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Ruebel ML, Zambelli F, Schall PZ, Barragan M, VandeVoort CA, Vassena R, Latham KE. Shared aspects of mRNA expression associated with oocyte maturation failure in humans and rhesus monkeys indicating compromised oocyte quality. Physiol Genomics 2021; 53:137-149. [PMID: 33554756 DOI: 10.1152/physiolgenomics.00155.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Oocyte maturation failure observed in assisted reproduction technology (ART) cycles can limit the number of quality oocytes obtained and present a pronounced barrier for some patients. The potential exists to use unmatured oocytes for ART through in vitro maturation. Understanding the molecular basis of oocyte maturation failure is pertinent to minimizing this loss of oocytes and considerations of whether such oocytes can be used safely for ART. We identified shared transcriptome abnormalities for rhesus monkey and human failed-to-mature (FTM) oocytes relative to healthy matured MII stage oocytes. We discovered that, although the number of shared affected genes was comparatively small, FTM oocytes in both species shared effects for several pathways and functions, including predicted activation of oxidative phosphorylation (OxPhos) with additional effects on mitochondrial function, lipid metabolism, transcription, nucleotide excision repair, endoplasmic reticulum stress, unfolded protein response, and cell viability. RICTOR emerged as a prominent upstream regulator with predicted inhibition across all analyses. Alterations in KDM5A, MTOR, MTORC1, INSR, CAB39L, and STK11 activities were implicated along with RICTOR in modulating mitochondrial activity and OxPhos. Defects in cell cycle progression were not a prominent feature of FTM oocytes. These results identify a common set of transcriptome abnormalities associated with oocyte maturation failure. While our results do not demonstrate causality, they indicate that fundamental aspects of cellular function are abnormal in FTM oocytes and raise significant concerns about the potential risks of using FTM oocytes for ART.
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Affiliation(s)
- Meghan L Ruebel
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | | | - Peter Z Schall
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | | | - Catherine A VandeVoort
- California National Primate Research Center, University of California, Davis, California.,Department of Obstetrics and Gynecology, University of California, Davis, California
| | | | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
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52
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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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53
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Assisted oocyte activation effects on the morphokinetic pattern of derived embryos. J Assist Reprod Genet 2021; 38:531-537. [PMID: 33405007 DOI: 10.1007/s10815-020-02025-9] [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: 07/17/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE Assisted oocyte activation (AOA) can restore fertilization rates after IVF/ICSI cycles with fertilization failure. AOA is an experimental technique, and its downstream effects remain poorly characterized. Clarifying the relationship between AOA and embryo, morphokinetics could offer complementary insights into the quality and viability of the embryos obtained with this technique. The aim of this study is to compare the preimplantation morphokinetic development of embryos derived from ICSI-AOA (experimental group) vs. ICSI cycles (control group). METHODS A retrospective cohort study was carried out with 141 embryos from fresh oocyte donation cycles performed between 2013 and 2017; 41 embryos were derived from 7 ICSI-AOA cycles and 100 embryos from 18 ICSI cycles. Morphokinetic development of all embryos was followed using a time-lapse system. RESULTS We show that embryos from both groups develop similarly for most milestones, with the exception of the time of second polar body extrusion (tPB2) and the time to second cell division (t3). CONCLUSIONS We conclude that ionomycin mediated AOA does not seem to affect the morphokinetic pattern of preimplantation embryo development, despite the alterations found in tPB2 and t3, which could directly reflect the use of a Ca2+ ionophore as a transient and quick non-physiologic increase of free intracytoplasmic Ca2+.
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54
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Timofeeva A, Drapkina Y, Fedorov I, Chagovets V, Makarova N, Shamina M, Kalinina E, Sukhikh G. Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage. Int J Mol Sci 2020; 21:ijms21249399. [PMID: 33321810 PMCID: PMC7764539 DOI: 10.3390/ijms21249399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
As part of the optimization of assisted reproductive technology programs, the aim of the study was to identify key small noncoding RNA (sncRNA) molecules that participate in maternal-to-zygotic transition and determine development potential and competence to form a healthy fetus. Small RNA deep sequencing followed by quantitative real-time RT-PCR was used to profile sncRNAs in 50 samples of spent culture medium from morula with different development potentials (no potential (degradation/developmental arrest), low potential (poor-quality blastocyst), and high potential (good/excellent quality blastocyst capable of implanting and leading to live birth)) obtained from 27 subfertile couples who underwent in vitro fertilization. We have shown that the quality of embryos at the morula stage is determined by secretion/uptake rates of certain sets of piRNAs and miRNAs, namely hsa_piR_011291, hsa_piR_019122, hsa_piR_001311, hsa_piR_015026, hsa_piR_015462, hsa_piR_016735, hsa_piR_019675, hsa_piR_020381, hsa_piR_020485, hsa_piR_004880, hsa_piR_000807, hsa-let-7b-5p, and hsa-let-7i-5p. Predicted gene targets of these sncRNAs included those globally decreased at the 8-cell–morula–blastocyst stage and critical to early embryo development. We show new original data on sncRNA profiling in spent culture medium from morula with different development potential. Our findings provide a view of a more complex network that controls human embryogenesis at the pre-implantation stage. Further research is required using reporter analysis to experimentally confirm interactions between identified sncRNA/gene target pairs.
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55
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Zhao C, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W, Zhang Y. A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos. Genome Biol 2020; 21:277. [PMID: 33198783 PMCID: PMC7667739 DOI: 10.1186/s13059-020-02189-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored. RESULTS Here, we present MethylTransition, a novel DNA methylation state transition model, for characterizing methylation changes during one or a few cell cycles at single-cell resolution. MethylTransition involves the creation of a transition matrix comprising three parameters that represent the probabilities of DNA methylation-modifying activities in order to link the methylation states before and after a cell cycle. We apply MethylTransition to single-cell DNA methylome data from human pre-implantation embryogenesis and elucidate that the DNA methylation heterogeneity that emerges at promoters during this process is largely an intrinsic output of a program with unique probabilities of DNA methylation-modifying activities. Moreover, we experimentally validate the effect of the initial DNA methylation on expression heterogeneity in pre-implantation mouse embryos. CONCLUSIONS Our study reveals the programmed DNA methylation heterogeneity during human pre-implantation embryogenesis through a novel mathematical model and provides valuable clues for identifying the driving factors of the first cell fate determination during this process.
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Affiliation(s)
- Chengchen Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Naiqian Zhang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209 China
| | - Yalin Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Nuermaimaiti Tuersunjiang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
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Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation. Nat Commun 2020; 11:4654. [PMID: 32943640 PMCID: PMC7498599 DOI: 10.1038/s41467-020-18508-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/24/2020] [Indexed: 11/08/2022] Open
Abstract
The shift from maternal to embryonic control is a critical developmental milestone in preimplantation development. Widespread transcriptomic and epigenetic remodeling facilitate this transition from terminally differentiated gametes to totipotent blastomeres, but the identity of transcription factors (TF) and genomic elements regulating embryonic genome activation (EGA) are poorly defined. The timing of EGA is species-specific, e.g., the timing of murine and human EGA differ significantly. To deepen our understanding of mammalian EGA, here we profile changes in open chromatin during bovine preimplantation development. Before EGA, open chromatin is enriched for maternal TF binding, similar to that observed in humans and mice. During EGA, homeobox factor binding becomes more prevalent and requires embryonic transcription. A cross-species comparison of open chromatin during preimplantation development reveals strong similarity in the regulatory circuitry underlying bovine and human EGA compared to mouse. Moreover, TFs associated with murine EGA are not enriched in cattle or humans, indicating that cattle may be a more informative model for human preimplantation development than mice. Preimplantation embryos undergo extensive transcriptomic and epigenomic remodeling. Here the authors assay open chromatin in bovine oocytes, embryos, and embryonic stem cells, and compare the transcriptomes and epigenomes of cattle, human and mouse embryos, revealing species-specific regulation of genome activation.
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57
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Haig D, Mainieri A. The Evolution of Imprinted microRNAs and Their RNA Targets. Genes (Basel) 2020; 11:genes11091038. [PMID: 32899179 PMCID: PMC7564603 DOI: 10.3390/genes11091038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/19/2022] Open
Abstract
Mammalian genomes contain many imprinted microRNAs. When an imprinted miRNA targets an unimprinted mRNA their interaction may have different fitness consequences for the loci encoding the miRNA and mRNA. In one possible outcome, the mRNA sequence evolves to evade regulation by the miRNA by a simple change of target sequence. Such a response is unavailable if the targeted sequence is strongly constrained by other functions. In these cases, the mRNA evolves to accommodate regulation by the imprinted miRNA. These evolutionary dynamics are illustrated using the examples of the imprinted C19MC cluster of miRNAs in primates and C2MC cluster in mice that are paternally expressed in placentas. The 3′ UTR of PTEN, a gene with growth-related and metabolic functions, appears to be an important target of miRNAs from both clusters.
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58
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Vergaro P, Tiscornia G, Zambelli F, Rodríguez A, Santaló J, Vassena R. Trophoblast attachment to the endometrial epithelium elicits compartment-specific transcriptional waves in an in-vitro model. Reprod Biomed Online 2020; 42:26-38. [PMID: 33051136 DOI: 10.1016/j.rbmo.2020.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 01/02/2023]
Abstract
RESEARCH QUESTION Which are the early compartment-specific transcriptional responses of the trophoblast and the endometrial epithelium throughout early attachment during implantation? DESIGN An endometrial epithelium proxy (cell line Ishikawa) was co-cultured with spheroids of a green fluorescent protein (GFP) expressing trophoblast cell line (JEG-3). After 0, 8 and 24 h of co-culture, the compartments were sorted by fluorescence-activated cell sorting; GFP+ (trophoblast), GFP- (epithelium) and non-co-cultured control populations were analysed (in triplicate) by RNA-seq and gene set enrichment analysis (GSEA). RESULTS Trophoblast challenge induced a wave of transcriptional changes in the epithelium that resulted in 295 differentially regulated genes involving epithelial to mesenchymal transition (EMT), cell movement, apoptosis, hypoxia, inflammation, allograft rejection, myogenesis and cell signalling at 8 h. Interestingly, many of the enriched pathways were subsequently de-enriched by 24 h (i.e. EMT, cell movement, allograft rejection, myogenesis and cell signalling). In the trophoblast, the co-culture induced more transcriptional changes and regulation of a variety of pathways. A total of 1247 and 481 genes were differentially expressed after 8 h and from 8 to 24 h, respectively. Angiogenesis and hypoxia were over-represented at both stages, while EMT and cell signalling only were at 8 h; from 8 to 24 h, inflammation and oestrogen response were enriched, while proliferation was under-represented. CONCLUSIONS Successful attachment produced a series of dynamic changes in gene expression, characterized by an overall early and transient transcriptional up-regulation in the receptive epithelium, in contrast to a more dynamic transcriptional response in the trophoblast.
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Affiliation(s)
- Paula Vergaro
- Clínica EUGIN Barcelona, Spain; Facultat de Biociències, Unitat de Biologia Cel•lular, Universitat Autònoma de Barcelona, Spain
| | - Gustavo Tiscornia
- Clínica EUGIN Barcelona, Spain; Centro de Investigação em Biomedicina (CBMR), Universidade do Algarve, Portugal
| | | | | | - Josep Santaló
- Facultat de Biociències, Unitat de Biologia Cel•lular, Universitat Autònoma de Barcelona, Spain
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Karpukhina A, Vassetzky Y. DUX4, a Zygotic Genome Activator, Is Involved in Oncogenesis and Genetic Diseases. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420030078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Williams K, Johnson MH. Adapting the 14-day rule for embryo research to encompass evolving technologies. REPRODUCTIVE BIOMEDICINE & SOCIETY ONLINE 2020; 10:1-9. [PMID: 32154395 PMCID: PMC7052500 DOI: 10.1016/j.rbms.2019.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 05/04/2023]
Abstract
We consider the scientific evidence that research on in-vitro development of embryos beyond 14 days is necessary. We then examine potential new developments in the use of stem cells to make embryoids or synthetic human entities with embryo-like features, and consider whether they also require legal control. Next, we consider the arguments advanced against extending the 14-day period during which research on human embryos is currently permitted, and find none of them to be convincing. We end by proposing a new objective limit that could serve as a mechanism for regulating the use of embryos for research in vitro.
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Affiliation(s)
- Kate Williams
- St John’s College, University of Cambridge, Cambridge, UK
| | - Martin H. Johnson
- School of Anatomy, Department of Physiology, Development and Neuroscience, Downing College, University of Cambridge, Cambridge, UK
- Corresponding author.
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Coticchio G, Lagalla C, Sturmey R, Pennetta F, Borini A. The enigmatic morula: mechanisms of development, cell fate determination, self-correction and implications for ART. Hum Reprod Update 2020; 25:422-438. [PMID: 30855681 DOI: 10.1093/humupd/dmz008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/20/2019] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Assisted reproduction technology offers the opportunity to observe the very early stages of human development. However, due to practical constraints, for decades morphological examination of embryo development has been undertaken at a few isolated time points at the stages of fertilisation (Day 1), cleavage (Day 2-3) and blastocyst (Day 5-6). Rather surprisingly, the morula stage (Day 3-4) has been so far neglected, despite its involvement in crucial cellular processes and developmental decisions. OBJECTIVE AND RATIONALE The objective of this review is to collate novel and unsuspected insights into developmental processes occurring during formation of the morula, highlighting the key importance of this stage for a better understanding of preimplantation development and an improvement of ART. SEARCH METHODS PubMed was used to search the MEDLINE database for peer-reviewed English-language original articles and reviews concerning the morula stage in mammals. Searches were performed by adopting 'embryo', 'morula', 'compaction', 'cell fate' and 'IVF/assisted reproduction' as main terms, in association with other keywords expressing concepts relevant to the subject (e.g. cell polarity). The most relevant publications, i.e. those concerning major phenomena occurring during formation of the morula in established experimental models and the human species, were assessed and discussed critically. OUTCOMES Novel live cell imaging technologies and cell biology studies have extended our understanding of morula formation as a key stage for the development of the blastocyst and determination of the inner cell mass (ICM) and the trophectoderm (TE). Cellular processes, such as dynamic formation of filopodia and cytoskeleton-mediated zippering cell-to-cell interactions, intervene to allow cell compaction (a geometrical requisite essential for development) and formation of the blastocoel, respectively. At the same time, differential orientation of cleavage planes, cell polarity and cortical tensile forces interact and cooperate to position blastomeres either internally or externally, thereby influencing their cellular fate. Recent time lapse microscopy (TLM) observations also suggest that in the human the process of compaction may represent an important checkpoint for embryo viability, through which chromosomally abnormal blastomeres are sensed and eliminated by the embryo. WIDER IMPLICATIONS In clinical embryology, the morula stage has been always perceived as a 'black box' in the continuum of preimplantation development. This has dictated its virtual exclusion from mainstream ART procedures. Recent findings described in this review indicate that the morula, and the associated process of compaction, as a crucial stage not only for the formation of the blastocyst, but also for the health of the conceptus. This understanding may open new avenues for innovative approaches to embryo manipulation, assessment and treatment.
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Affiliation(s)
| | - Cristina Lagalla
- 9.Baby, Family and Fertility Center, Via Dante 15, Bologna, Italy
| | - Roger Sturmey
- Centre for Cardiovascular Metabolic Research, Hull York Medical School, University of Hull, Hull, United Kingdom
| | | | - Andrea Borini
- 9.Baby, Family and Fertility Center, Via Dante 15, Bologna, Italy
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Next-generation sequencing analysis of each blastomere in good-quality embryos: insights into the origins and mechanisms of embryonic aneuploidy in cleavage-stage embryos. J Assist Reprod Genet 2020; 37:1711-1718. [PMID: 32445153 DOI: 10.1007/s10815-020-01803-9] [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: 09/25/2019] [Accepted: 04/28/2020] [Indexed: 01/06/2023] Open
Abstract
PURPOSE To explore the whole-chromosome status, origins, and mechanisms of chromosomal abnormalities in good-quality cleavage embryos using multiple annealing and looping-based amplification cycle (MALBAC) sequencing. METHODS The embryos studied came from7 patients (maternal aged 26-35) who had healthy birth from the same IVF cycles. These 21 frozen day 3 good-quality embryos were thawed and disaggregated into individual blastomere. Each blastomere was collected and analyzed by MALBAC sequencing. RESULTS Conclusive results were obtained from a high percentage of blastomeres (95.3%). A total of 46.6% of blastomeres were diploid, 53.4% were abnormal, and 28.0% had complex aneuploidy. Out of 21 embryos, 3 (14.3%) were normal and 18 (85.7%) were mosaics, showing the occurrence of mitotic errors; aneuploidy was confirmed in all cells of 4 of the 18 embryos, which showed the coexistence of meiotic errors. Conclusive results were obtained from all blastomeres of 15 embryos (71.4%, 15/21), which enabled us to reconstruct the cell lineage on the basis of the chromosomal content of the blastomeres in each division. There were 9 mitotic errors (8.7%, 9/103): nondisjunction accounted for 88.9% (8/9), and endoreplication accounted for 11.1% (1/9). CONCLUSIONS In good-quality embryos, there was a high rate and diverse array of chromosomal abnormalities. Morphological evaluation does not appear to assist in the reduction in meiotic errors from parental origins. Mitotic errors were common, and nondisjunction was found to be the main mechanism causing malsegregation during the cleavage divisions.
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Ivanova E, Canovas S, Garcia-Martínez S, Romar R, Lopes JS, Rizos D, Sanchez-Calabuig MJ, Krueger F, Andrews S, Perez-Sanz F, Kelsey G, Coy P. DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes. Clin Epigenetics 2020; 12:64. [PMID: 32393379 PMCID: PMC7216732 DOI: 10.1186/s13148-020-00857-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended such analysis to two key livestock species, the pig and the cow. We generated genome-wide DNA methylation and whole-transcriptome datasets from gametes to blastocysts in both species. In oocytes from both species, a distinctive bimodal methylation landscape is present, with hypermethylated domains prevalent over hypomethylated domains, similar to human, while in the mouse the proportions are reversed. An oocyte-like pattern of methylation persists in the cleavage stages, albeit with some reduction in methylation level, persisting to blastocysts in cow, while pig blastocysts have a highly hypomethylated landscape. In the pig, there was evidence of transient de novo methylation at the 8–16 cell stages of domains unmethylated in oocytes, revealing a complex dynamic of methylation reprogramming. The methylation datasets were used to identify germline differentially methylated regions (gDMRs) of known imprinted genes and for the basis of detection of novel imprinted loci. Strikingly in the pig, we detected a consistent reduction in gDMR methylation at the 8–16 cell stages, followed by recovery to the blastocyst stage, suggesting an active period of imprint stabilization in preimplantation embryos. Transcriptome analysis revealed absence of expression in oocytes of both species of ZFP57, a key factor in the mouse for gDMR methylation maintenance, but presence of the alternative imprint regulator ZNF445. In conclusion, our study reveals species differences in DNA methylation reprogramming and suggests that porcine or bovine models may be closer to human in key aspects than in the mouse model.
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Affiliation(s)
- Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Sebastian Canovas
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Soledad Garcia-Martínez
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | - Raquel Romar
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Jordana S Lopes
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | | | | | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Fernando Perez-Sanz
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Pilar Coy
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain. .,Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain.
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Schall PZ, Ruebel ML, Midic U, VandeVoort CA, Latham KE. Temporal patterns of gene regulation and upstream regulators contributing to major developmental transitions during Rhesus macaque preimplantation development. Mol Hum Reprod 2020; 25:111-123. [PMID: 30698740 DOI: 10.1093/molehr/gaz001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/11/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
The preimplantation period of life in mammals encompasses a tremendous amount of restructuring and remodeling of the embryonic genome and reprogramming of gene expression. These vast changes support metabolic activation and cellular processes that drive early cleavage divisions and enable the creation of the earliest primitive cell lineages. A major question in mammalian embryology is how such vast, sweeping changes in gene expression are orchestrated, so that changes in gene expression are exactly appropriate to meet the developmental needs of the embryo over time. Using the rhesus macaque as an experimentally tractable model species closely related to the human, we combined high quality RNA-seq libraries, in-depth sequencing and advanced systems analysis to discover the underlying mechanisms that drive major changes in gene regulation during preimplantation development. We identified the major changes in mRNA population and the biological pathways and processes impacted by those changes. Most importantly, we identified 24 key upstream regulators that are themselves modulated during development and that are associated with the regulation of over 1000 downstream genes. Through their roles in extensive gene networks, these 24 upstream regulators are situated to either drive major changes in target gene expression or modify the cellular environment in which other genes function, thereby directing major developmental transitions in the preimplantation embryo. The data presented here highlight some of the specific molecular features that likely drive preimplantation development in a nonhuman primate species and provides an extensive database for novel hypothesis-driven studies.
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Affiliation(s)
- Peter Z Schall
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA.,Comparative Medicine and Integrative Biology Program, Michigan State University, East Lansing, MI, USA
| | - Meghan L Ruebel
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Uros Midic
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
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Chromosome Missegregation in Single Human Oocytes Is Related to the Age and Gene Expression Profile. Int J Mol Sci 2020; 21:ijms21061934. [PMID: 32178390 PMCID: PMC7139522 DOI: 10.3390/ijms21061934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
The growing trend for women to postpone childbearing has resulted in a dramatic increase in the incidence of aneuploid pregnancies. Despite the importance to human reproductive health, the events precipitating female age-related meiotic errors are poorly understood. To gain new insight into the molecular basis of age-related chromosome missegregation in human oocytes, we combined the transcriptome profiles of twenty single oocytes (derived from females divided into two groups according to age <35 and ≥35 years) with their chromosome status obtained by array comparative genomic hybridization (aCGH). Furthermore, we compared the transcription profile of the single oocyte with the surrounding cumulus cells (CCs). RNA-seq data showed differences in gene expression between young and old oocytes. Dysregulated genes play a role in important biological processes such as gene transcription regulation, cytoskeleton organization, pathways related to RNA maturation and translation. The comparison of the transcription profile of the oocyte and the corresponding CCs highlighted the differential expression of genes belonging to the G protein-coupled receptor superfamily. Finally, we detected the loss of a X chromosome in two oocytes derived from women belonging to the ≥35 years age group. These aneuploidies may be caused by the detriment of REEP4, an endoplasmic reticulum protein, in women aged ≥35 years. Here we gained new insight into the complex regulatory circuit between the oocyte and the surrounding CCs and uncovered a new putative molecular basis of age-related chromosome missegregation in human oocytes.
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66
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Srinivasan R, Nady N, Arora N, Hsieh LJ, Swigut T, Narlikar GJ, Wossidlo M, Wysocka J. Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage. SCIENCE ADVANCES 2020; 6:eaaz9115. [PMID: 32219172 PMCID: PMC7083622 DOI: 10.1126/sciadv.aaz9115] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/02/2020] [Indexed: 05/07/2023]
Abstract
Zinc finger protein Zscan4 is selectively expressed in mouse two-cell (2C) embryos undergoing zygotic genome activation (ZGA) and in a rare subpopulation of embryonic stem cells with 2C-like features. Here, we show that Zscan4 specifically recognizes a subset of (CA)n microsatellites, repeat sequences prone to genomic instability. Zscan4-associated microsatellite regions are characterized by low nuclease sensitivity and high histone occupancy. In vitro, Zscan4 binds nucleosomes and protects them from disassembly upon torsional strain. Furthermore, Zscan4 depletion leads to elevated DNA damage in 2C mouse embryos in a transcription-dependent manner. Together, our results identify Zscan4 as a DNA sequence-dependent microsatellite binding factor and suggest a developmentally regulated mechanism, which protects fragile genomic regions from DNA damage at a time of embryogenesis associated with high transcriptional burden and genomic stress.
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Affiliation(s)
- Rajini Srinivasan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nataliya Nady
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura J. Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mark Wossidlo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Cell and Developmental Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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67
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Wen L, Liu Q, Xu J, Liu X, Shi C, Yang Z, Zhang Y, Xu H, Liu J, Yang H, Huang H, Qiao J, Tang F, Chen ZJ. Recent advances in mammalian reproductive biology. SCIENCE CHINA. LIFE SCIENCES 2020; 63:18-58. [PMID: 31813094 DOI: 10.1007/s11427-019-1572-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023]
Abstract
Reproductive biology is a uniquely important topic since it is about germ cells, which are central for transmitting genetic information from generation to generation. In this review, we discuss recent advances in mammalian germ cell development, including preimplantation development, fetal germ cell development and postnatal development of oocytes and sperm. We also discuss the etiologies of female and male infertility and describe the emerging technologies for studying reproductive biology such as gene editing and single-cell technologies.
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Affiliation(s)
- Lu Wen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qiang Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingjing Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Xixi Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Chaoyi Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Zuwei Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Yili Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Hong Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Hefeng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Zi-Jiang Chen
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250021, China.
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68
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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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A. Lea R, K. Niakan K. Human germline genome editing. Nat Cell Biol 2019; 21:1479-1489. [DOI: 10.1038/s41556-019-0424-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/25/2019] [Indexed: 12/14/2022]
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Warrier S, Taelman J, Tilleman L, Van der Jeught M, Duggal G, Lierman S, Popovic M, Van Soom A, Peelman L, Van Nieuwerburgh F, Deforce D, Chuva de Sousa Lopes SM, De Sutter P, Heindryckx B. Transcriptional landscape changes during human embryonic stem cell derivation. Mol Hum Reprod 2019; 24:543-555. [PMID: 30239859 DOI: 10.1093/molehr/gay039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/14/2018] [Indexed: 01/06/2023] Open
Abstract
STUDY QUESTION What are the transcriptional changes occurring during the human embryonic stem cell (hESC) derivation process, from the inner cell mass (ICM) to post-ICM intermediate stage (PICMI) to hESC stage, that have downstream effects on pluripotency states and differentiation? SUMMARY ANSWER We reveal that although the PICMI is transcriptionally similar to the hESC profile and distinct from ICM, it exhibits upregulation of primordial germ cell (PGC) markers, dependence on leukemia inhibitory factor (LIF) signaling, upregulation of naïve pluripotency-specific signaling networks and appears to be an intermediate switching point from naïve to primed pluripotency. WHAT IS KNOWN ALREADY It is currently known that the PICMI exhibits markers of early and late-epiblast stage. It is suggested that hESCs acquire primed pluripotency features due to the upregulation of post-implantation genes in the PICMI which renders them predisposed towards differentiation cues. Despite this current knowledge, the transcriptional landscape changes during hESC derivation from ICM to hESC and the effect of PICMI on pluripotent state is still not well defined. STUDY DESIGN, SIZE, DURATION To gain insight into the signaling mechanisms that may govern the ICM to PICMI to hESC transition, comparative RNA sequencing (RNA-seq) analysis was performed on preimplantation ICMs, PICMIs and hESCs in biological and technical triplicates (n = 3). PARTICIPANTS/MATERIALS, SETTING, AND METHODS Primed hESCs (XX) were maintained in feeder-free culture conditions on Matrigel for two passages and approximately 50 cells were collected in biological and technical triplicates (n = 3). For ICM sample collection, Day 3, frozen-thawed human embryos were cultured up to day five blastocyst stage and only good quality blastocysts were subjected to laser-assisted micromanipulation for ICM collection (n = 3). Next, day six expanded blastocysts were cultured on mouse embryonic fibroblasts and manual dissection was performed on the PICMI outgrowths between post-plating Day 6 and Day 10 (n = 3). Sequencing of these samples was performed on NextSeq500 and statistical analysis was performed using edgeR (false discovery rate (FDR) < 0.05). MAIN RESULTS AND THE ROLE OF CHANCE Comparative RNA-seq data analysis revealed that 634 and 560 protein-coding genes were significantly up and downregulated in hESCs compared to ICM (FDR < 0.05), respectively. Upon ICM to PICMI transition, 471 genes were expressed significantly higher in the PICMI compared to ICM, while 296 genes were elevated in the ICM alone (FDR < 0.05). Principle component analysis showed that the ICM was completely distinct from the PICMI and hESCs while the latter two clustered in close proximity to each other. Increased expression of E-CADHERIN1 (CDH1) in ICM and intermediate levels in the PICMI was observed, while CDH2 was higher in hESCs, suggesting a role of extracellular matrix components in facilitating pluripotency transition during hESC derivation. The PICMI also showed regulation of naïve-specific LIF and bone morphogenetic protein signaling, differential regulation of primed pluripotency-specific fibroblast growth factor and NODAL signaling pathway components, upregulation of phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway (PI3K/AKT/mTORC), as well as predisposition towards the germ cell lineage, further confirmed by gene ontology analysis. Hence, the data suggest that the PICMI may serve as an intermediate pluripotency stage which, when subjected to an appropriate culture niche, could aid in enhancing naïve hESC derivation and germ cell differentiation efficiency. LARGE-SCALE DATA Gene Expression Omnibus (GEO) Accession number GSE119378. LIMITATIONS, REASONS FOR CAUTION Owing to the limitation in sample availability, the sex of ICM and PICMI have not been taken into consideration. Obtaining cells from the ICM and maintaining them in culture is not feasible as it will hamper the formation of PICMI and hESC derivation. Single-cell quantitative real-time PCR on low ICM and PICMI cell numbers, although challenging due to limited availability of human embryos, will be advantageous to further corroborate the RNA-seq data on transcriptional changes during hESC derivation process. WIDER IMPLICATIONS OF THE FINDINGS We elucidate the dynamics of transcriptional network changes from the naïve ICM to the intermediate PICMI stage and finally the primed hESC lines. We provide an in-depth understanding of the PICMI and its role in conferring the type of pluripotent state which may have important downstream effects on differentiation, specifically towards the PGC lineage. This knowledge contributes to our limited understanding of the true nature of the human pluripotent state in vitro. STUDY FUNDING/COMPETING INTEREST(S) This research is supported by the Concerted Research Actions funding from Bijzonder Onderzoeksfonds University Ghent (BOF GOA 01G01112).The authors declare no conflict of interest.
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Affiliation(s)
- S Warrier
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - J Taelman
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - L Tilleman
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - M Van der Jeught
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - G Duggal
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium.,Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - S Lierman
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - M Popovic
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - A Van Soom
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - L Peelman
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - F Van Nieuwerburgh
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - D Deforce
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - S M Chuva de Sousa Lopes
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - P De Sutter
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
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Takahashi K, Ross PJ, Sawai K. The necessity of ZSCAN4 for preimplantation development and gene expression of bovine embryos. J Reprod Dev 2019; 65:319-326. [PMID: 31019155 PMCID: PMC6708851 DOI: 10.1262/jrd.2019-039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Zinc finger and SCAN domain containing 4 (Zscan4) is a gene that is specifically expressed during zygotic genome activation (ZGA) in mouse preimplantation embryos, and a
reduction of Zscan4 transcripts leads to developmental failure. In mouse embryonic stem cells (ESCs), Zscan4 is expressed transiently in as little as 1–5%
of the cell population. Zscan4 has also been shown to enhance the efficiency of mouse induced pluripotent stem cells (iPSCs) generation and their quality. Although ZSCAN4
plays important roles in murine embryos and stem cells, its expression and role in bovine embryos is unknown. This study examines ZSCAN4 transcripts in bovine embryos at
various developmental stages and attempts to elucidate the functions of ZSCAN4 during bovine preimplantation development. ZSCAN4 transcripts were found to be upregulated at
the 8- and 16-cell stages. We next attempted ZSCAN4 downregulation in bovine early embryos by RNA interference and evaluated developmental competency and transcripts levels
of genes involved in ZGA and iPSCs generation. Although the bovine embryos injected with ZSCAN4-siRNA could develop to the 8-cell stage, very few were developing beyond the
16-cell stage. PIWIL2 expression was reduced in ZSCAN4 downregulated embryos. It is possible that ZSCAN4 downregulated embryos fail to
regulate gene expression during ZGA. Our results indicate that ZSCAN4 is an important factor for the preimplantation development of bovine embryos.
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Affiliation(s)
- Kazuki Takahashi
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate 020-8550, Japan
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, CA 95616, U. S. A
| | - Ken Sawai
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate 020-8550, Japan.,Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan
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Roles of MicroRNAs in Establishing and Modulating Stem Cell Potential. Int J Mol Sci 2019; 20:ijms20153643. [PMID: 31349654 PMCID: PMC6696000 DOI: 10.3390/ijms20153643] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Early embryonic development in mammals, from fertilization to implantation, can be viewed as a process in which stem cells alternate between self-renewal and differentiation. During this process, the fates of stem cells in embryos are gradually specified, from the totipotent state, through the segregation of embryonic and extraembryonic lineages, to the molecular and cellular defined progenitors. Most of those stem cells with different potencies in vivo can be propagated in vitro and recapitulate their differentiation abilities. Complex and coordinated regulations, such as epigenetic reprogramming, maternal RNA clearance, transcriptional and translational landscape changes, as well as the signal transduction, are required for the proper development of early embryos. Accumulated studies suggest that Dicer-dependent noncoding RNAs, including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs), are involved in those regulations and therefore modulate biological properties of stem cells in vitro and in vivo. Elucidating roles of these noncoding RNAs will give us a more comprehensive picture of mammalian embryonic development and enable us to modulate stem cell potencies. In this review, we will discuss roles of miRNAs in regulating the maintenance and cell fate potential of stem cells in/from mouse and human early embryos.
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Abstract
Having been debated for many years, the presence and role of spermatozoal RNAs is resolving, and their contribution to development is now appreciated. Data from different species continue show that sperm contain a complex suite of coding and noncoding RNAs that play a role in an individual's life course. Mature sperm RNAs provide a retrospective of spermatogenesis, with their presence and abundance reflecting sperm maturation, fertility potential, and the paternal contribution to the developmental path the offspring may follow.Sperm RNAs delivered upon fertilization provide some of the initial contacts with the oocyte, directly confront the maternal with the paternal contribution as a prelude to genome consolidation. Following syngamy, early embryo development may in part be modulated by paternal RNAs that can include epidydimal passengers. This provides a direct path to relay an experience and then initiate a paternal response to the environment to the oocyte and beyond. Their epigenetic impact is likely felt prior to embryonic genome activation when the population of sperm delivered transcripts markedly changes. Here, we review the insights gained from sperm RNAs over the years, the subtypes, and the caveats of the RNAs described. We discuss the role of sperm RNAs in fertilization and embryo development, and their possible mechanism(s) influencing offspring phenotype. Approaches to meet the future challenges as the study of sperm RNAs continues, include, elucidating the potential mechanisms underlying how paternal allostatic load, the constant adaptation of health to external conditions, may be relayed by sperm RNAs to affect future generations.
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Affiliation(s)
- Marta Gòdia
- Animal Genomics Group, Center for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Cerdanyola del Vallès (Barcelona), Catalonia, Spain
| | - Grace Swanson
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan, USA
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74
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Gentsch GE, Owens NDL, Smith JC. The Spatiotemporal Control of Zygotic Genome Activation. iScience 2019; 16:485-498. [PMID: 31229896 PMCID: PMC6593175 DOI: 10.1016/j.isci.2019.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/07/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the midblastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal, and BMP signaling together generate most of the spatiotemporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.
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Affiliation(s)
- George E Gentsch
- Developmental Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK.
| | - Nick D L Owens
- Department of Stem Cell and Developmental Biology, Pasteur Institute, Paris 75015, France
| | - James C Smith
- Developmental Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK.
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75
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Aberkane A, Essahib W, Spits C, De Paepe C, Sermon K, Adriaenssens T, Mackens S, Tournaye H, Brosens JJ, Van de Velde H. Expression of adhesion and extracellular matrix genes in human blastocysts upon attachment in a 2D co-culture system. Mol Hum Reprod 2019; 24:375-387. [PMID: 29846687 DOI: 10.1093/molehr/gay024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/25/2018] [Indexed: 12/15/2022] Open
Abstract
STUDY QUESTION What are the changes in human embryos, in terms of morphology and gene expression, upon attachment to endometrial epithelial cells? SUMMARY ANSWER Apposition and adhesion of human blastocysts to endometrial epithelial cells are predominantly initiated at the embryonic pole and these steps are associated with changes in expression of adhesion and extracellular matrix (ECM) genes in the embryo. WHAT IS KNOWN ALREADY Both human and murine embryos have been co-cultured with Ishikawa cells, although embryonic gene expression associated with attachment has not yet been investigated in an in vitro implantation model. STUDY DESIGN, SIZE, DURATION Vitrified human blastocysts were warmed and co-cultured for up to 48 h with Ishikawa cells, a model cell line for receptive endometrial epithelium. PARTICIPANTS/MATERIALS, SETTING, METHODS Six days post-fertilization (6dpf) human embryos were co-cultured with Ishikawa cells for 12, 24 (7dpf) or 48 h (8dpf) and attachment rate and morphological development investigated. Expression of 84 adhesion and ECM genes was analysed by quantitative PCR. Immunofluorescence microscopy was used to assess the expression of three informative genes at the protein level. Data are reported on 145 human embryos. Mann-Whitney U was used for statistical analysis between two groups, with P < 0.05 considered significant. MAIN RESULTS AND THE ROLE OF CHANCE The majority of embryos attached to Ishikawa cells at the level of the polar trophectoderm; 41% of co-cultured embryos were loosely attached after 12 h and 86% firmly attached after 24 h. Outgrowth of hCG-positive embryonic cells at 8dpf indicated differentiation of trophectoderm into invasive syncytiotrophoblast. Gene expression analysis was performed on loosely attached and unattached embryos co-cultured with Ishikawa cells for 12 h. In contrast to unattached embryos, loosely attached embryos expressed THBS1, TNC, COL12A1, CTNND2, ITGA3, ITGAV and LAMA3 and had significantly higher CD44 and TIMP1 transcript levels (P = 0.014 and P = 0.029, respectively). LAMA3, THBS1 and TNC expressions were validated at the protein level in firmly attached 7dpf embryos. Thrombospondin 1 (THBS1) resided in the cytoplasm of embryonic cells whereas laminin subunit alpha 3 (LAMA3) and tenascin C (TNC) were expressed on the cell surface of trophectoderm cells. Incubation with a neutralizing TNC antibody did not affect the rate of embryo attachment or hCG secretion. LARGE SCALE DATA None. LIMITATIONS, REASONS FOR CAUTION This in vitro study made use of an endometrial adenocarcinoma cell line to mimic receptive luminal epithelium. Also, the number of embryos was limited. Contamination of recovered embryos with Ishikawa cells was unlikely based on their differential gene expression profiles. WIDER IMPLICATIONS OF THE FINDINGS Taken together, we provide a 'proof of concept' that initiation of the implantation process coincides with the induction of specific embryonic genes. Genome-wide expression profiling of a larger sample set may provide insights into the molecular embryonic pathways underlying successful or failed implantation. STUDY FUNDING AND COMPETING INTEREST(S) A.A. was supported by a grant from the 'Instituut voor Innovatie door Wetenschap en Technologie' (IWT, 121716, Flanders, Belgium). This work was supported by the 'Wetenschappelijk Fonds Willy Gepts' (WFWG G142 and G170, Universitair Ziekenhuis Brussel). The authors declare no conflict of interest.
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Affiliation(s)
- A Aberkane
- Research Group Reproduction and Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - W Essahib
- Research Group Reproduction and Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - C Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - C De Paepe
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - T Adriaenssens
- Research Group Follicle Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - S Mackens
- Research Group Reproduction and Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,Centre for Reproductive Medicine, Brussels University Hospital, Brussels, Belgium
| | - H Tournaye
- Centre for Reproductive Medicine, Brussels University Hospital, Brussels, Belgium
| | - J J Brosens
- Division of Biomedical Sciences, Clinical Science Research Laboratories, Warwick Medical School, University of Warwick, Coventry, UK.,Tommy's National Centre for Miscarriage Research, University Hospitals Coventry & Warwickshire, Coventry CV2 2DX, UK
| | - H Van de Velde
- Research Group Reproduction and Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,Centre for Reproductive Medicine, Brussels University Hospital, Brussels, Belgium
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76
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Madissoon E, Damdimopoulos A, Katayama S, Krjutškov K, Einarsdottir E, Mamia K, De Groef B, Hovatta O, Kere J, Damdimopoulou P. Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development. Sci Rep 2019; 9:8411. [PMID: 31182756 PMCID: PMC6557853 DOI: 10.1038/s41598-019-44882-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023] Open
Abstract
Pleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in cancer and growth. We discovered a de novo DNA motif containing a PLAG1 binding site in the promoters of genes activated during zygotic genome activation (ZGA) in human embryos. This motif was located within an Alu element in a region that was conserved in the murine B1 element. We show that maternally provided Plag1 is needed for timely mouse preimplantation embryo development. Heterozygous mouse embryos lacking maternal Plag1 showed disrupted regulation of 1,089 genes, spent significantly longer time in the 2-cell stage, and started expressing Plag1 ectopically from the paternal allele. The de novo PLAG1 motif was enriched in the promoters of the genes whose activation was delayed in the absence of Plag1. Further, these mouse genes showed a significant overlap with genes upregulated during human ZGA that also contain the motif. By gene ontology, the mouse and human ZGA genes with de novo PLAG1 motifs were involved in ribosome biogenesis and protein synthesis. Collectively, our data suggest that PLAG1 affects embryo development in mice and humans through a conserved DNA motif within Alu/B1 elements located in the promoters of a subset of ZGA genes.
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Affiliation(s)
- Elo Madissoon
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden.
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, 50410, Tartu, Estonia.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Katariina Mamia
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Bert De Groef
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden. .,Research Programs Unit, Molecular Neurology, University of Helsinki, and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, WC2R 2LS, UK.
| | - Pauliina Damdimopoulou
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden. .,Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden.
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77
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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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78
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McCollin A, Swann RL, Summers MC, Handyside AH, Ottolini CS. Abnormal cleavage and developmental arrest of human preimplantation embryos in vitro. Eur J Med Genet 2019; 63:103651. [PMID: 30995534 DOI: 10.1016/j.ejmg.2019.04.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/01/2019] [Accepted: 04/09/2019] [Indexed: 02/08/2023]
Abstract
Despite improvements in culture conditions and laboratory techniques still only about 50% of human embryos reach the blastocyst stage of development in vitro. While many factors influence embryo development, aberrant cleavage divisions have only recently been shown to directly affect the genome in individual cells of human embryos resulting in chromosome loss, mosaicism and cell arrest. In this article we review the current literature in the area of aberrant cleavage in human embryos and its effect on blastocyst development. Further to this, we propose a series of common abnormal cleavage events, with particular attention to timing and frequency, and illustrate how these might influence a number of different embryo fates.
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Affiliation(s)
- Abeo McCollin
- London Women's Clinic, One St Thomas Street, London, SE1 9RY, UK
| | | | - Michael C Summers
- London Women's Clinic, One St Thomas Street, London, SE1 9RY, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Alan H Handyside
- London Women's Clinic, One St Thomas Street, London, SE1 9RY, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Christian S Ottolini
- The Evewell, 61 Harley Street, London, W1G 8QU, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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79
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Smith HL, Stevens A, Minogue B, Sneddon S, Shaw L, Wood L, Adeniyi T, Xiao H, Lio P, Kimber SJ, Brison DR. Systems based analysis of human embryos and gene networks involved in cell lineage allocation. BMC Genomics 2019; 20:171. [PMID: 30836937 PMCID: PMC6399968 DOI: 10.1186/s12864-019-5558-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell population. Notably, there is a lack of understanding of how transcriptional networks arise during reorganisation of the embryonic genome post-fertilisation. RESULTS We identified a hierarchical structure of preimplantation gene network modules around the time of embryonic genome activation (EGA). Using network models along with eukaryotic initiation factor (EIF) and epigenetic-associated gene expression we defined two sets of blastomeres that exhibited diverging tendencies towards ICM or TE. Analysis of the developmental networks demonstrated stage specific EIF expression and revealed that histone modifications may be an important epigenetic regulatory mechanism in preimplantation human embryos. Comparison to published RNAseq data confirmed that during EGA the individual 8-cell blastomeres are transcriptionally primed for the first lineage decision in development towards ICM or TE. CONCLUSIONS Using multiple systems biology approaches to compare developmental stages in the early human embryo with single cell transcript data from blastomeres, we have shown that blastomeres considered to be totipotent are not transcriptionally equivalent. Furthermore we have linked the developmental interactome to individual blastomeres and to later cell lineage. This has clinical implications for understanding the impact of fertility treatments and developmental programming of long term health.
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Affiliation(s)
- H. L. Smith
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL 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, Oxford Road, Manchester, M13 9WL UK
| | - A. Stevens
- Division of Developmental Biology & Medicine, School of Medical Sciences, University of Manchester, Manchester Academic Health Sciences Centre, 5th Floor Research, Royal Manchester Children’s Hospital, Oxford Road, Manchester, M13 9WL UK
| | - B. Minogue
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL 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, Oxford Road, Manchester, M13 9WL UK
| | - S. Sneddon
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL 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, Oxford Road, Manchester, M13 9WL UK
| | - L. Shaw
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL 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, Oxford Road, Manchester, M13 9WL UK
| | - L. Wood
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - T. Adeniyi
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - H. Xiao
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - P. Lio
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - S. 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, Oxford Road, Manchester, M13 9WL UK
| | - D. R. Brison
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
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80
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Vendrell X, Escribà MJ. The model of "genetic compartments": a new insight into reproductive genetics. J Assist Reprod Genet 2019; 36:363-369. [PMID: 30421342 PMCID: PMC6439105 DOI: 10.1007/s10815-018-1366-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/02/2018] [Indexed: 12/20/2022] Open
Abstract
Currently, we are witnessing revolutionary advances in the analytical power of genetic tools. An enormous quantity of data can now be obtained from samples; however, the translation of genetic findings to the general status of individuals, or their offspring, should be done with caution. This is especially relevant in the reproductive context, where the concepts of "transmission" and "inheritability" of a trait are crucial. Against this background, we offer new insight based on a systemic view of genetic constitution in the compartmentalized organism, that is, the human body. This model considers the coexistence of "different" genomes in the same individual and the repercussion of this on reproductive efficacy and offspring. Herein, we review the major differences between somatic, germinal, embryonic, and fetal/placental genomes and their contribution to the next generation and its reproductive efficacy. The major novelty of our approach is the holistic interaction between microsystems within a macrosystem (i.e., the reproductive system). This panoramic model allows us to sketch the future implications of genetic results in function of the origin (compartment) of the sample: peripheral blood or other somatic tissues, gametes, zygotes, preimplantation embryos, fetus, or placenta. We believe this perspective can be of great use in the context of reproductive genetic counseling.
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Affiliation(s)
- X Vendrell
- Reproductive Genetics Unit, Sistemas Genómicos, Parc Tecnològic de Paterna, G. Marconi 6, 46980, València, Spain.
| | - M J Escribà
- IVF Laboratory, IVIRMA-Valencia, Plaça de la Policia Local, 3, 46015, València, Spain
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81
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Dabiri Y, Gama-Brambila RA, Taškova K, Herold K, Reuter S, Adjaye J, Utikal J, Mrowka R, Wang J, Andrade-Navarro MA, Cheng X. Imidazopyridines as Potent KDM5 Demethylase Inhibitors Promoting Reprogramming Efficiency of Human iPSCs. iScience 2019; 12:168-181. [PMID: 30685712 PMCID: PMC6354736 DOI: 10.1016/j.isci.2019.01.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/11/2018] [Accepted: 01/08/2019] [Indexed: 02/06/2023] Open
Abstract
Pioneering human induced pluripotent stem cell (iPSC)-based pre-clinical studies have raised safety concerns and pinpointed the need for safer and more efficient approaches to generate and maintain patient-specific iPSCs. One approach is searching for compounds that influence pluripotent stem cell reprogramming using functional screens of known drugs. Our high-throughput screening of drug-like hits showed that imidazopyridines—analogs of zolpidem, a sedative-hypnotic drug—are able to improve reprogramming efficiency and facilitate reprogramming of resistant human primary fibroblasts. The lead compound (O4I3) showed a remarkable OCT4 induction, which at least in part is due to the inhibition of H3K4 demethylase (KDM5, also known as JARID1). Experiments demonstrated that KDM5A, but not its homolog KDM5B, serves as a reprogramming barrier by interfering with the enrichment of H3K4Me3 at the OCT4 promoter. Thus our results introduce a new class of KDM5 chemical inhibitors and provide further insight into the pluripotency-related properties of KDM5 family members. O4I3 supports the maintenance and generation of human iPSCs O4I3 is a potent H3K4 demethylase KDM5 inhibitor in vitro and in cells KDM5A, but not KDM5B, serves as an epigenetic barrier of reprogramming Chemical or genetic inhibition of KDM5A tends to promote the reprogramming efficiency
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Affiliation(s)
- Yasamin Dabiri
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, ImNeuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Rodrigo A Gama-Brambila
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, ImNeuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Katerina Taškova
- Faculty of Biology, University Mainz, Gresemundweg 2, 55128 Mainz, Germany; Institute of Molecular Biology GmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Kristina Herold
- Experimentelle Nephrologie, KIM III, Universitätsklinikum, 07743 Jena, Germany
| | - Stefanie Reuter
- Experimentelle Nephrologie, KIM III, Universitätsklinikum, 07743 Jena, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ) and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Ralf Mrowka
- Experimentelle Nephrologie, KIM III, Universitätsklinikum, 07743 Jena, Germany
| | - Jichang Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China
| | - Miguel A Andrade-Navarro
- Faculty of Biology, University Mainz, Gresemundweg 2, 55128 Mainz, Germany; Institute of Molecular Biology GmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Xinlai Cheng
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, ImNeuenheimer Feld 364, 69120 Heidelberg, Germany.
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82
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Mazilina MA, Komarova EM, Baranov VS. RNA in Human Sperm and Some Problems of Male Fertility. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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83
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Global, Survival, and Apoptotic Transcriptome during Mouse and Human Early Embryonic Development. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5895628. [PMID: 30515407 PMCID: PMC6236930 DOI: 10.1155/2018/5895628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/24/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022]
Abstract
Survival and cell death signals are crucial for mammalian embryo preimplantation development. However, the knowledge on the molecular mechanisms underlying their regulation is still limited. Mouse studies are widely used to understand preimplantation embryo development, but extrapolation of these results to humans is questionable. Therefore, we wanted to analyse the global expression profiles during early mouse and human development with a special focus on genes involved in the regulation of the apoptotic and survival pathways. We used DNA microarray technology to analyse the global gene expression profiles of preimplantation human and mouse embryos (metaphase II oocytes, embryos at the embryonic genome activation stage, and blastocysts). Components of the major apoptotic and survival signalling pathways were expressed during early human and mouse embryonic development; however, most expression profiles were species-specific. Particularly, the expression of genes encoding components and regulators of the apoptotic machinery were extremely stable in mouse embryos at all analysed stages, while it was more stage-specific in human embryos. CASP3, CASP9, and AIF were the only apoptosis-related genes expressed in both species and at all studied stages. Moreover, numerous transcripts related to the apoptotic and survival pathway were reported for the first time such as CASP6 and IL1RAPL1 that were specific to MII oocytes; CASP2, ENDOG, and GFER to blastocysts in human. These findings open new perspectives for the characterization and understanding of the survival and apoptotic signalling pathways that control early human and mouse embryonic development.
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84
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Ladstätter S, Tachibana K. Genomic insights into chromatin reprogramming to totipotency in embryos. J Cell Biol 2018; 218:70-82. [PMID: 30257850 PMCID: PMC6314560 DOI: 10.1083/jcb.201807044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
Ladstätter and Tachibana discuss changes in DNA methylation, chromatin accessibility, and topological architecture occurring during the reprogramming to totipotency in the early embryo. The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.
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Affiliation(s)
- Sabrina Ladstätter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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85
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Chang JY, Yu WH, Juan HF, Huang HC. Dynamics of alternative polyadenylation in human preimplantation embryos. Biochem Biophys Res Commun 2018; 504:727-733. [PMID: 30217451 DOI: 10.1016/j.bbrc.2018.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023]
Abstract
Alternative polyadenylation (APA) affects the length of the 3' untranslated region (3'-UTR) and the regulation of microRNAs. Previous studies have shown that cancer cells tend to have shorter 3'-UTRs than normal cells. A plausible explanation for this is that it enables cancer cells to escape the regulation of microRNAs. Here, we extend this concept to an opposing context: changes in 3'-UTR length in the development of the human preimplantation embryo. Unlike cancer cells, during early development 3'-UTRs tended to become longer, and gene expression was negatively correlated with 3'-UTR length. Moreover, our functional enrichment results showed that length changes are part of the development mechanism. We also investigated the analogy of 3'-UTR length variation with respect to lncRNAs and found that, similarly, lncRNA length tended to increase during embryo development.
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Affiliation(s)
- Jen-Yun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Wen-Hsuan Yu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Hsueh-Fen Juan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan; Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
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86
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Gonzalez-Munoz E, Cibelli JB. Somatic Cell Reprogramming Informed by the Oocyte. Stem Cells Dev 2018; 27:871-887. [DOI: 10.1089/scd.2018.0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Elena Gonzalez-Munoz
- LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
- Department of Cell Biology, Genetics and Physiology, University of Málaga, Málaga, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBN), Málaga, Spain
| | - Jose B. Cibelli
- LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
- Department of Animal Science, Michigan State University, East Lansing, MI
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI
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87
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Castillo J, Jodar M, Oliva R. The contribution of human sperm proteins to the development and epigenome of the preimplantation embryo. Hum Reprod Update 2018; 24:535-555. [DOI: 10.1093/humupd/dmy017] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/25/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Judit Castillo
- Molecular Biology of Reproduction and Development Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain
- Biochemistry and Molecular Genetics Service, Hospital Clínic, Villarroel, Barcelona, Spain
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88
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Tsai TS, St John JC. The effects of mitochondrial DNA supplementation at the time of fertilization on the gene expression profiles of porcine preimplantation embryos. Mol Reprod Dev 2018; 85:490-504. [PMID: 29663563 DOI: 10.1002/mrd.22985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/10/2018] [Indexed: 01/20/2023]
Abstract
Mitochondrial DNA (mtDNA) deficient metaphase II porcine oocytes are less likely to fertilize and more likely to arrest during preimplantation development. However, they can be supplemented with autologous populations of mitochondria at the time of fertilization, which significantly increases mtDNA copy number by the 2-cell stage due to the modulation of DNA methylation at a CpG island of the gene encoding the mtDNA-specific polymerase, POLG, and promotes preimplantation development. Although mitochondrial supplementation does not increase development rates or mtDNA copy number in oocytes with normal levels of mtDNA copy number, we tested whether this approach would also impact on chromosomal gene expression patterns in these oocytes at each stage of preimplantation development. Here, we have compared the gene expression profiles of embryos produced by mitochondrial supplementation at the time of fertilization with embryos produced by in vitro fertilization (IVF) using a panel of genes associated with different stages of preimplantation development. When compared to IVF-derived embryos, 27 (34%) genes were differentially expressed in supplemented embryos but this was restricted to one or two developmental stages. However, 53 (66%) genes were comparably expressed across all six stages and by the blastocyst stage 4 (5%) genes were differentially expressed. We conclude that additional copies of mtDNA can induce changes in gene expression at various stages of preimplantation development with the first changes occurring prior to maternal-to-zygotic transition (MZT). However, these changes appear to be transitory suggesting that some genomic resetting is taking place.
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Affiliation(s)
- Te-Sha Tsai
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Australia.,Centre for Genetic Diseases, Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Australia.,Centre for Genetic Diseases, Department of Molecular and Translational Science, Monash University, Clayton, Australia
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89
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Eckersley-Maslin MA, Alda-Catalinas C, Reik W. Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. Nat Rev Mol Cell Biol 2018; 19:436-450. [DOI: 10.1038/s41580-018-0008-z] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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90
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Barragán M, Pons J, Ferrer-Vaquer A, Cornet-Bartolomé D, Schweitzer A, Hubbard J, Auer H, Rodolosse A, Vassena R. The transcriptome of human oocytes is related to age and ovarian reserve. Mol Hum Reprod 2018; 23:535-548. [PMID: 28586423 DOI: 10.1093/molehr/gax033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 06/03/2017] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION How does the human oocyte transcriptome change with age and ovarian reserve? SUMMARY ANSWER Specific sets of human oocyte messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) are affected independently by age and ovarian reserve. WHAT IS KNOWN ALREADY Although it is well established that the ovarian reserve diminishes with increasing age, and that a woman's age is correlated with lower oocyte quality, the interplay of a diminished reserve and age on oocyte developmental competence is not clear. After maturation, oocytes are mostly transcriptionally quiescent, and developmental competence prior to embryonic genome activationrelies on maternal RNA and proteins. STUDY DESIGN, SIZE, DURATION A total of 36 vitrified/warmed MII oocytes from 30 women undergoing oocyte donation were included in this study, processed and analyzed individually. PARTICIPANTS/MATERIALS, SETTING, METHODS Total RNA from each oocyte was independently isolated, amplified, labeled, and hybridized on HTA 2.0 arrays (Affymetrix). Data were analyzed using TAC software, in four groups, each including nine oocytes, according to the woman's age and antral follicular count (AFC) (mean ± SD): Young with High AFC (YH; age 21 ± 1 years and 24 ± 3 follicles); Old with High AFC (OH; age 32 ± 2 years and 29 ± 7 follicles); Young with Low AFC (YL; age 24 ± 2 years and 8 ± 2 follicles); Old with Low AFC (OL; age 34 ± 1 years and 7 ± 1 follicles). qPCR was performed to validate arrays. MAIN RESULTS AND THE ROLE OF CHANCE We identified a set of 30 differentially expressed mRNAs when comparing oocytes from women with different ages and AFC. In addition, 168 non-coding RNAs (ncRNAs) were differentially expressed in relation to age and/or AFC. Few mRNAs have been identified as differentially expressed transcripts, and among ncRNAs, a set of Piwi-interacting RNAs clusters (piRNAs-c) and precursor microRNAs (pre-miRNAs) were identified as increased in high AFC and old groups, respectively. Our results indicate that age and ovarian reserve are associated with specific ncRNA profiles, suggesting that oocyte quality might be mediated by ncRNA pathways. LARGE SCALE DATA Data can be found via GEO accession number GSE87201. LIMITATIONS, REASONS FOR CAUTION The oldest woman included in the study was 35 years old, thus our results cannot readily be extrapolated to women older than 35 or infertile women. WIDER IMPLICATIONS OF THE FINDINGS We show, for the first time, that several non-coding RNAs, usually regulating DNA transcription, are differentially expressed in relation to age and/or ovarian reserve. Interestingly, the mRNA transcriptome of in vivo matured oocytes remains remarkably stable across ages and ovarian reserve, suggesting the possibility that changes in the non-coding transcriptome might regulate some post-transcriptional/translational mechanisms which might, in turn, affect oocyte developmental competence. STUDY FUNDING AND COMPETING INTEREST(S) This work was supported by intramural funding of Clinica EUGIN and by the Secretary for Universities and Research of the Ministry of Economy and Knowledge of the Government of Catalonia. J.H. and A.S. are employees of Affymetrix, otherwise there are no competing interests.
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Affiliation(s)
- M Barragán
- Clínica EUGIN, Travessera de les Corts 322, 08029 Barcelona, Spain
| | - J Pons
- Functional Genomics Core, Institute for Research in Biomedicine (IRB) Barcelona, Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - A Ferrer-Vaquer
- Clínica EUGIN, Travessera de les Corts 322, 08029 Barcelona, Spain
| | | | - A Schweitzer
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA 95051, USA
| | - J Hubbard
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA 95051, USA
| | - H Auer
- Functional GenOmics Consulting, Bellavista 53, 08753 Pallejà, Spain
| | - A Rodolosse
- Functional Genomics Core, Institute for Research in Biomedicine (IRB) Barcelona, Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - R Vassena
- Clínica EUGIN, Travessera de les Corts 322, 08029 Barcelona, Spain
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91
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Exploring timing activation of functional pathway based on differential co-expression analysis in preimplantation embryogenesis. Oncotarget 2018; 7:74120-74131. [PMID: 27705919 PMCID: PMC5342040 DOI: 10.18632/oncotarget.12339] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/17/2016] [Indexed: 12/15/2022] Open
Abstract
Recent genome-wide omics studies have confirmed the early embryogenesis strictly dependent on the rigorous spatiotemporal activation and multilevel regulation. However, the full effect of functional pathway was not considered. To obtain complete understanding of the gene activation during early development, we performed systematic comparisons based on differential co-expression analysis for bovine preimplantation embryo development (PED). The results confirmed that the functional pathways actively transcribes as early as the 2-cell and 4-cell waves, which Basal transcription factor, Endocytosis and Spliceosome pathway can represent first signs of embryonic activity. Endocytosis act as one of master activators for uncovering a series of successive waves of maternal pioneer signal regulator with the help of Spliceosome complex. Furthermore, the results showed that pattern recognition receptors began to perform its essential function at 4-cell stage, which might be needed to coordinate the later major activation. And finally, our work presented a probable dynamic landscape of key functional pathways for embryogenesis. A clearer understanding of early embryo development will be helpful for Assisted Reproductive Technology (ART) and Regenerative Medicine (RM).
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92
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Li RS, Hwu YM, Lee RKK, Li SH, Lin MH. Day 4 good morula embryo transfer provided compatible live birth rate with day 5 blastocyst embryo in fresh IVF/ET cycles. Taiwan J Obstet Gynecol 2018; 57:52-57. [DOI: 10.1016/j.tjog.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2017] [Indexed: 11/15/2022] Open
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93
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Wang Y, Zhao C, Hou Z, Yang Y, Bi Y, Wang H, Zhang Y, Gao S. Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state. eLife 2018; 7:29518. [PMID: 29381138 PMCID: PMC5807049 DOI: 10.7554/elife.29518] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 01/29/2018] [Indexed: 12/22/2022] Open
Abstract
Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental biology studies and therapeutic manipulations. However, the molecular mechanisms involved in the establishment and maintenance of human naïve pluripotency remain poorly understood. Using the human inducible reprogramming system together with the 5iLAF naïve induction strategy, integrative analysis of transcriptional and epigenetic dynamics across the transition from human fibroblasts to naïve iPSCs revealed ordered waves of gene network activation sharing signatures with those found during embryonic development from late embryogenesis to pre-implantation stages. More importantly, Transcriptional analysis showed a significant transient reactivation of transcripts with 8-cell-stage-like characteristics in the late stage of reprogramming, suggesting transient activation of gene network with human zygotic genome activation (ZGA)-like signatures during the establishment of naïve pluripotency. Together, Dissecting the naïve reprogramming dynamics by integrative analysis improves the understanding of the molecular features involved in the generation of naïve pluripotency directly from somatic cells.
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Affiliation(s)
- Yixuan Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chengchen Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhenzhen Hou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuanyuan Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yan Bi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yong Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
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94
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Theunissen TW, Jaenisch R. Mechanisms of gene regulation in human embryos and pluripotent stem cells. Development 2018; 144:4496-4509. [PMID: 29254992 DOI: 10.1242/dev.157404] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pluripotent stem cells have broad utility in biomedical research and their molecular regulation has thus garnered substantial interest. While the principles that establish and regulate pluripotency have been well defined in the mouse, it has been difficult to extrapolate these insights to the human system due to species-specific differences and the distinct developmental identities of mouse versus human embryonic stem cells. In this Review, we examine genome-wide approaches to elucidate the regulatory principles of pluripotency in human embryos and stem cells, and highlight where differences exist in the regulation of pluripotency in mice and humans. We review recent insights into the nature of human pluripotent cells in vivo, obtained by the deep sequencing of pre-implantation embryos. We also present an integrated overview of the principal layers of global gene regulation in human pluripotent stem cells. Finally, we discuss the transcriptional and epigenomic remodeling events associated with cell fate transitions into and out of human pluripotency.
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Affiliation(s)
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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95
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96
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Tardat M, Déjardin J. Telomere chromatin establishment and its maintenance during mammalian development. Chromosoma 2017; 127:3-18. [PMID: 29250704 PMCID: PMC5818603 DOI: 10.1007/s00412-017-0656-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Telomeres are specialized structures that evolved to protect the end of linear chromosomes from the action of the cell DNA damage machinery. They are composed of tandem arrays of repeated DNA sequences with a specific heterochromatic organization. The length of telomeric repeats is dynamically regulated and can be affected by changes in the telomere chromatin structure. When telomeres are not properly controlled, the resulting chromosomal alterations can induce genomic instability and ultimately the development of human diseases, such as cancer. Therefore, proper establishment, regulation, and maintenance of the telomere chromatin structure are required for cell homeostasis. Here, we review the current knowledge on telomeric chromatin dynamics during cell division and early development in mammals, and how its proper regulation safeguards genome stability.
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Affiliation(s)
- Mathieu Tardat
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Jérôme Déjardin
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
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97
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Svoboda P. Mammalian zygotic genome activation. Semin Cell Dev Biol 2017; 84:118-126. [PMID: 29233752 DOI: 10.1016/j.semcdb.2017.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/22/2017] [Accepted: 12/08/2017] [Indexed: 12/14/2022]
Abstract
Zygotic genome activation (ZGA) denotes the initiation of gene expression after fertilization. It is part of the complex oocyte-to-embryo transition (OET) in which a highly specialized cell - the oocyte - is fertilized and transformed into a zygote that gives rise to an embryo that will develop into a newborn. From the perspective of gene expression, the OET reflects reprogramming of germ cell gene expression into the new developmental program of the zygote. This reprogramming occurs at transcriptional and post-transcriptional levels. This review will discuss selected aspects of mammalian ZGA, highlighting shared features and evolved differences observed in commonly investigated mammals and non-mammalian model animals.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20, Prague 4, Czech Republic.
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98
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Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:1291-1303. [PMID: 28966118 PMCID: PMC5639460 DOI: 10.1016/j.stemcr.2017.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 01/21/2023] Open
Abstract
Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage. We identify SETα to be rapidly downregulated during ESC differentiation SETα is regulated by pluripotency factors and replaced by SETβ during differentiation SETα/SETβ switch is crucial for ESC differentiation SETα regulates chromatin plasticity in ESCs
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99
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Boroviak T, Nichols J. Primate embryogenesis predicts the hallmarks of human naïve pluripotency. Development 2017; 144:175-186. [PMID: 28096211 PMCID: PMC5430762 DOI: 10.1242/dev.145177] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Naïve pluripotent mouse embryonic stem cells (ESCs) resemble the preimplantation epiblast and efficiently contribute to chimaeras. Primate ESCs correspond to the postimplantation embryo and fail to resume development in chimaeric assays. Recent data suggest that human ESCs can be ‘reset’ to an earlier developmental stage, but their functional capacity remains ill defined. Here, we discuss how the naïve state is inherently linked to preimplantation epiblast identity in the embryo. We hypothesise that distinctive features of primate development provide stringent criteria to evaluate naïve pluripotency in human and other primate cells. Based on our hypothesis, we define 12 key hallmarks of naïve pluripotency, five of which are specific to primates. These hallmarks may serve as a functional framework to assess human naïve ESCs. Summary: This Hypothesis article highlights several fundamental differences between rodent and primate early development and exploits these to predict key hallmarks of naïve pluripotency in primates.
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Affiliation(s)
- Thorsten Boroviak
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 4BG, UK
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100
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Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing. Sci Rep 2017; 7:10794. [PMID: 28883481 PMCID: PMC5589911 DOI: 10.1038/s41598-017-11044-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/18/2017] [Indexed: 12/16/2022] Open
Abstract
In female mammals, one X chromosome is transcriptionally inactivated (XCI), leading to dosage compensation between sexes, fundamental for embryo viability. A previous study using single-cell RNA-sequencing (scRNA-seq) data proposed that female human preimplantation embryos achieve dosage compensation by downregulating both Xs, a phenomenon named dampening of X expression. Using a novel pipeline on those data, we identified a decrease in the proportion of biallelically expressed X-linked genes during development, consistent with XCI. Moreover, we show that while the expression sum of biallelically expressed X-linked genes decreases with embryonic development, their median expression remains constant, rejecting the hypothesis of X dampening. In addition, analyses of a different dataset of scRNA-seq suggest the appearance of X-linked monoallelic expression by the late blastocyst stage in females, another hallmark of initiation of XCI. Finally, we addressed the issue of dosage compensation between the single active X and autosomes in males and females for the first time during human preimplantation development, showing emergence of X to autosome dosage compensation by the upregulation of the active X chromosome in both male and female embryonic stem cells. Our results show compelling evidence of an early process of X chromosome inactivation during human preimplantation development.
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