prognosis, and are characterized by a lack of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark. Recently, we reported overexpression of chromosome X open reading frame 67 (CXorf67) as a hallmark of PFA ependymoma and showed that CXorf67 can interact with enhancer of zeste homolog 2 (EZH2), thereby inhibiting polycomb repressive complex 2 (PRC2), but the mechanism of action remained unclear. METHODS We performed mass spectrometry and peptide modeling analyses to identify the functional domain of CXorf67 responsible for binding and inhibition of EZH2. Our findings were validated by immunocytochemistry, western blot, and methyltransferase assays. RESULTS We find that the inhibitory mechanism of CXorf67 is similar to diffuse midline gliomas harboring H3K27M mutations. A small, highly conserved peptide sequence located in the C-terminal region of CXorf67 mimics the sequence of K27M mutated histones and binds to the SET domain (Su(var)3-9/enhancer-of-zeste/trithorax) of EZH2. This interaction blocks EZH2 methyltransferase activity and inhibits PRC2 function, causing de-repression of PRC2 target genes, including genes involved in neurodevelopment. CONCLUSIONS Expression of CXorf67 is an oncogenic mechanism that drives H3K27 hypomethylation in PFA tumors by mimicking K27M mutated histones. Disrupting the interaction between CXorf67 and EZH2 may serve as a novel targeted therapy for PFA tumors but also for other tumors that overexpress CXorf67. Based on its function, we have renamed CXorf67 as "EZH Inhibitory Protein" (EZHIP).
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Affiliation(s)
- Jens-Martin Hübner
- Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Torsten Müller
- Division of Proteomics of Stem Cells and Cancer, DKFZ, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monika Mauermann
- Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, DKFZ, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Robert B Russell
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Bioquant, Heidelberg University, Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center, Heidelberg, Germany
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35
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Rosales M, Nuñez M, Abdala A, Mesch V, Mendeluk G. Thyroid hormones in ovarian follicular fluid: Association with oocyte retrieval in women undergoing assisted fertilization procedures. JBRA Assist Reprod 2020; 24:245-249. [PMID: 32155015 PMCID: PMC7365548 DOI: 10.5935/1518-0557.20200004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objective: Our aim was to analyze the role of thyroid hormones in follicular fluid (FF) in relation to the number of oocytes retrieved in women recruited for an assisted fertilization procedure. Methods: Retrospective cohort study of 51 women 37.5±3.3 years, range 29-42, evaluated after a controlled ovarian stimulation protocol in a University Hospital. FF was sampled by transvaginal ultrasound-guided aspiration after ovarian hyperstimulation and we measured T3 (T3f), T4 (T4f), TSH (TSHf) and free T4 (T4ff). The oocyte maturation rate was calculated as: Number of metaphase II oocytes/Number of oocytes retrieved x 100. Statistical analysis was performed using the SPSS-19 software. Results: Hormone levels in FF were: TSHf 1.3µIU/ml (0.4 - 2.7), T3f: 1.52±0.46 nmol/L, T4f 88.8±30.9nmol/L and T4ff: 15.44±2.57pmol/L. The number of oocytes recovered was dependent onT4f following the equation: Log (oocyte) = 0.379+0.042*T4f (r:0.352, p=0.012). After a logistic regression model analysis, T3f showed a tendency to be associated with the OMR: OR (95 % CI)= 0.977 (0.954 to 1.001), p=0.057. Conclusions: The correlation found between thyroid hormones and the number of oocytes retrieved suggests an interaction between thyroid and gonadal axes in relation to follicular development.
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Affiliation(s)
- Mónica Rosales
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Bioquímica Clínica, Cátedra de Bioquímica Clínica I, Laboratorio de Endocrinología. Buenos Aires, Argentina.,Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC). Buenos Aires, Argentina
| | - Myriam Nuñez
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC). Buenos Aires, Argentina
| | - Andrea Abdala
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Matemática. Buenos Aires, Argentina
| | - Viviana Mesch
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Bioquímica Clínica, Cátedra de Bioquímica Clínica I, Laboratorio de Endocrinología. Buenos Aires, Argentina.,Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC). Buenos Aires, Argentina
| | - Gabriela Mendeluk
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC). Buenos Aires, Argentina.,5Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Bioquímica Clínica, Cátedra de Bioquímica Clínica II, Laboratorio de Fertilidad Masculina. Buenos Aires, Argentina
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36
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Chakraborty C, Bhattacharya M, Agoramoorthy G. Single-cell sequencing of miRNAs: A modified technology. Cell Biol Int 2020; 44:1773-1780. [PMID: 32379363 DOI: 10.1002/cbin.11376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 03/07/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
The recent development of next-generation sequencing technologies has offered valuable insights into individual cells. This technology is centered on the characterization of single cells for epigenomics, genomics, and transcriptomics. Ever since the first report appeared in 2009, the single-cell RNA-sequencing saga started to explore deeper into the mechanics intrigued within a single cell. microRNA (miRNA) has been increasingly recognized as an essential molecule triggering an additional layer for gene regulation. Therefore, single-cell sequencing of miRNAs is crucial to explore the logical riddles surrounding the epigenomics, genomics, and transcriptomics of an individual cell. Scientists from the Vienna Biocenter Campus have lately performed single-cell sequencing of miRNAs in the fly, Drosophila, and nematode, Caenorhabditis elegans. In this review, we present the latest scientific explorations supported by all-inclusive data on this novel subject matter of next-generation sequencing.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, Odisha, India
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Gallardo-Fuentes L, Santos-Pereira JM, Tena JJ. Functional Conservation of Divergent p63-Bound cis-Regulatory Elements. Front Genet 2020; 11:339. [PMID: 32411176 PMCID: PMC7200997 DOI: 10.3389/fgene.2020.00339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/20/2020] [Indexed: 11/26/2022] Open
Abstract
The transcription factor p63 is an essential regulator of vertebrate ectoderm development, including epidermis, limbs, and craniofacial tissues. Here, we have investigated the evolutionary conservation of p63 binding sites (BSs) between zebrafish and human. First, we have analyzed sequence conservation of p63 BSs by comparing ChIP-seq data from human keratinocytes and zebrafish embryos, observing a very poor conservation. Next, we compared the gene regulatory network orchestrated by p63 in both species and found a high overlap between them, suggesting a high degree of functional conservation during evolution despite sequence divergence and the large evolutionary distance. Finally, we used transgenic reporter assays in zebrafish embryos to functionally validate a set of equivalent p63 BSs from zebrafish and human located close to genes involved in epidermal development. Reporter expression was driven by human and zebrafish BSs to many common tissues related to p63 expression domains. Therefore, we conclude that the gene regulatory network controlled by p63 is highly conserved across vertebrates despite the fact that p63-bound regulatory elements show high divergence.
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Affiliation(s)
- Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - José M Santos-Pereira
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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38
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ROCK and RHO Playlist for Preimplantation Development: Streaming to HIPPO Pathway and Apicobasal Polarity in the First Cell Differentiation. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2020; 229:47-68. [PMID: 29177764 DOI: 10.1007/978-3-319-63187-5_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In placental mammalian development, the first cell differentiation produces two distinct lineages that emerge according to their position within the embryo: the trophectoderm (TE, placenta precursor) differentiates in the surface, while the inner cell mass (ICM, fetal body precursor) forms inside. Here, we discuss how such position-dependent lineage specifications are regulated by the RHOA subfamily of small GTPases and RHO-associated coiled-coil kinases (ROCK). Recent studies in mouse show that activities of RHO/ROCK are required to promote TE differentiation and to concomitantly suppress ICM formation. RHO/ROCK operate through the HIPPO signaling pathway, whose cell position-specific modulation is central to establishing unique gene expression profiles that confer cell fate. In particular, activities of RHO/ROCK are essential in outside cells to promote nuclear localization of transcriptional co-activators YAP/TAZ, the downstream effectors of HIPPO signaling. Nuclear localization of YAP/TAZ depends on the formation of apicobasal polarity in outside cells, which requires activities of RHO/ROCK. We propose models of how RHO/ROCK regulate lineage specification and lay out challenges for future investigations to deepen our understanding of the roles of RHO/ROCK in preimplantation development. Finally, as RHO/ROCK may be inhibited by certain pharmacological agents, we discuss their potential impact on human preimplantation development in relation to fertility preservation in women.
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Naddafpour A, Ghazvini Zadegan F, Hajian M, Hosseini SM, Jafarpour F, Rahimi M, Habibi R, Nasr Esfahani MH. Effects of abundances of OCT-4 mRNA transcript on goat pre-implantation embryonic development. Anim Reprod Sci 2020; 215:106286. [PMID: 32216939 DOI: 10.1016/j.anireprosci.2020.106286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 12/18/2019] [Accepted: 01/16/2020] [Indexed: 12/27/2022]
Abstract
Unlike in mice, the function of pluripotent markers in early embryonic development of domestic animals remains to be elucidated and this may account for the failure to establish embryonic stem cell lines for these species. To study the functions of the OCT-4 protein which has important actions in maintenance of pluripotent and self-renewal processes during early embryonic development, there was induced reduction in relative abundance of OCT-4 mRNA transcript during goat early embryonic development by using RNA interference techniques. The injection of OCT-4 siRNA into goat IVF presumptive zygotes resulted in a decrease in the relative abundance of OCT-4 mRNA transcript; however, there was development of these embryos to the blastocyst stage at the same rate as there was in the control group. The blastocysts from the treated groups had a similar number of TE, ICM, and total cells compared to those from the control group. Although there was a greater relative abundance of NANOG, REX1, and CDX2 mRNA transcript in the embryos injected with siRNA at the 8-16 cell stage, the relative transcript abundances were similar for the control and treatment groups at the blastocyst stage. The relative abundance of SOX2 mRNA transcript was similar for the treatment and control group. It, therefore, is concluded that inhibition of abundances of OCT-4 mRNA transcript to about 20 % of that of the untreated control group did not affect blastocyst formation rate in goats. The functions of OCT-4 in maintaining ICM and TE integrity, however, remains to be assessed.
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Affiliation(s)
- Azadeh Naddafpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; Department of Biology, University of Science and Culture, Tehran, Iran
| | - Faezeh Ghazvini Zadegan
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mehdi Hajian
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sayyed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohsen Rahimi
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Razieh Habibi
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; Department of Biology, University of Science and Culture, Tehran, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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Abstract
PURPOSE OF REVIEW Altered epigenetics is central to oncogenesis in many pediatric cancers. Aberrant epigenetic states are induced by mutations in histones or epigenetic regulatory genes, aberrant expression of genes regulating chromatin complexes, altered DNA methylation patterns, or dysregulated expression of noncoding RNAs. Developmental contexts of dysregulated epigenetic states are equally important for initiation and progression of many childhood cancers. As an improved understanding of disease-specific roles and molecular consequences of epigenetic alterations in oncogenesis is emerging, targeting these mechanisms of disease in childhood cancers is increasingly becoming important. RECENT FINDINGS In addition to disease-causing epigenetic events, DNA methylation patterns and specific oncohistone mutations are being utilized for the diagnosis of pediatric central nervous system (CNS) and solid tumors. These discoveries have improved the classification of poorly differentiated tumors and laid the foundation for future improved clinical management. On the therapeutic side, the first therapies targeting epigenetic alterations have recently entered clinical trials. Current clinical trials include pharmacological inhibition of histone and DNA modifiers in aggressive types of pediatric cancer. SUMMARY Targeting novel epigenetic vulnerabilities, either by themselves, or coupled with targeting altered transcriptional states, developmental cell states or immunomodulation will result in innovative approaches for treating deadly pediatric cancers.
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Affiliation(s)
- Eshini Panditharatna
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA.,Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts, USA
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Han X, Xiang J, Li C, Wang J, Wang C, Zhang Y, Li Z, Lu Z, Yue Y, Li X. MLL1 combined with GSK3 and MAP2K inhibition improves the development of in vitro-fertilized embryos. Theriogenology 2020; 146:58-70. [PMID: 32059151 DOI: 10.1016/j.theriogenology.2020.01.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/15/2020] [Accepted: 01/26/2020] [Indexed: 10/25/2022]
Abstract
The MM-102 compound prevents the interaction between mixed lineage leukemia 1 (MLL1) and WD Trp-Asp repeat domain 5 (WDR5) and results in the inhibition of MLL1 H3K4 histone methyltransferase (HMT) activity. The inhibition of the FGFR signaling pathway and activation of the WNT pathway by small molecule inhibitors (known as 2i) improves blastocyst development. However, studies on the effects of MLL1 combined with GSK3 and MAP2K inhibition (3i) on the development of embryos have not been reported. Our results show that 3i improves bovine and mouse IVF development only when added at the appropriate time point and affects ICM-related gene (OCT4, SOX2 and NANOG) expression in a concentration-dependent manner. 3i increases the expression of blastocyst-related genes such as PRDM14, KLF4 and KLF17 and decreases the expression of the de novo DNA methyltransferase genes DNMT3L and DNMT1 in bovines, but increases Prdm14, Stella, Klf2 and Klf4 expression and significantly decreases Dnmt3l, Dnmt3b, and Dnmt1 expression in mice. The analysis of transcription data showed that the expression of DNMTs increases slightly later than that of PRDM14 during embryo development, which indicates that PRDM14 is the upstream regulator. 3i upregulates PRDM14 and then downregulates DNMTs to affect IVF embryo development. When 3i-treated mouse embryos were transplanted, the morphology and body weight of the offspring were not significantly different from those of the control group. These offspring were as fertile as normal mice. 3i improves the development of bovine and mouse IVF embryos but does not affect the quality of the embryos. The application of 3i provides a new method for improving IVF embryo production in domestic animals.
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Affiliation(s)
- Xuejie Han
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Jinzhu Xiang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Chen Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Jing Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Chen Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Yuanyuan Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Zihong Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Zhenyu Lu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Yongli Yue
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
| | - Xueling Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot, China.
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Fan J, Campioli E, Sottas C, Zirkin B, Papadopoulos V. Amhr2-Cre-Mediated Global Tspo Knockout. J Endocr Soc 2020; 4:bvaa001. [PMID: 32099945 PMCID: PMC7031085 DOI: 10.1210/jendso/bvaa001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 12/27/2022] Open
Abstract
Although the role of translocator protein (TSPO) in cholesterol transport in steroid-synthesizing cells has been studied extensively, recent studies of TSPO genetic depletion have questioned its role. Amhr2-Cre mice have been used to generate Leydig cell-specific Tspo conditional knockout (cKO) mice. Using the same Cre line, we were unable to generate Tspo cKO mice possibly because of genetic linkage between Tspo and Amhr2 and coexpression of Amhr2-Cre and Tspo in early embryonic development. We found that Amhr2-Cre is expressed during preimplantation stages, resulting in global heterozygous mice (gHE; Amhr2-Cre+/–,Tspo–/+). Two gHE mice were crossed, generating Amhr2-Cre–mediated Tspo global knockout (gKO; Tspo–/–) mice. We found that 33.3% of blastocysts at E3.5 to E4.5 showed normal morphology, whereas 66.7% showed delayed development, which correlates with the expected Mendelian proportions of Tspo+/+ (25%), Tspo–/– (25%), and Tspo+/– (50%) genotypes from crossing 2 Tspo–/+ mice. Adult Tspo gKO mice exhibited disturbances in neutral lipid homeostasis and reduced intratesticular and circulating testosterone levels, but no change in circulating basal corticosterone levels. RNA-sequencing data from mouse adrenal glands and lungs revealed transcriptome changes in response to the loss of TSPO, including changes in several cholesterol-binding and transfer proteins. This study demonstrates that Amhr2-Cre can be used to produce Tspo gKO mice instead of cKO, and can serve as a new global “Cre deleter.” Moreover, our results show that Tspo deletion causes delayed preimplantation embryonic development, alters neutral lipid storage and steroidogenesis, and leads to transcriptome changes that may reflect compensatory mechanisms in response to the loss of function of TSPO.
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Affiliation(s)
- Jinjiang Fan
- The Research Institute of the McGill University Health Centre.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Enrico Campioli
- The Research Institute of the McGill University Health Centre.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Chantal Sottas
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, US
| | - Barry Zirkin
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, US
| | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre.,Department of Medicine, McGill University, Montreal, Quebec, Canada.,Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, US
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Villanueva-Cañas JL, Horvath V, Aguilera L, González J. Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster. Nucleic Acids Res 2020; 47:6842-6857. [PMID: 31175824 PMCID: PMC6649756 DOI: 10.1093/nar/gkz490] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 12/25/2022] Open
Abstract
Although transposable elements are an important source of regulatory variation, their genome-wide contribution to the transcriptional regulation of stress-response genes has not been studied yet. Stress is a major aspect of natural selection in the wild, leading to changes in the transcriptional regulation of a variety of genes that are often triggered by one or a few transcription factors. In this work, we take advantage of the wealth of information available for Drosophila melanogaster and humans to analyze the role of transposable elements in six stress regulatory networks: immune, hypoxia, oxidative, xenobiotic, heat shock, and heavy metal. We found that transposable elements were enriched for caudal, dorsal, HSF, and tango binding sites in D. melanogaster and for NFE2L2 binding sites in humans. Taking into account the D. melanogaster population frequencies of transposable elements with predicted binding motifs and/or binding sites, we showed that those containing three or more binding motifs/sites are more likely to be functional. For a representative subset of these TEs, we performed in vivo transgenic reporter assays in different stress conditions. Overall, our results showed that TEs are relevant contributors to the transcriptional regulation of stress-response genes.
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Affiliation(s)
| | - Vivien Horvath
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Laura Aguilera
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Gross N, Strillacci MG, Peñagaricano F, Khatib H. Characterization and functional roles of paternal RNAs in 2-4 cell bovine embryos. Sci Rep 2019; 9:20347. [PMID: 31889064 PMCID: PMC6937301 DOI: 10.1038/s41598-019-55868-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022] Open
Abstract
Embryos utilize oocyte-donated RNAs until they become capable of producing RNAs through embryonic genome activation (EGA). The sperm's influence over pre-EGA RNA content of embryos remains unknown. Recent studies have revealed that sperm donate non-genomic components upon fertilization. Thus, sperm may also contribute to RNA presence in pre-EGA embryos. The first objective of this study was to investigate whether male fertility status is associated with the RNAs present in the bovine embryo prior to EGA. A total of 65 RNAs were found to be differentially expressed between 2-4 cell bovine embryos derived from high and low fertility sires. Expression patterns were confirmed for protein phosphatase 1 regulatory subunit 36 (PPP1R36) and ataxin 2 like (ATXN2L) in three new biological replicates. The knockdown of ATXN2L led to a 22.9% increase in blastocyst development. The second objective of this study was to characterize the parental origin of RNAs present in pre-EGA embryos. Results revealed 472 sperm-derived RNAs, 2575 oocyte-derived RNAs, 2675 RNAs derived from both sperm and oocytes, and 663 embryo-exclusive RNAs. This study uncovers an association of male fertility with developmentally impactful RNAs in 2-4 cell embryos. This study also provides an initial characterization of paternally-contributed RNAs to pre-EGA embryos. Furthermore, a subset of 2-4 cell embryo-specific RNAs was identified.
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Affiliation(s)
- Nicole Gross
- University of Wisconsin, Department of Animal Sciences, Madison, WI, 53706, USA
| | | | | | - Hasan Khatib
- University of Wisconsin, Department of Animal Sciences, Madison, WI, 53706, USA.
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Pang CY, Bai MZ, Zhang C, Chen J, Lu XR, Deng TX, Ma XY, Duan AQ, Liang SS, Huang YQ, Xiu Z, Liang XW. Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo. PeerJ 2019; 7:e8185. [PMID: 31824777 PMCID: PMC6894430 DOI: 10.7717/peerj.8185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/10/2019] [Indexed: 12/03/2022] Open
Abstract
Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
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Affiliation(s)
- Chun-Ying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Ming-Zhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Junhui Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Xing-Rong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Ting-Xian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Xiao-Ya Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - An-Qin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Sha-Sha Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Yun-Qi Huang
- Shandong Agricultural University, Taian, PR China
| | - Zhihui Xiu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Xian-Wei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
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Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
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Adult Pgf -/- mice behaviour and neuroanatomy are altered by neonatal treatment with recombinant placental growth factor. Sci Rep 2019; 9:9285. [PMID: 31243296 PMCID: PMC6594955 DOI: 10.1038/s41598-019-45824-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/12/2019] [Indexed: 12/20/2022] Open
Abstract
Offspring of preeclamptic pregnancies have cognitive alterations. Placental growth factor (PGF), is low in preeclampsia; reduced levels may affect brain development. PGF-null mice differ from normal congenic controls in cerebrovasculature, neuroanatomy and behavior. Using brain imaging and behavioral testing, we asked whether developmentally asynchronous (i.e. neonatal) PGF supplementation alters the vascular, neuroanatomic and/or behavioral status of Pgf−/− mice at adulthood. C57BL/6-Pgf−/− pups were treated intraperitoneally on postnatal days 1–10 with vehicle or PGF at 10 pg/g, 70 pg/g or 700 pg/g. These mice underwent behavioral testing and perfusion for MRI and analysis of retinal vasculature. A second cohort of vehicle- or PGF-treated mice was perfused for micro-CT imaging. 10 pg/g PGF-treated mice exhibited less locomotor activity and greater anxiety-like behavior relative to vehicle-treated mice. Depressive-like behavior showed a sex-specific, dose-dependent decrease and was lowest in 700 pg/g PGF-treated females relative to vehicle-treated females. Spatial learning did not differ. MRI revealed smaller volume of three structures in the 10 pg/g group, larger volume of seven structures in the 70 pg/g group and smaller volume of one structure in the 700 pg/g group. No cerebral or retinal vascular differences were detected. Overall, neonatal PGF replacement altered behavior and neuroanatomy of adult Pgf−/− mice.
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Hu B, Zheng L, Long C, Song M, Li T, Yang L, Zuo Y. EmExplorer: a database for exploring time activation of gene expression in mammalian embryos. Open Biol 2019; 9:190054. [PMID: 31164042 PMCID: PMC6597754 DOI: 10.1098/rsob.190054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding early development offers a striking opportunity to investigate genetic disease, stem cell and assisted reproductive technology. Recent advances in high-throughput sequencing technology have led to the rising influx of omics data, which have rapidly boosted our understanding of mammalian developmental mechanisms. Here, we review the database EmExplorer (a database for exploring time activation of gene expression in mammalian embryos), which systematically organizes the genes from development-related pathways, and which we have already established and continue to update it. The current version of EmExplorer incorporates over 26 000 genes obtained from 306 functional pathways in five species. The function annotations of development-related genes were also integrated into EmExplorer. To facilitate data extraction, the database also contains the following information. (i) The dynamic expression values for each development stage are matched to the corresponding genes. (ii) A two-layer search tool which supports multi-option searching, such as by official symbol, pathway name and function annotation. The returned entries can directly link to the analysis results for the corresponding gene or pathway in the analysis module. (iii) The analysis module provides different gene comparisons at the multi-species level and functional pathway level, which shows the species specificity and stage specificity at the gene or pathway level. (iv) The analysis based on the hypergeometric distribution test reveals the enrichment of gene functions at a particular stage of one organism's pathway. (v) The browser is designed for users with ambiguous searching goals and greatly helps new users to get a general idea of the contents of the database. (vi) The experimentally validated pathways are manually curated and shown on the home page. EmExplorer will be helpful for elucidating early developmental mechanisms and exploring time activation genes. EmExplorer is freely available at http://bioinfor.imu.edu.cn/emexplorer.
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Affiliation(s)
- Bosu Hu
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Lei Zheng
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Chunshen Long
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Mingmin Song
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Tao Li
- 2 College of Life Sciences, Inner Mongolia Agricultural University , Hohhot 010018 , People's Republic of China
| | - Lei Yang
- 3 College of Bioinformatics Science and Technology, Harbin Medical University , Harbin 150081 , People's Republic of China
| | - Yongchun Zuo
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
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Feng M, Dang N, Bai Y, Wei H, Meng L, Wang K, Zhao Z, Chen Y, Gao F, Chen Z, Li L, Zhang S. Differential expression profiles of long non‑coding RNAs during the mouse pronuclear stage under normal gravity and simulated microgravity. Mol Med Rep 2018; 19:155-164. [PMID: 30483791 PMCID: PMC6297735 DOI: 10.3892/mmr.2018.9675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 10/19/2018] [Indexed: 01/22/2023] Open
Abstract
Pronuclear migration, which is the initial stage of embryonic development and the marker of zygote formation, is a crucial process during mammalian preimplantation embryonic development. Recent studies have revealed that long non-coding RNAs (lncRNAs) serve an important role in early embryonic development. However, the functional regulation of lncRNAs in this process has yet to be elucidated, largely due to the difficulty of assessing gene expression alterations during the very short time in which pronuclear migration occurs. It has previously been reported that migration of the pronucleus of a zygote can be obstructed by simulated microgravity. To investigate pronuclear migration in mice, a rotary cell culture system was employed, which generates simulated microgravity, in order to interfere with murine pronuclear migration. Subsequently, lncRNA sequencing was performed to investigate the mechanism underlying this process. In the present study, a comprehensive analysis of lncRNA profile during the mouse pronuclear stage was conducted, in which 3,307 lncRNAs were identified based on single-cell RNA sequencing data. Furthermore, 52 lncRNAs were identified that were significantly differentially expressed. Subsequently, 10 lncRNAs were selected for validation by reverse transcription-quantitative polymerase chain reaction, in which the same relative expression pattern was observed. The results revealed that 12 lncRNAs (lnc006745, lnc007956, lnc013100, lnc013782, lnc017097, lnc019869, lnc025838, lnc027046, lnc005454, lnc007956, lnc019410 and lnc019607), with tubulin β 4B class IVb or actinin α 4 as target genes, may be associated with the expression of microtubule and microfilament proteins. Binding association was confirmed using a dual-luciferase reporter assay. Finally, Gene Ontology analysis revealed that the target genes of the differentially expressed lncRNAs participated in cellular processes associated with protein transport, binding, catalytic activity, membrane-bounded organelle, protein complex and the cortical cytoskeleton. These findings suggested that these lncRNAs may be associated with migration of the mouse pronucleus.
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Affiliation(s)
- Meiying Feng
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Nannan Dang
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Yinshan Bai
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Hengxi Wei
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Li Meng
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Kai Wang
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Zhihong Zhao
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Yun Chen
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Fenglei Gao
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Zhilin Chen
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Li Li
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
| | - Shouquan Zhang
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, P.R. China
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Biase FH, Wu Q, Calandrelli R, Rivas-Astroza M, Zhou S, Chen Z, Zhong S. Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. iScience 2018; 7:16-29. [PMID: 30267678 PMCID: PMC6135740 DOI: 10.1016/j.isci.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 08/01/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell transcriptomes. We triggered lineage tracking in each blastomere at the 2-cell stage, observed microscopically inequivalent contributions of the progeny to the two embryonic poles at the blastocyst stage, and analyzed every single cell at either 4- or 8-cell stage with deep paired-end sequencing of full-length transcripts. Although lineage difference was not marked unequivocally at a single-gene level, it became clear when the transcriptome was analyzed as a whole. Moreover, several groups of novel transcript isoforms with embedded repeat sequences exhibited lineage difference, suggesting a possible link between DNA demethylation and cell fate decision. Rainbow-seq bridged a critical gap between division history and single-cell RNA-seq assays.
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Affiliation(s)
- Fernando H Biase
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Qiuyang Wu
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA; Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Shuigeng Zhou
- School of Computer Science, Fudan University, Shanghai 200433, China
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA.
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