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Gunne-Braden A, Sullivan A, Gharibi B, Sheriff RSM, Maity A, Wang YF, Edwards A, Jiang M, Howell M, Goldstone R, Wollman R, East P, Santos SDM. GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells. Cell Stem Cell 2020; 26:693-706.e9. [PMID: 32302522 PMCID: PMC7487786 DOI: 10.1016/j.stem.2020.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/19/2019] [Accepted: 03/09/2020] [Indexed: 01/08/2023]
Abstract
During early development, extrinsic triggers prompt pluripotent cells to begin the process of differentiation. When and how human embryonic stem cells (hESCs) irreversibly commit to differentiation is a fundamental yet unanswered question. By combining single-cell imaging, genomic approaches, and mathematical modeling, we find that hESCs commit to exiting pluripotency unexpectedly early. We show that bone morphogenetic protein 4 (BMP4), an important differentiation trigger, induces a subset of early genes to mirror the sustained, bistable dynamics of upstream signaling. Induction of one of these genes, GATA3, drives differentiation in the absence of BMP4. Conversely, GATA3 knockout delays differentiation and prevents fast commitment to differentiation. We show that positive feedback at the level of the GATA3-BMP4 axis induces fast, irreversible commitment to differentiation. We propose that early commitment may be a feature of BMP-driven fate choices and that interlinked feedback is the molecular basis for an irreversible transition from pluripotency to differentiation. Irreversible commitment to BMP4-driven hESC differentiation is fast SMAD activation is sustained, bistable, and irreversible due to positive feedback GATA3 mirrors SMAD dynamics and mediates fast commitment to differentiation GATA3 is an early commitment gene
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Affiliation(s)
| | | | | | - Rahuman S M Sheriff
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK
| | - Alok Maity
- University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | | | | | | | | | | | - Roy Wollman
- University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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A framework for high-resolution phenotyping of candidate male infertility mutants: from human to mouse. Hum Genet 2020; 140:155-182. [PMID: 32248361 DOI: 10.1007/s00439-020-02159-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 03/27/2020] [Indexed: 12/18/2022]
Abstract
Male infertility is a heterogeneous condition of largely unknown etiology that affects at least 7% of men worldwide. Classical genetic approaches and emerging next-generation sequencing studies support genetic variants as a frequent cause of male infertility. Meanwhile, the barriers to transmission of this disease mean that most individual genetic cases will be rare, but because of the large percentage of the genome required for spermatogenesis, the number of distinct causal mutations is potentially large. Identifying bona fide causes of male infertility thus requires advanced filtering techniques to select for high-probability candidates, including the ability to test causality in animal models. The mouse remains the gold standard for defining the genotype-phenotype connection in male fertility. Here, we present a best practice guide consisting of (a) major points to consider when interpreting next-generation sequencing data performed on infertile men, and, (b) a systematic strategy to categorize infertility types and how they relate to human male infertility. Phenotyping infertility in mice can involve investigating the function of multiple cell types across the testis and epididymis, as well as sperm function. These findings will feed into the diagnosis and treatment of male infertility as well as male health broadly.
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53
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Naddafpour A, Ghazvini Zadegan F, Hajian M, Hosseini SM, Jafarpour F, Rahimi M, Habibi R, Nasr Esfahani MH. Effects of abundances of OCT-4 mRNA transcript on goat pre-implantation embryonic development. Anim Reprod Sci 2020; 215:106286. [PMID: 32216939 DOI: 10.1016/j.anireprosci.2020.106286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 12/18/2019] [Accepted: 01/16/2020] [Indexed: 12/27/2022]
Abstract
Unlike in mice, the function of pluripotent markers in early embryonic development of domestic animals remains to be elucidated and this may account for the failure to establish embryonic stem cell lines for these species. To study the functions of the OCT-4 protein which has important actions in maintenance of pluripotent and self-renewal processes during early embryonic development, there was induced reduction in relative abundance of OCT-4 mRNA transcript during goat early embryonic development by using RNA interference techniques. The injection of OCT-4 siRNA into goat IVF presumptive zygotes resulted in a decrease in the relative abundance of OCT-4 mRNA transcript; however, there was development of these embryos to the blastocyst stage at the same rate as there was in the control group. The blastocysts from the treated groups had a similar number of TE, ICM, and total cells compared to those from the control group. Although there was a greater relative abundance of NANOG, REX1, and CDX2 mRNA transcript in the embryos injected with siRNA at the 8-16 cell stage, the relative transcript abundances were similar for the control and treatment groups at the blastocyst stage. The relative abundance of SOX2 mRNA transcript was similar for the treatment and control group. It, therefore, is concluded that inhibition of abundances of OCT-4 mRNA transcript to about 20 % of that of the untreated control group did not affect blastocyst formation rate in goats. The functions of OCT-4 in maintaining ICM and TE integrity, however, remains to be assessed.
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Affiliation(s)
- Azadeh Naddafpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; Department of Biology, University of Science and Culture, Tehran, Iran
| | - Faezeh Ghazvini Zadegan
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mehdi Hajian
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sayyed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohsen Rahimi
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Razieh Habibi
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; Department of Biology, University of Science and Culture, Tehran, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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54
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Tam PPL, Ho JWK. Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes. Development 2020; 147:147/2/dev179788. [PMID: 31980483 DOI: 10.1242/dev.179788] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Single cell RNA-sequencing (scRNA-seq) technology has matured to the point that it is possible to generate large single cell atlases of developing mouse embryos. These atlases allow the dissection of developmental cell lineages and molecular changes during embryogenesis. When coupled with single cell technologies for profiling the chromatin landscape, epigenome, proteome and metabolome, and spatial tissue organisation, these scRNA-seq approaches can now collect a large volume of multi-omic data about mouse embryogenesis. In addition, advances in computational techniques have enabled the inference of developmental lineages of differentiating cells, even without explicitly introduced genetic markers. This Spotlight discusses recent advent of single cell experimental and computational methods, and key insights from applying these methods to the study of mouse embryonic development. We highlight challenges in analysing and interpreting these data to complement and expand our knowledge from traditional developmental biology studies in relation to cell identity, diversity and lineage differentiation.
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Affiliation(s)
- Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW 2145, Australia .,The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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55
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Uehara R, Cerritelli SM, Hasin N, Sakhuja K, London M, Iranzo J, Chon H, Grinberg A, Crouch RJ. Two RNase H2 Mutants with Differential rNMP Processing Activity Reveal a Threshold of Ribonucleotide Tolerance for Embryonic Development. Cell Rep 2019; 25:1135-1145.e5. [PMID: 30380406 PMCID: PMC6309994 DOI: 10.1016/j.celrep.2018.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/18/2018] [Accepted: 10/03/2018] [Indexed: 11/30/2022] Open
Abstract
RNase H2 has two distinct functions: initiation of the ribonucleotide excision repair (RER) pathway by cleaving ribonucleotides (rNMPs) incorporated during DNA replication and processing the RNA portion of an R-loop formed during transcription. An RNase H2 mutant lacking RER activity but supporting R-loop removal revealed that rNMPs in DNA initiate p53-dependent DNA damage response and early embryonic arrest in mouse. However, an RNase H2 AGS-related mutant with residual RER activity develops to birth. Estimations of the number of rNMPs in DNA in these two mutants define a ribonucleotide threshold above which p53 induces apoptosis. Below the threshold, rNMPs in DNA trigger an innate immune response. Compound heterozygous cells, containing both defective enzymes, retain rNMPs above the threshold, indicative of competition for RER substrates between active and inactive enzymes, suggesting that patients with compound heterozygous mutations in RNASEH2 genes may not reflect the properties of recombinantly expressed proteins. Uehara et al. use RNase H2 mice with differing activity levels for removal of rNMPs embedded in DNA. Moderate levels of rNMPs lead to perinatal lethality activating the cGAS-Sting DNA sensing innate immune response. Exceeding a threshold, high abundance of rNMPs activates p53-dependent DNA damage, causing early embryonic lethality.
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Affiliation(s)
- Ryo Uehara
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Naushaba Hasin
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Kiran Sakhuja
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Mariya London
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Jaime Iranzo
- NCBI, National Library of Medicine, Bethesda, MD, USA
| | - Hyongi Chon
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Alexander Grinberg
- Mouse Core, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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56
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Cerritelli SM, Crouch RJ. RNase H2-RED carpets the path to eukaryotic RNase H2 functions. DNA Repair (Amst) 2019; 84:102736. [PMID: 31761672 PMCID: PMC6936605 DOI: 10.1016/j.dnarep.2019.102736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022]
Abstract
Eukaryotic RNases H2 have dual functions in initiating the removal of ribonucleoside monophosphates (rNMPs) incorporated by DNA polymerases during DNA synthesis and in cleaving the RNA moiety of RNA/DNA hybrids formed during transcription and retrotransposition. The other major cellular RNase H, RNase H1, shares the hybrid processing activity, but not all substrates. After RNase H2 incision at the rNMPs in DNA the Ribonucleotide Excision Repair (RER) pathway completes the removal, restoring dsDNA. The development of the RNase H2-RED (Ribonucleotide Excision Defective) mutant enzyme, which can process RNA/DNA hybrids but is unable to cleave rNMPs embedded in DNA has unlinked the two activities and illuminated the roles of RNase H2 in cellular metabolism. Studies mostly in Saccharomyces cerevisiae, have shown both activities of RNase H2 are necessary to maintain genome integrity and that RNase H1 and H2 have overlapping as well as distinct RNA/DNA hybrid substrates. In mouse RNase H2-RED confirmed that rNMPs in DNA during embryogenesis induce lethality in a p53-dependent DNA damage response. In mammalian cell cultures, RNase H2-RED helped identifying DNA lesions produced by Top1 cleavage at rNMPs and led to determine that RNase H2 participates in the retrotransposition of LINE-1 elements. In this review, we summarize the studies and conclusions reached by utilization of RNase H2-RED enzyme in different model systems.
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Affiliation(s)
- Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Abstract
Early embryogenesis is characterized by the segregation of cell lineages that fulfill critical roles in the establishment of pregnancy and development of the fetus. The formation of the blastocyst marks the emergence of extraembryonic precursors, needed for implantation, and of pluripotent cells, which differentiate toward the major lineages of the adult organism. The coordinated emergence of these cell types shows that these processes are broadly conserved in mammals. However, developmental heterochrony and changes in gene regulatory networks highlight unique evolutionary adaptations that may explain the diversity in placentation and in the mechanisms controlling pluripotency in mammals. The incorporation of new technologies, including single-cell omics, imaging, and gene editing, is instrumental for comparative embryology. Broadening the knowledge of mammalian embryology will provide new insights into the mechanisms driving evolution and development. This knowledge can be readily translated into biomedical and biotechnological applications in humans and livestock, respectively.
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Affiliation(s)
- Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
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58
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Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J, He A. CoBATCH for High-Throughput Single-Cell Epigenomic Profiling. Mol Cell 2019; 76:206-216.e7. [DOI: 10.1016/j.molcel.2019.07.015] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/17/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022]
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59
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Martyn I, Siggia ED, Brivanlou AH. Mapping cell migrations and fates in a gastruloid model to the human primitive streak. Development 2019; 146:dev.179564. [PMID: 31427289 DOI: 10.1242/dev.179564] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022]
Abstract
Although fate maps of early embryos exist for nearly all model organisms, a fate map of the gastrulating human embryo remains elusive. Here, we use human gastruloids to piece together a rudimentary fate map for the human primitive streak (PS). This is possible because differing levels of BMP, WNT and NODAL lead to self-organization of gastruloids into homogenous subpopulations of endoderm and mesoderm, and comparative analysis of these gastruloids, together with the fate map of the mouse embryo, allows the organization of these subpopulations along an anterior-posterior axis. We also developed a novel cell tracking technique that detected robust fate-dependent cell migrations in our gastruloids comparable with those found in the mouse embryo. Taken together, our fate map and recording of cell migrations provides a first coarse view of what the human PS may resemble in vivo.
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Affiliation(s)
- Iain Martyn
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA.,Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - Eric D Siggia
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - Ali H Brivanlou
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
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60
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Miyazawa H, Muramatsu Y, Makino H, Yamaguchi Y, Miura M. Temporal regulation of Lin28a during mammalian neurulation contributes to neonatal body size control. Dev Dyn 2019; 248:931-941. [PMID: 31301196 DOI: 10.1002/dvdy.87] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/22/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The timing of developmental events is tightly regulated along a time axis for normal development. Although the RNA-binding protein Lin28a plays a crucial role in the regulation of developmental timing in Caenorhabditis elegans, how the timing of Lin28a expression affects the rate and/or duration of developmental events during mammalian development remains to be addressed. RESULTS In this study, we discovered that the timing and the duration of Lin28a expression affect embryonic growth. During the neurulation stage of mouse development, endogenous Lin28a levels start to drop. When Lin28a expression was maintained transiently using the inducible tetracycline-regulated gene expression (Tet-ON) system [doxycycline (Dox)-inducible Lin28a transgenic (iLin28a Tg) mice] with Dox administration at E8.5 and E9.5, it resulted in neonatal lethality, increased body weight (organomegaly), and an increased number of caudal vertebrae at birth. On the other hand, Lin28a induction only at E8.5 caused neonatal lethality and organomegaly, but did not affect the caudal vertebra number. Of note, although Dox treatment before or after neurulation still caused neonatal lethality, it neither caused organomegaly nor the increased caudal vertebra number in iLin28a Tg neonates. CONCLUSIONS Temporal regulation of Lin28a expression during neurulation affects developmental events such as cessation of axial elongation and embryonic growth in mice.
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Affiliation(s)
- Hidenobu Miyazawa
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Muramatsu
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hatsune Makino
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshifumi Yamaguchi
- Hibernation Metabolism, Physiology and Development Group, Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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61
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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62
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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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63
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Ortiz WG, Rizo JA, Carvalheira LR, Ahmed BMS, Estrada-Cortes E, Harstine BR, Bromfield JJ, Hansen PJ. Effects of intrauterine infusion of seminal plasma at artificial insemination on fertility of lactating Holstein cows. J Dairy Sci 2019; 102:6587-6594. [PMID: 31103294 DOI: 10.3168/jds.2019-16251] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/27/2019] [Indexed: 01/02/2023]
Abstract
An inflammatory response is induced in the reproductive tract by deposition of semen during natural mating. This response might facilitate establishment and maintenance of pregnancy and alter the phenotype of the offspring by modifying the microenvironment of the reproductive tract. Here, we hypothesized that intrauterine infusion of 0.5 mL of seminal plasma at the time of artificial insemination (AI) in first-service lactating Holstein cows will improve pregnancy success after insemination. Cows were inseminated (511 primiparous cows inseminated with X-sorted semen, 554 multiparous cows inseminated with X-sorted semen, and 627 multiparous cows inseminated with conventional semen) using the Double-Ovsynch protocol. Cows were randomly assigned to receive intrauterine infusion of either 0.5 mL of seminal plasma or saline immediately after AI. There was no overall effect of seminal plasma infusion on the percentage of inseminated cows diagnosed pregnant at d 32 or 60 after AI, pregnancy loss, or percent of inseminated cows calving. If cows were inseminated with conventional semen, seminal plasma reduced pregnancies at d 32 and tended to reduce calvings. There was no effect of seminal plasma if cows were inseminated with X-sorted semen. Seminal plasma infusion increased the birth weight of heifer calves born using X-sorted semen but not conventional semen. These results do not support a beneficial effect of seminal plasma on pregnancy success after AI, but exposure to seminal plasma may program fetal development to affect phenotype at birth.
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Affiliation(s)
- W G Ortiz
- Department of Animal Sciences and D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611-0910
| | - J A Rizo
- Department of Animal Sciences and D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611-0910
| | - L R Carvalheira
- Departmento de Clínica e Cirurgia Veterinárias, Universidade Federal de Minas Gerais, BeloHorizonte, MG, Brazil CEP 31270-901
| | - B M S Ahmed
- Department of Animal Sciences and D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611-0910
| | - E Estrada-Cortes
- Department of Animal Sciences and D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611-0910
| | | | - J J Bromfield
- Department of Animal Sciences and D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611-0910
| | - P J Hansen
- Department of Animal Sciences and D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611-0910.
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Hu J, Li S, Sun X, Fang Z, Wang L, Xiao F, Shao M, Ge L, Tang F, Gu J, Yu H, Guo Y, Guo X, Liao B, Jin Y. Stk40 deletion elevates c-JUN protein level and impairs mesoderm differentiation. J Biol Chem 2019; 294:9959-9972. [PMID: 31092598 DOI: 10.1074/jbc.ra119.007840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
Mesoderm development is a finely tuned process initiated by the differentiation of pluripotent epiblast cells. Serine/threonine kinase 40 (STK40) controls the development of several mesoderm-derived cell types, its overexpression induces differentiation of mouse embryonic stem cells (mESCs) toward the extraembryonic endoderm, and Stk40 knockout (KO) results in multiple organ failure and is lethal at the perinatal stage in mice. However, molecular mechanisms underlying the physiological functions of STK40 in mesoderm differentiation remain elusive. Here, we report that Stk40 ablation impairs mesoderm differentiation both in vitro and in vivo Mechanistically, STK40 interacts with both the E3 ubiquitin ligase mammalian constitutive photomorphogenesis protein 1 (COP1) and the transcriptional regulator proto-oncogene c-Jun (c-JUN), promoting c-JUN protein degradation. Consequently, Stk40 knockout leads to c-JUN protein accumulation, which, in turn, apparently suppresses WNT signaling activity and impairs the mesoderm differentiation process. Overall, this study reveals that STK40, together with COP1, represents a previously unknown regulatory axis that modulates the c-JUN protein level within an appropriate range during mesoderm differentiation from mESCs. Our findings provide critical insights into the molecular mechanisms regulating the c-JUN protein level and may have potential implications for managing cellular disorders arising from c-JUN dysfunction.
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Affiliation(s)
- Jing Hu
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Shuang Li
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Xiaozhi Sun
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Zhuoqing Fang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Lina Wang
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Feng Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Min Shao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Laixiang Ge
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Fan Tang
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Junjie Gu
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Hongyao Yu
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Bing Liao
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China,
| | - Ying Jin
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China, .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China, and
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65
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Sybirna A, Wong FCK, Surani MA. Genetic basis for primordial germ cells specification in mouse and human: Conserved and divergent roles of PRDM and SOX transcription factors. Curr Top Dev Biol 2019; 135:35-89. [PMID: 31155363 DOI: 10.1016/bs.ctdb.2019.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Primordial germ cells (PGCs) are embryonic precursors of sperm and egg that pass on genetic and epigenetic information from one generation to the next. In mammals, they are induced from a subset of cells in peri-implantation epiblast by BMP signaling from the surrounding tissues. PGCs then initiate a unique developmental program that involves comprehensive epigenetic resetting and repression of somatic genes. This is orchestrated by a set of signaling molecules and transcription factors that promote germ cell identity. Here we review significant findings on mammalian PGC biology, in particular, the genetic basis for PGC specification in mice and human, which has revealed an evolutionary divergence between the two species. We discuss the importance and potential basis for these differences and focus on several examples to illustrate the conserved and divergent roles of critical transcription factors in mouse and human germline.
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Affiliation(s)
- Anastasiya Sybirna
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
| | - Frederick C K Wong
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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66
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Estill MS, Hauser R, Krawetz SA. RNA element discovery from germ cell to blastocyst. Nucleic Acids Res 2019; 47:2263-2275. [PMID: 30576549 PMCID: PMC6411832 DOI: 10.1093/nar/gky1223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/31/2018] [Accepted: 11/24/2018] [Indexed: 12/19/2022] Open
Abstract
Recent studies have shown that tissue-specific transcriptomes contain multiple types of RNAs that are transcribed from intronic and intergenic sequences. The current study presents a tool for the discovery of transcribed, unannotated sequence elements from RNA-seq libraries. This RNA Element (RE) discovery algorithm (REDa) was applied to a spectrum of tissues and cells representing germline, embryonic, and somatic tissues and examined as a function of differentiation through the first set of cell divisions of human development. This highlighted extensive transcription throughout the genome, yielding previously unidentified human spermatogenic RNAs. Both exonic and novel X-chromosome REs were subject to robust meiotic sex chromosome inactivation, although an extensive de-repression occurred in the post-meiotic stages of spermatogenesis. Surprisingly, 2.4% of the 10,395 X chromosome exonic REs were present in mature sperm. Transcribed genomic repetitive sequences, including simple centromeric repeats, HERVE and HSAT1, were also shown to be associated with RE expression during spermatogenesis. These results suggest that pervasive intergenic repetitive sequence expression during human spermatogenesis may play a role in regulating chromatin dynamics. Repetitive REs switching repeat classes during differentiation upon fertilization and embryonic genome activation was evident.
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MESH Headings
- Algorithms
- Blastocyst/cytology
- Blastocyst/metabolism
- Cell Differentiation
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomes, Human, X/genetics
- Embryonic Development/genetics
- Exons/genetics
- Female
- Fertilization
- Gene Expression Regulation, Developmental
- Genomics
- Humans
- Liver/cytology
- Liver/metabolism
- Male
- Meiosis/genetics
- Oocytes/cytology
- Oocytes/metabolism
- Poly A/analysis
- Poly A/genetics
- Poly A/isolation & purification
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- Regulatory Sequences, Ribonucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, RNA
- Spermatogenesis/genetics
- Spermatozoa/cytology
- Spermatozoa/metabolism
- Transcription, Genetic
- X Chromosome Inactivation
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Affiliation(s)
- Molly S Estill
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
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67
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Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J. The single-cell transcriptional landscape of mammalian organogenesis. Nature 2019; 566:496-502. [PMID: 30787437 PMCID: PMC6434952 DOI: 10.1038/s41586-019-0969-x] [Citation(s) in RCA: 1908] [Impact Index Per Article: 381.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022]
Abstract
Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting 'mouse organogenesis cell atlas' (MOCA) provides a global view of developmental processes during this critical window. We use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes. We explore the dynamics of gene expression within cell types and trajectories over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle.
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Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Malte Spielmann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaojie Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Andrew J Hill
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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68
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Salvador-Martínez I, Grillo M, Averof M, Telford MJ. Is it possible to reconstruct an accurate cell lineage using CRISPR recorders? eLife 2019; 8:e40292. [PMID: 30688650 PMCID: PMC6349403 DOI: 10.7554/elife.40292] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/11/2019] [Indexed: 02/02/2023] Open
Abstract
Cell lineages provide the framework for understanding how cell fates are decided during development. Describing cell lineages in most organisms is challenging; even a fruit fly larva has ~50,000 cells and a small mammal has >1 billion cells. Recently, the idea of applying CRISPR to induce mutations during development, to be used as heritable markers for lineage reconstruction, has been proposed by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated. Here, we use computer simulations to estimate the performance of these approaches under different conditions. We incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters - variable cell division rates, skewed mutational outcomes, target dropouts and different sequencing strategies. Our approach reveals the limitations of published CRISPR recorders, and indicates how future implementations can be optimised. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Irepan Salvador-Martínez
- Centre for Life’s Origins and Evolution, Department of Genetics Evolution and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Marco Grillo
- Institut de Génomique Fonctionnelle de Lyon (IGFL)École Normale Supérieure de LyonLyonFrance
- Centre National de la Recherche Scientifique (CNRS)ParisFrance
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon (IGFL)École Normale Supérieure de LyonLyonFrance
- Centre National de la Recherche Scientifique (CNRS)ParisFrance
| | - Maximilian J Telford
- Centre for Life’s Origins and Evolution, Department of Genetics Evolution and EnvironmentUniversity College LondonLondonUnited Kingdom
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69
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Abstract
Mammalian target of rapamycin (mTOR) is a conserved serine/threonine kinase of the phosphatidylinositol kinase-related kinase family that regulates cell growth, metabolism, and autophagy. Extensive research has linked mTOR to several human diseases including cancer, neurodegenerative disorders, and aging. In this review, recent publications regarding the mechanisms underlying the role of mTOR in female reproduction under physiological and pathological conditions are summarized. Moreover, we assess whether strategies to improve or suppress mTOR expression could have therapeutic potential for reproductive diseases like premature ovarian failure, polycystic ovarian syndrome, and endometriosis.
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70
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Gatie MI, Assabgui AR, Kelly GM. The Zen of XEN: insight into differentiation, metabolism and genomic integrity. Cell Death Dis 2018; 9:1075. [PMID: 30349040 PMCID: PMC6197270 DOI: 10.1038/s41419-018-1120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Mohamed I Gatie
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada.,Collaborative Graduate Specialization in Developmental Biology, The University of Western Ontario, London, ON, Canada
| | - Amy R Assabgui
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada.,Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON, Canada
| | - Gregory M Kelly
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada. .,Collaborative Graduate Specialization in Developmental Biology, The University of Western Ontario, London, ON, Canada. .,Department of Paediatrics, The University of Western Ontario, London, ON, Canada. .,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada. .,Child Health Research Institute, London, ON, Canada. .,Ontario Institute for Regenerative Medicine, Toronto, ON, Canada.
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71
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Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation. Nat Cell Biol 2018; 20:1278-1289. [PMID: 30323188 DOI: 10.1038/s41556-018-0211-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/06/2018] [Indexed: 11/08/2022]
Abstract
The morphogenetic remodelling of embryo architecture after implantation culminates in pro-amniotic cavity formation. Despite its key importance, how this transformation occurs remains unknown. Here, we apply high-resolution imaging of embryos developing in vivo and in vitro, spatial RNA sequencing and 3D trophoblast stem cell models to determine the sequence and mechanisms of these remodelling events. We show that cavitation of the embryonic tissue is followed by folding of extra-embryonic tissue to mediate the formation of a second extra-embryonic cavity. Concomitantly, at the boundary between embryonic and extra-embryonic tissues, a hybrid 3D rosette forms. Resolution of this rosette enables the embryonic cavity to invade the extra-embryonic tissue. Subsequently, β1-integrin signalling mediates the formation of multiple extra-embryonic 3D rosettes. Podocalyxin exocytosis leads to their polarized resolution, permitting the extension of embryonic and extra-embryonic cavities and their fusion into a unified pro-amniotic cavity. These morphogenetic transformations of embryogenesis reveal a previously unappreciated mechanism for lumen expansion and fusion.
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72
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Barratt KS, Diamand KEM, Arkell RM. Identification of reference genes suitable for RT-qPCR studies of murine gastrulation and patterning. Mamm Genome 2018; 29:656-662. [PMID: 30094508 DOI: 10.1007/s00335-018-9769-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/20/2018] [Indexed: 11/26/2022]
Abstract
Quantitative reverse transcriptase PCR (RT-qPCR), a powerful and efficient means of rapidly comparing gene expression between experimental conditions, is routinely used as a phenotyping tool in developmental biology. The accurate comparison of gene expression across multiple embryonic stages requires normalisation to reference genes that have stable expression across the time points to be examined. As the embryo and its constituent tissues undergo rapid growth and differentiation during development, reference genes known to be stable across some time points cannot be assumed to be stable across all developmental stages. The immediate post-implantation events of gastrulation and patterning are characterised by a rapid expansion in cell number and increasing specialisation of cells. The optimal reference genes for comparative gene expression studies at these specific stages have not been experimentally identified. In this study, the expression of five commonly used reference genes (H2afz, Ubc, Actb, Tbp and Gapdh) was measured across murine gastrulation and patterning (6.5-9.5 dpc) and analysed with the normalisation tools geNorm, Bestkeeper and Normfinder. The results, validated by RT-qPCR analysis of two genes with well-documented expression patterns across these stages, indicated the best strategy for RT-qPCR studies spanning murine gastrulation and patterning utilises the concurrent reference genes H2afz and Ubc.
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Affiliation(s)
- Kristen S Barratt
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Koula E M Diamand
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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73
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Bowling S, Di Gregorio A, Sancho M, Pozzi S, Aarts M, Signore M, D Schneider M, Martinez-Barbera JP, Gil J, Rodríguez TA. P53 and mTOR signalling determine fitness selection through cell competition during early mouse embryonic development. Nat Commun 2018; 9:1763. [PMID: 29720666 PMCID: PMC5932021 DOI: 10.1038/s41467-018-04167-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/06/2018] [Indexed: 01/08/2023] Open
Abstract
Ensuring the fitness of the pluripotent cells that will contribute to future development is important both for the integrity of the germline and for proper embryogenesis. Consequently, it is becoming increasingly apparent that pluripotent cells can compare their fitness levels and signal the elimination of those cells that are less fit than their neighbours. In mammals the nature of the pathways that communicate fitness remain largely unknown. Here we identify that in the early mouse embryo and upon exit from naive pluripotency, the confrontation of cells with different fitness levels leads to an inhibition of mTOR signalling in the less fit cell type, causing its elimination. We show that during this process, p53 acts upstream of mTOR and is required to repress its activity. Finally, we demonstrate that during normal development around 35% of cells are eliminated by this pathway, highlighting the importance of this mechanism for embryonic development.
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Affiliation(s)
- Sarah Bowling
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- Cell Proliferation Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Cell Proliferation Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Aida Di Gregorio
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Margarida Sancho
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sara Pozzi
- Developmental Biology and Cancer Programme, Newlife Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N, UK
| | - Marieke Aarts
- Cell Proliferation Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Cell Proliferation Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Massimo Signore
- Developmental Biology and Cancer Programme, Newlife Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N, UK
| | - Michael D Schneider
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Juan Pedro Martinez-Barbera
- Developmental Biology and Cancer Programme, Newlife Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N, UK
| | - Jesús Gil
- Cell Proliferation Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.
- Cell Proliferation Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Tristan A Rodríguez
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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74
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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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75
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Embryonic lethality in mice lacking Trim59 due to impaired gastrulation development. Cell Death Dis 2018; 9:302. [PMID: 29467473 PMCID: PMC5833458 DOI: 10.1038/s41419-018-0370-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/21/2018] [Accepted: 02/01/2018] [Indexed: 01/13/2023]
Abstract
TRIM family members have been implicated in a variety of biological processes such as differentiation and development. We here found that Trim59 plays a critical role in early embryo development from blastocyst stage to gastrula. There existed delayed development and empty yolk sacs from embryonic day (E) 8.5 in Trim59−/− embryos. No viable Trim59−/− embryos were observed beyond E9.5. Trim59 deficiency affected primary germ layer formation at the beginning of gastrulation. At E6.5 and E7.5, the expression of primary germ layer formation-associated genes including Brachyury, lefty2, Cer1, Otx2, Wnt3, and BMP4 was reduced in Trim59−/− embryos. Homozygous mutant embryonic epiblasts were contracted and the mesoderm was absent. Trim59 could interact with actin- and myosin-associated proteins. Its deficiency disturbed F-actin polymerization during inner cell mass differentiation. Trim59-mediated polymerization of F-actin was via WASH K63-linked ubiquitination. Thus, Trim59 may be a critical regulator for early embryo development from blastocyst stage to gastrula through modulating F-actin assembly.
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76
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Morgani SM, Metzger JJ, Nichols J, Siggia ED, Hadjantonakis AK. Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning. eLife 2018; 7:e32839. [PMID: 29412136 PMCID: PMC5807051 DOI: 10.7554/elife.32839] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/02/2018] [Indexed: 12/29/2022] Open
Abstract
During gastrulation epiblast cells exit pluripotency as they specify and spatially arrange the three germ layers of the embryo. Similarly, human pluripotent stem cells (PSCs) undergo spatially organized fate specification on micropatterned surfaces. Since in vivo validation is not possible for the human, we developed a mouse PSC micropattern system and, with direct comparisons to mouse embryos, reveal the robust specification of distinct regional identities. BMP, WNT, ACTIVIN and FGF directed mouse epiblast-like cells to undergo an epithelial-to-mesenchymal transition and radially pattern posterior mesoderm fates. Conversely, WNT, ACTIVIN and FGF patterned anterior identities, including definitive endoderm. By contrast, epiblast stem cells, a developmentally advanced state, only specified anterior identities, but without patterning. The mouse micropattern system offers a robust scalable method to generate regionalized cell types present in vivo, resolve how signals promote distinct identities and generate patterns, and compare mechanisms operating in vivo and in vitro and across species.
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Affiliation(s)
- Sophie M Morgani
- Developmental Biology ProgramSloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Wellcome Trust-Medical Research Council Centre for Stem Cell ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Jakob J Metzger
- Center for Studies in Physics and BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Centre for Stem Cell ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric D Siggia
- Center for Studies in Physics and BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology ProgramSloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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77
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Lima A, Burgstaller J, Sanchez-Nieto JM, Rodríguez TA. The Mitochondria and the Regulation of Cell Fitness During Early Mammalian Development. Curr Top Dev Biol 2017; 128:339-363. [PMID: 29477168 DOI: 10.1016/bs.ctdb.2017.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
From fertilization until the onset of gastrulation the early mammalian embryo undergoes a dramatic series of changes that converts a single fertilized cell into a remarkably complex organism. Much attention has been given to the molecular changes occurring during this process, but here we will review what is known about the changes affecting the mitochondria and how they impact on the energy metabolism and apoptotic response of the embryo. We will also focus on understanding what quality control mechanisms ensure optimal mitochondrial activity in the embryo, and in this way provide an overview of the importance of the mitochondria in determining cell fitness during early mammalian development.
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Affiliation(s)
- Ana Lima
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom; Cell Stress Group, MRC London Institute of Medical Sciences (LMS), London, United Kingdom
| | - Jörg Burgstaller
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom; Biotechnology in Animal Production, Department for Agrobiotechnology, IFA Tulln, Tulln, Austria
| | - Juan M Sanchez-Nieto
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Tristan A Rodríguez
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom.
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78
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Milewski R, Szpila M, Ajduk A. Dynamics of cytoplasm and cleavage divisions correlates with preimplantation embryo development. Reproduction 2017; 155:1-14. [PMID: 28993454 DOI: 10.1530/rep-17-0230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 01/27/2023]
Abstract
In vitro fertilization has become increasingly popular as an infertility treatment. In order to improve efficiency of this procedure, there is a strong need for a refinement of existing embryo assessment methods and development of novel, robust and non-invasive selection protocols. Studies conducted on animal models can be extremely helpful here, as they allow for more extensive research on the potential biomarkers of embryo quality. In the present paper, we subjected mouse embryos to non-invasive time-lapse imaging and combined the Particle Image Velocimetry analysis of cytoplasmic dynamics in freshly fertilized oocytes with the morphokinetic analysis of recordings covering 5 days of preimplantation development. Our results indicate that parameters describing cytoplasmic dynamics and cleavage divisions independently correspond to mouse embryo's capacity to form a high-quality blastocyst. We also showed for the first time that these parameters are associated with the percentage of abnormal embryonic cells with fragmented nuclei and with embryo's ability to form primitive endoderm, one of the cell lineages differentiated during preimplantation development. Finally, we present a model that links selected cytoplasmic and morphokinetic parameters reflecting frequency of fertilization-induced Ca2+-oscillations and timing of 4-cell stage and compaction with viability of the embryo assessed as the total number of cells at the end of its preimplantation development. Our results indicate that a combined analysis of cytoplasmic dynamics and morphokinetics may facilitate the assessment of embryo's ability to form high-quality blastocysts.
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Affiliation(s)
- Robert Milewski
- Department of Statistics and Medical InformaticsMedical University of Bialystok, Bialystok, Poland
| | - Marcin Szpila
- Department of EmbryologyFaculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Ajduk
- Department of EmbryologyFaculty of Biology, University of Warsaw, Warsaw, Poland
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79
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Jukam D, Shariati SAM, Skotheim JM. Zygotic Genome Activation in Vertebrates. Dev Cell 2017; 42:316-332. [PMID: 28829942 PMCID: PMC5714289 DOI: 10.1016/j.devcel.2017.07.026] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
The first major developmental transition in vertebrate embryos is the maternal-to-zygotic transition (MZT) when maternal mRNAs are degraded and zygotic transcription begins. During the MZT, the embryo takes charge of gene expression to control cell differentiation and further development. This spectacular organismal transition requires nuclear reprogramming and the initiation of RNAPII at thousands of promoters. Zygotic genome activation (ZGA) is mechanistically coordinated with other embryonic events, including changes in the cell cycle, chromatin state, and nuclear-to-cytoplasmic component ratios. Here, we review progress in understanding vertebrate ZGA dynamics in frogs, fish, mice, and humans to explore differences and emphasize common features.
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Affiliation(s)
- David Jukam
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - S Ali M Shariati
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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80
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Peng G, Tam PPL, Jing N. Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Establishment of progenitor cell populations and lineage diversity during embryogenesis and the differentiation of pluripotent stem cells is a fascinating and intricate biological process. Conceptually, an understanding of this developmental process provides a framework to integrate stem-cell pluripotency, cell competence and differentiating potential with the activity of extrinsic and intrinsic molecular determinants. The recent advent of enabling technologies of high-resolution transcriptome analysis at the cellular, population and spatial levels proffers the capability of gaining deeper insights into the attributes of the gene regulatory network and molecular signaling in lineage specification and differentiation. In this review, we provide a snapshot of the emerging enabling genomic technologies that contribute to the study of development and stem-cell biology.
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Affiliation(s)
- Guangdun Peng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Patrick P. L. Tam
- Embryology Unit, Children's Medical Research Institute, School of Medical Sciences, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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81
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Rossant J, Tam PPL. New Insights into Early Human Development: Lessons for Stem Cell Derivation and Differentiation. Cell Stem Cell 2017; 20:18-28. [PMID: 28061351 DOI: 10.1016/j.stem.2016.12.004] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pathways underlying mouse embryonic development have always informed efforts to derive, maintain, and drive differentiation of human pluripotent stem cells. However, direct application of mouse embryology to the human system has not always been successful because of fundamental developmental differences between species. The naive pluripotent state of mouse embryonic stem cells (ESCs), in particular, has been difficult to capture in human ESCs, and appears to be transitory in the human embryo itself. Further studies of human and non-human primate embryo development are needed to untangle the complexities of pluripotency networks across mammalian species.
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Affiliation(s)
- Janet Rossant
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada.
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute and School of Medical Sciences, Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia.
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82
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Singh AP, Foley J, Tandon A, Phadke D, Karimi Kinyamu H, Archer TK. A role for BRG1 in the regulation of genes required for development of the lymphatic system. Oncotarget 2017; 8:54925-54938. [PMID: 28903392 PMCID: PMC5589631 DOI: 10.18632/oncotarget.18976] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/16/2017] [Indexed: 12/02/2022] Open
Abstract
Lymphatic vasculature is an important part of the cardiovascular system with multiple functions, including regulation of the return of interstitial fluid (lymph) to the bloodstream, immune responses, and fat absorption. Consequently, lymphatic vasculature defects are involved in many pathological processes, including tumor metastasis and lymphedema. BRG1 is an important player in the developmental window when the lymphatic system is initiated. In the current study, we used tamoxifen inducible Rosa26CreERT2-BRG1floxed/floxed mice that allowed temporal analysis of the impact of BRG1 inactivation in the embryo. The BRG1floxed/floxed/Cre-TM embryos exhibited edema and hemorrhage at embryonic day-13 and began to die. BRG1 deficient embryos had abnormal lymphatic sac linings with fewer LYVE1 positive lymphatic endothelial cells. Indeed, loss of BRG1 attenuated expression of a subset of lymphatic genes in-vivo. Furthermore, BRG1 binds at the promoters of COUP-TFII and LYVE1, suggesting that BRG1 modulates expression of these genes in the developing embryos. Conversely, re-expression of BRG1 in cells lacking endogenous BRG1 resulted in induction of lymphatic gene expression in-vitro, suggesting that BRG1 was both required and sufficient for lymphatic gene expression. These studies provide important insights into intrinsic regulation of BRG1-mediated lymphatic-gene expression, and further an understanding of lymphatic gene dysregulation in lymphedema and other disease conditions.
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Affiliation(s)
- Ajeet Pratap Singh
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.,Present address: Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
| | - Julie Foley
- Special Techniques Group, Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Arpit Tandon
- Sciome.com, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Dhiral Phadke
- Sciome.com, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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83
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Simunovic M, Brivanlou AH. Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis. Development 2017; 144:976-985. [PMID: 28292844 PMCID: PMC5358114 DOI: 10.1242/dev.143529] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells have an intrinsic ability to self-assemble and self-organize into complex and functional tissues and organs. By taking advantage of this ability, embryoids, organoids and gastruloids have recently been generated in vitro, providing a unique opportunity to explore complex embryological events in a detailed and highly quantitative manner. Here, we examine how such approaches are being used to answer fundamental questions in embryology, such as how cells self-organize and assemble, how the embryo breaks symmetry, and what controls timing and size in development. We also highlight how further improvements to these exciting technologies, based on the development of quantitative platforms to precisely follow and measure subcellular and molecular events, are paving the way for a more complete understanding of the complex events that help build the human embryo.
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Affiliation(s)
- Mijo Simunovic
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Ali H Brivanlou
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
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84
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Peng G, Jing N. The genome-wide molecular regulation of mouse gastrulation embryo. SCIENCE CHINA-LIFE SCIENCES 2017; 60:363-369. [PMID: 28251461 DOI: 10.1007/s11427-016-0285-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/25/2016] [Indexed: 11/24/2022]
Abstract
The diverse morphologies among vertebrate species stems from the evolution of a basic body plan that is constituted by a spatially organized ensemble of tissue lineage progenitors. At gastrulation, this body plan is established through a coordinated morphogenetic process and the delineation of tissue lineages that are driven by the activity of the genome. To explore the molecular mechanisms, in a comprehensive context, it is imperative to glean an understanding of the region- and population-specific genetic activity underpinning this fundamental developmental process. In this review, we outline the recent progresses and the future directions in studies of genome activity for the regulation of mouse embryogenesis at gastrulation.
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Affiliation(s)
- Guangdun Peng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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85
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Kim J, Kim SH, Jun JH. Prediction of blastocyst development and implantation potential in utero based on the third cleavage and compaction times in mouse pre-implantation embryos. J Reprod Dev 2016; 63:117-125. [PMID: 27980237 PMCID: PMC5401804 DOI: 10.1262/jrd.2016-129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytokinesis and cell division during pre-implantation embryonic development occur as an orchestrated spatiotemporal program. Cleavage, compaction, and
blastulation in pre-implantation embryos are essential for successful implantation and pregnancy. Their alteration is associated with chromosomal imbalance and
loss of developmental competence. In this study, we evaluated the time of cleavage and compaction as predictors for in vitro pre- and
peri-implantation development and in utero implantation potential by time-lapse monitoring. Mouse 2-cell embryos were collected on 1.5 days
post coitum (dpc) and were individually cultured to the outgrowth (OG) stage (7.5 dpc). Developmental stages were classified as 3-cell,
4-cell, 8-cell, morula, blastocyst, and OG. Cut-off times for successful blastocyst development were determined by receiver operating characteristic curve
analysis. When cut-off times were set as 9 h for the third cleavage from the 2- to 4-cell stage, and 40 h for compaction from the 2-cell to morula stage,
blastocyst and OG development rates, respectively, were significantly higher (P < 0.0001). Embryos were grouped according to the above cut-off time and
transferred to the contralateral uterine horn on 3.5 dpc. Implantation rates in utero on 5.5 dpc were significantly higher in early third
cleaved (≤ 9 h from 2- to 4-cell) and early compacted embryos (≤ 40 h from 2-cell to morula) than those in delayed embryos (P < 0.05). Therefore, the time of
the third cleavage from 2- to the 4-cell stage and compaction from 2-cell to morula stage may be a useful morphokinetic parameter for predicting developmental
potential, including successful implantation and pregnancy in human in vitro fertilization-embryo transfer programs.
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Affiliation(s)
- Jihyun Kim
- Department of Senior Healthcare, BK21 Plus Program, Graduated School, Eulji University, Gyeonggi-do 461-713, Korea
| | - Seok Hyun Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jin Hyun Jun
- Department of Senior Healthcare, BK21 Plus Program, Graduated School, Eulji University, Gyeonggi-do 461-713, Korea.,Department of Biomedical Laboratory Science, Graduate School of Health Science, Eulji University, Gyeonggi-do 461-713, Korea.,Eulji Medi-Bio Research Institute (EMBRI), Eulji University, Gyeonggi-do 461-713, Korea
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86
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Abstract
Three-dimensional organoid constructs serve as increasingly widespread in vitro models for development and disease modeling. Current approaches to recreate morphogenetic processes in vitro rely on poorly controllable and ill-defined matrices, thereby largely overlooking the contribution of biochemical and biophysical extracellular matrix (ECM) factors in promoting multicellular growth and reorganization. Here, we show how defined synthetic matrices can be used to explore the role of the ECM in the development of complex 3D neuroepithelial cysts that recapitulate key steps in early neurogenesis. We demonstrate how key ECM parameters are involved in specifying cytoskeleton-mediated symmetry-breaking events that ultimately lead to neural tube-like patterning along the dorsal-ventral (DV) axis. Such synthetic materials serve as valuable tools for studying the discrete action of extrinsic factors in organogenesis, and allow for the discovery of relationships between cytoskeletal mechanobiology and morphogenesis.
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87
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Affiliation(s)
- Cristina Clavería
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain;
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain;
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88
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Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biol 2016; 17:173. [PMID: 27534536 PMCID: PMC4989499 DOI: 10.1186/s13059-016-1033-x] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 07/27/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individual stem cells exit the pluripotent state and transition towards their respective progenitor states. RESULTS Here, we analyze the transcriptomes of human embryonic stem cell-derived lineage-specific progenitors by single-cell RNA-sequencing (scRNA-seq). We identify a definitive endoderm (DE) transcriptomic signature that leads us to pinpoint a critical time window when DE differentiation is enhanced by hypoxia. The molecular mechanisms governing the emergence of DE are further examined by time course scRNA-seq experiments, employing two new statistical tools to identify stage-specific genes over time (SCPattern) and to reconstruct the differentiation trajectory from the pluripotent state through mesendoderm to DE (Wave-Crest). Importantly, presumptive DE cells can be detected during the transitory phase from Brachyury (T) (+) mesendoderm toward a CXCR4 (+) DE state. Novel regulators are identified within this time window and are functionally validated on a screening platform with a T-2A-EGFP knock-in reporter engineered by CRISPR/Cas9. Through loss-of-function and gain-of-function experiments, we demonstrate that KLF8 plays a pivotal role modulating mesendoderm to DE differentiation. CONCLUSIONS We report the analysis of 1776 cells by scRNA-seq covering distinct human embryonic stem cell-derived progenitor states. By reconstructing a differentiation trajectory at single-cell resolution, novel regulators of the mesendoderm transition to DE are elucidated and validated. Our strategy of combining single-cell analysis and genetic approaches can be applied to uncover novel regulators governing cell fate decisions in a variety of systems.
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Affiliation(s)
- Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.
| | - Ning Leng
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.,Present address: Genentech, Inc., South San Francisco, CA, USA
| | - Jue Zhang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Zhonggang Hou
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.,Present address: Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - David T Vereide
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Jeea Choi
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA. .,Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA, USA.
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89
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Peng G, Suo S, Chen J, Chen W, Liu C, Yu F, Wang R, Chen S, Sun N, Cui G, Song L, Tam PPL, Han JDJ, Jing N. Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Dev Cell 2016; 36:681-97. [PMID: 27003939 DOI: 10.1016/j.devcel.2016.02.020] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 02/10/2016] [Accepted: 02/22/2016] [Indexed: 10/22/2022]
Abstract
Gastrulation of the mouse embryo entails progressive restriction of lineage potency and the organization of the lineage progenitors into a body plan. Here we performed a high-resolution RNA sequencing analysis on single mid-gastrulation mouse embryos to collate a spatial transcriptome that correlated with the regionalization of cell fates in the embryo. 3D rendition of the quantitative data enabled the visualization of the spatial pattern of all expressing genes in the epiblast in a digital whole-mount in situ format. The dataset also identified genes that (1) are co-expressed in a specific cell population, (2) display similar global pattern of expression, (3) have lineage markers, (4) mark domains of transcriptional and signaling activity associated with cell fates, and (5) can be used as zip codes for mapping the position of single cells isolated from the mid-gastrula stage embryo and the embryo-derived stem cells to the equivalent epiblast cells for delineating their prospective cell fates.
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Affiliation(s)
- Guangdun Peng
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Chen
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Weiyang Chen
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chang Liu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fang Yu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ran Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shirui Chen
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Sun
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guizhong Cui
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu Song
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute and School of Medical Sciences, Sydney Medical School, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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90
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Nguyen H, Sokpor G, Pham L, Rosenbusch J, Stoykova A, Staiger JF, Tuoc T. Epigenetic regulation by BAF (mSWI/SNF) chromatin remodeling complexes is indispensable for embryonic development. Cell Cycle 2016; 15:1317-24. [PMID: 26986003 DOI: 10.1080/15384101.2016.1160984] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The multi-subunit chromatin-remodeling SWI/SNF (known as BAF for Brg/Brm-associated factor) complexes play essential roles in development. Studies have shown that the loss of individual BAF subunits often affects local chromatin structure and specific transcriptional programs. However, we do not fully understand how BAF complexes function in development because no animal mutant had been engineered to lack entire multi-subunit BAF complexes. Importantly, we recently reported that double conditional knock-out (dcKO) of the BAF155 and BAF170 core subunits in mice abolished the presence of the other BAF subunits in the developing cortex. The generated dcKO mutant provides a novel and powerful tool for investigating how entire BAF complexes affect cortical development. Using this model, we found that BAF complexes globally control the key heterochromatin marks, H3K27me2 and -3, by directly modulating the enzymatic activity of the H3K27 demethylases, Utx and Jmjd3. Here, we present further insights into how the scaffolding ability of the BAF155 and BAF170 core subunits maintains the stability of BAF complexes in the forebrain and throughout the embryo during development. Furthermore, we show that the loss of BAF complexes in the above-described model up-regulates H3K27me3 and impairs forebrain development and embryogenesis. These findings improve our understanding of epigenetic mechanisms and their modulation by the chromatin-remodeling SWI/SNF complexes that control embryonic development.
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Affiliation(s)
- Huong Nguyen
- a University Medical Center , Georg-August-University Goettingen , Germany
| | - Godwin Sokpor
- a University Medical Center , Georg-August-University Goettingen , Germany
| | - Linh Pham
- a University Medical Center , Georg-August-University Goettingen , Germany
| | - Joachim Rosenbusch
- a University Medical Center , Georg-August-University Goettingen , Germany
| | - Anastassia Stoykova
- b Max-Planck-Institute for Biophysical Chemistry , Goettingen ; Germany.,c DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB) , Goettingen , Germany
| | - Jochen F Staiger
- a University Medical Center , Georg-August-University Goettingen , Germany.,c DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB) , Goettingen , Germany
| | - Tran Tuoc
- a University Medical Center , Georg-August-University Goettingen , Germany.,c DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB) , Goettingen , Germany
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91
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Balmer S, Nowotschin S, Hadjantonakis AK. Notochord morphogenesis in mice: Current understanding & open questions. Dev Dyn 2016; 245:547-57. [PMID: 26845388 DOI: 10.1002/dvdy.24392] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 12/25/2022] Open
Abstract
The notochord is a structure common to all chordates, and the feature that the phylum Chordata has been named after. It is a rod-like mesodermal structure that runs the anterior-posterior length of the embryo, adjacent to the ventral neural tube. The notochord plays a critical role in embryonic tissue patterning, for example the dorsal-ventral patterning of the neural tube. The cells that will come to form the notochord are specified at gastrulation. Axial mesodermal cells arising at the anterior primitive streak migrate anteriorly as the precursors of the notochord and populate the notochordal plate. Yet, even though a lot of interest has centered on investigating the functional and structural roles of the notochord, we still have a very rudimentary understanding of notochord morphogenesis. The events driving the formation of the notochord are rapid, taking place over the period of approximately a day in mice. In this commentary, we provide an overview of our current understanding of mouse notochord morphogenesis, from the initial specification of axial mesendodermal cells at the primitive streak, the emergence of these cells at the midline on the surface of the embryo, to their submergence and organization of the stereotypically positioned notochord. We will also discuss some key open questions. Developmental Dynamics 245:547-557, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sophie Balmer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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92
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Qiu Z, Elsayed Z, Peterkin V, Alkatib S, Bennett D, Landry JW. Ino80 is essential for proximal-distal axis asymmetry in part by regulating Bmp4 expression. BMC Biol 2016; 14:18. [PMID: 26975355 PMCID: PMC4790052 DOI: 10.1186/s12915-016-0238-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 02/16/2016] [Indexed: 12/12/2022] Open
Abstract
Background Understanding how embryos specify asymmetric axes is a major focus of biology. While much has been done to discover signaling pathways and transcription factors important for axis specification, comparatively little is known about how epigenetic regulators are involved. Epigenetic regulators operate downstream of signaling pathways and transcription factors to promote nuclear processes, most prominently transcription. To discover novel functions for these complexes in axis establishment during early embryonic development, we characterized phenotypes of a mouse knockout (KO) allele of the chromatin remodeling Ino80 ATPase. Results Ino80 KO embryos implant, but fail to develop beyond the egg cylinder stage. Ino80 KO embryonic stem cells (ESCs) are viable and maintain alkaline phosphatase activity, which is suggestive of pluripotency, but they fail to fully differentiate as either embryoid bodies or teratomas. Gene expression analysis of Ino80 KO early embryos by in situ hybridization and embryoid bodies by RT-PCR shows elevated Bmp4 expression and reduced expression of distal visceral endoderm (DVE) markers Cer1, Hex, and Lefty1. In culture, Bmp4 maintains stem cell pluripotency and when overexpressed is a known negative regulator of DVE differentiation in the early embryo. Consistent with the early embryo, we observed upregulated Bmp4 expression and down-regulated Cer1, Hex, and Lefty1 expression when Ino80 KO ESCs are differentiated in a monolayer. Molecular studies in these same cells demonstrate that Ino80 bound to the Bmp4 promoter regulates its chromatin structure, which correlates with enhanced SP1 binding. These results in combination suggest that Ino80 directly regulates the chromatin structure of the Bmp4 promoter with consequences to gene expression. Conclusions In contrast to Ino80 KO differentiated cells, our experiments show that undifferentiated Ino80 KO ESCs are viable, but fail to differentiate in culture and in the early embryo. Ino80 KO ESCs and the early embryo up-regulate Bmp4 expression and down-regulate the expression of DVE markers Cer1, Hex and Lefty1. Based on this data, we propose a model where the Ino80 chromatin remodeling complex represses Bmp4 expression in the early embryo, thus promoting DVE differentiation and successful proximal-distal axis establishment. These results are significant because they show that epigenetic regulators have specific roles in establishing embryonic axes. By further characterizing these complexes, we will deepen our understanding of how the mammalian embryo is patterned by epigenetic regulators. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0238-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhijun Qiu
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Zeinab Elsayed
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Veronica Peterkin
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Suehyb Alkatib
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Dorothy Bennett
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA.
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93
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Mallol A, Piqué L, Santaló J, Ibáñez E. Morphokinetics of cloned mouse embryos treated with epigenetic drugs and blastocyst prediction. Reproduction 2015; 151:203-14. [PMID: 26621919 DOI: 10.1530/rep-15-0354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/30/2015] [Indexed: 12/31/2022]
Abstract
Time-lapse monitoring of somatic cell nuclear transfer (SCNT) embryos may help to predict developmental success and increase birth and embryonic stem cells (ESC) derivation rates. Here, the development of ICSI fertilized embryos and of SCNT embryos, non-treated or treated with either psammaplin A (PsA) or vitamin C (VitC), was monitored, and the ESC derivation rates from the resulting blastocysts were determined. Blastocyst rates were similar among PsA-treated and VitC-treated SCNT embryos and ICSI embryos, but lower for non-treated SCNT embryos. ESC derivation rates were higher in treated SCNT embryos than in non-treated or ICSI embryos. Time-lapse microscopy analysis showed that non-treated SCNT embryos had a delayed development from the second division until compaction, lower number of blastomeres at compaction and longer compaction and cavitation durations compared with ICSI ones. Treatment of SCNT embryos with PsA further increased this delay whereas treatment with VitC slightly reduced it, suggesting that both treatments act through different mechanisms, not necessarily related to their epigenetic effects. Despite these differences, the time of completion of the third division, alone or combined with the duration of compaction and/or the presence of fragmentation, had a strong predictive value for blastocyst formation in all groups. In contrast, we failed to predict ESC derivation success from embryo morphokinetics. Time-lapse technology allows the selection of SCNT embryos with higher developmental potential and could help to increase cloning outcomes. Nonetheless, further studies are needed to find reliable markers for full-term development and ESC derivation success.
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Affiliation(s)
- Anna Mallol
- Unitat de Biologia Cel.lularDepartament de Biologia Cel.lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Laia Piqué
- Unitat de Biologia Cel.lularDepartament de Biologia Cel.lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Josep Santaló
- Unitat de Biologia Cel.lularDepartament de Biologia Cel.lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Elena Ibáñez
- Unitat de Biologia Cel.lularDepartament de Biologia Cel.lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Xu Q, Wang F, Xiang Y, Zhang X, Zhao ZA, Gao Z, Liu W, Lu X, Liu Y, Yu XJ, Wang H, Huang J, Yi Z, Gao S, Li L. Maternal BCAS2 protects genomic integrity in mouse early embryonic development. Development 2015; 142:3943-53. [PMID: 26428007 DOI: 10.1242/dev.129841] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/24/2015] [Indexed: 11/20/2022]
Abstract
Mammalian early embryos maintain accurate genome integrity for proper development within a programmed timeline despite constant assaults on their DNA by replication, DNA demethylation and genetic defects transmitted from germ cells. However, how genome integrity is safeguarded during mammalian early embryonic development remains unclear. BCAS2 (breast carcinoma amplified sequence 2), a core component of the PRP19 complex involved in pre-mRNA splicing, plays an important role in the DNA damage response through the RPA complex, a key regulator in the maintenance of genome integrity. Currently, the physiological role of BCAS2 in mammals is unknown. We now report that BCAS2 responds to endogenous and exogenous DNA damage in mouse zygotes. Maternal depletion of BCAS2 compromises the DNA damage response in early embryos, leading to developmental arrest at the two- to four-cell stage accompanied by the accumulation of damaged DNA and micronuclei. Furthermore, BCAS2 mutants that are unable to bind RPA1 fail in DNA repair during the zygotic stage. In addition, phosphorylated RPA2 cannot localise to the DNA damage sites in mouse zygotes with disrupted maternal BCAS2. These data suggest that BCAS2 might function through the RPA complex during DNA repair in zygotes. Together, our results reveal that maternal BCAS2 maintains the genome integrity of early embryos and is essential for female mouse fertility.
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Affiliation(s)
- Qianhua Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yunlong Xiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen-Ao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusheng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xing-Jiang Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haibin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhenjiang 310058, China
| | - Zhaohong Yi
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Carneiro K, de Brito JM, Rossi MID. Development by three-dimensional approaches and four-dimensional imaging: to the knowledge frontier and beyond. ACTA ACUST UNITED AC 2015; 105:1-8. [PMID: 25789860 DOI: 10.1002/bdrc.21089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many advances have been taken on elucidating embryonic development and tissue homeostasis and repair by the use of experimental strategies that preserve the three-dimensional (3D) organization and allow quantitative analysis of images over time (four-dimensional). Ranging from the understanding about the relationship between blastomeres and the events that take place during gastrulation by the use of time-lapse imaging through 3D cultures that mimic organogenesis, the advances in this area are of critical value. The studies on embryonic development without disrupting the original architecture and the development of 3D organoid cultures pave a new avenue for unprecedented experimental advances that will positively impact the emergence of new treatments applying regenerative principles for both tissue repair and organ transplant.
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Affiliation(s)
- Katia Carneiro
- Biomedical Institute of Sciences, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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