101
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Tardat M, Déjardin J. Telomere chromatin establishment and its maintenance during mammalian development. Chromosoma 2017; 127:3-18. [PMID: 29250704 PMCID: PMC5818603 DOI: 10.1007/s00412-017-0656-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Telomeres are specialized structures that evolved to protect the end of linear chromosomes from the action of the cell DNA damage machinery. They are composed of tandem arrays of repeated DNA sequences with a specific heterochromatic organization. The length of telomeric repeats is dynamically regulated and can be affected by changes in the telomere chromatin structure. When telomeres are not properly controlled, the resulting chromosomal alterations can induce genomic instability and ultimately the development of human diseases, such as cancer. Therefore, proper establishment, regulation, and maintenance of the telomere chromatin structure are required for cell homeostasis. Here, we review the current knowledge on telomeric chromatin dynamics during cell division and early development in mammals, and how its proper regulation safeguards genome stability.
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Affiliation(s)
- Mathieu Tardat
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Jérôme Déjardin
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
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102
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Svoboda P. Mammalian zygotic genome activation. Semin Cell Dev Biol 2017; 84:118-126. [PMID: 29233752 DOI: 10.1016/j.semcdb.2017.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/22/2017] [Accepted: 12/08/2017] [Indexed: 12/14/2022]
Abstract
Zygotic genome activation (ZGA) denotes the initiation of gene expression after fertilization. It is part of the complex oocyte-to-embryo transition (OET) in which a highly specialized cell - the oocyte - is fertilized and transformed into a zygote that gives rise to an embryo that will develop into a newborn. From the perspective of gene expression, the OET reflects reprogramming of germ cell gene expression into the new developmental program of the zygote. This reprogramming occurs at transcriptional and post-transcriptional levels. This review will discuss selected aspects of mammalian ZGA, highlighting shared features and evolved differences observed in commonly investigated mammals and non-mammalian model animals.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20, Prague 4, Czech Republic.
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103
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Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:1291-1303. [PMID: 28966118 PMCID: PMC5639460 DOI: 10.1016/j.stemcr.2017.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 01/21/2023] Open
Abstract
Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage. We identify SETα to be rapidly downregulated during ESC differentiation SETα is regulated by pluripotency factors and replaced by SETβ during differentiation SETα/SETβ switch is crucial for ESC differentiation SETα regulates chromatin plasticity in ESCs
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104
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Boroviak T, Nichols J. Primate embryogenesis predicts the hallmarks of human naïve pluripotency. Development 2017; 144:175-186. [PMID: 28096211 PMCID: PMC5430762 DOI: 10.1242/dev.145177] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Naïve pluripotent mouse embryonic stem cells (ESCs) resemble the preimplantation epiblast and efficiently contribute to chimaeras. Primate ESCs correspond to the postimplantation embryo and fail to resume development in chimaeric assays. Recent data suggest that human ESCs can be ‘reset’ to an earlier developmental stage, but their functional capacity remains ill defined. Here, we discuss how the naïve state is inherently linked to preimplantation epiblast identity in the embryo. We hypothesise that distinctive features of primate development provide stringent criteria to evaluate naïve pluripotency in human and other primate cells. Based on our hypothesis, we define 12 key hallmarks of naïve pluripotency, five of which are specific to primates. These hallmarks may serve as a functional framework to assess human naïve ESCs. Summary: This Hypothesis article highlights several fundamental differences between rodent and primate early development and exploits these to predict key hallmarks of naïve pluripotency in primates.
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Affiliation(s)
- Thorsten Boroviak
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 4BG, UK
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105
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Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing. Sci Rep 2017; 7:10794. [PMID: 28883481 PMCID: PMC5589911 DOI: 10.1038/s41598-017-11044-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/18/2017] [Indexed: 12/16/2022] Open
Abstract
In female mammals, one X chromosome is transcriptionally inactivated (XCI), leading to dosage compensation between sexes, fundamental for embryo viability. A previous study using single-cell RNA-sequencing (scRNA-seq) data proposed that female human preimplantation embryos achieve dosage compensation by downregulating both Xs, a phenomenon named dampening of X expression. Using a novel pipeline on those data, we identified a decrease in the proportion of biallelically expressed X-linked genes during development, consistent with XCI. Moreover, we show that while the expression sum of biallelically expressed X-linked genes decreases with embryonic development, their median expression remains constant, rejecting the hypothesis of X dampening. In addition, analyses of a different dataset of scRNA-seq suggest the appearance of X-linked monoallelic expression by the late blastocyst stage in females, another hallmark of initiation of XCI. Finally, we addressed the issue of dosage compensation between the single active X and autosomes in males and females for the first time during human preimplantation development, showing emergence of X to autosome dosage compensation by the upregulation of the active X chromosome in both male and female embryonic stem cells. Our results show compelling evidence of an early process of X chromosome inactivation during human preimplantation development.
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106
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Weissbein U, Plotnik O, Vershkov D, Benvenisty N. Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells. PLoS Genet 2017; 13:e1006979. [PMID: 28837588 PMCID: PMC5587343 DOI: 10.1371/journal.pgen.1006979] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 09/06/2017] [Accepted: 08/16/2017] [Indexed: 11/18/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are an important player in disease modeling and regenerative medicine. Nonetheless, multiple studies uncovered their inherent genetic instability upon prolonged culturing, where specific chromosomal aberrations provide cells with a growth advantage. These positively selected modifications have dramatic effects on multiple cellular characteristics. Epigenetic aberrations also possess the potential of changing gene expression and altering cellular functions. In the current study we assessed the landscape of DNA methylation aberrations during prolonged culturing of hPSCs, and defined a set of genes which are recurrently hypermethylated and silenced. We further focused on one of these genes, testis-specific Y-encoded like protein 5 (TSPYL5), and demonstrated that when silenced, differentiation-related genes and tumor-suppressor genes are downregulated, while pluripotency- and growth promoting genes are upregulated. This process is similar to the hypermethylation-mediated inactivation of certain genes during tumor development. Our analysis highlights the existence and importance of recurrent epigenetic aberrations in hPSCs during prolonged culturing.
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Affiliation(s)
- Uri Weissbein
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Omer Plotnik
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
- * E-mail:
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107
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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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108
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Zuo Y, Su G, Cheng L, Liu K, Feng Y, Wei Z, Bai C, Cao G, Li G. Coexpression analysis identifies nuclear reprogramming barriers of somatic cell nuclear transfer embryos. Oncotarget 2017; 8:65847-65859. [PMID: 29029477 PMCID: PMC5630377 DOI: 10.18632/oncotarget.19504] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/30/2017] [Indexed: 11/25/2022] Open
Abstract
The success of cloned animal "Dolly Sheep" demonstrated the somatic cell nuclear transfer (SCNT) technique holds huge potentials for mammalian asexual reproduction. However, the extremely poor development of SCNT embryos indicates their molecular mechanism remain largely unexplored. Deciphering the spatiotemporal patterns of gene expression in SCNT embryos is a crucial step toward understanding the mechanisms associated with nuclear reprogramming. In this study, a valuable transcriptome recourse of SCNT embryos was firstly established, which derived from different inter-/intra donor cells. The gene co-expression analysis identified 26 cell-specific modules, and a series of regulatory pathways related to reprogramming barriers were further enriched. Compared to the intra-SCNT embryos, the inter-SCNT embryos underwent only complete partially reprogramming. As master genome trigger genes, the transcripts related to TFIID subunit, RNA polymerase and mediators were incomplete activated in inter-SCNT embryos. The inter-SCNT embryos only wasted the stored maternal mRNA of master regulators, but failed to activate their self-sustained pathway of RNA polymerases. The KDM family of epigenetic regulator also seriously delayed in inter-SCNT embryo reprogramming process. Our study provided new insight into understanding of the mechanisms of nuclear reprogramming.
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Affiliation(s)
- Yongchun Zuo
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.,College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guanghua Su
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Lei Cheng
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Kun Liu
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Yu Feng
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Zhuying Wei
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Chunling Bai
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangpeng Li
- The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
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109
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Otte J, Wruck W, Adjaye J. New insights into human primordial germ cells and early embryonic development from single-cell analysis. FEBS Lett 2017. [PMID: 28627120 DOI: 10.1002/1873-3468.12716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human preimplantation developmental studies are difficult to accomplish due to associated ethical and moral issues. Preimplantation cells are rare and exist only in transient cell states. From a single cell, it is very challenging to analyse the origination of the heterogeneity and complexity inherent to the human body. However, recent advances in single-cell technology and data analysis have provided new insights into the process of early human development and germ cell specification. In this Review, we examine the latest single-cell datasets of human preimplantation embryos and germ cell development, compare them to bulk cell analyses, and interpret their biological implications.
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Affiliation(s)
- Jörg Otte
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
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110
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Durruthy-Durruthy J, Wossidlo M, Pai S, Takahashi Y, Kang G, Omberg L, Chen B, Nakauchi H, Reijo Pera R, Sebastiano V. Spatiotemporal Reconstruction of the Human Blastocyst by Single-Cell Gene-Expression Analysis Informs Induction of Naive Pluripotency. Dev Cell 2017; 38:100-15. [PMID: 27404362 DOI: 10.1016/j.devcel.2016.06.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 05/25/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
Human preimplantation embryo development involves complex cellular and molecular events that lead to the establishment of three cell lineages in the blastocyst: trophectoderm, primitive endoderm, and epiblast. Owing to limited resources of biological specimens, our understanding of how the earliest lineage commitments are regulated remains narrow. Here, we examined gene expression in 241 individual cells from early and late human blastocysts to delineate dynamic gene-expression changes. We distinguished all three lineages and further developed a 3D model of the inner cell mass and trophectoderm in which individual cells were mapped into distinct expression domains. We identified in silico precursors of the epiblast and primitive endoderm lineages and revealed a role for MCRS1, TET1, and THAP11 in epiblast formation and their ability to induce naive pluripotency in vitro. Our results highlight the potential of single-cell gene-expression analysis in human preimplantation development to instruct human stem cell biology.
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Affiliation(s)
- Jens Durruthy-Durruthy
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark Wossidlo
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sunil Pai
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Yusuke Takahashi
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Gugene Kang
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | | | - Bertha Chen
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Renee Reijo Pera
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
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111
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Zakharova FM, Zakharov VV. Identification of brain proteins BASP1 and GAP-43 in mouse oocytes and zygotes. Russ J Dev Biol 2017. [DOI: 10.1134/s1062360417030110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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112
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Li J, Han W, Shen X, Han S, Ye H, Huang G. DNA methylation signature of long noncoding RNA genes during human pre-implantation embryonic development. Oncotarget 2017; 8:56829-56838. [PMID: 28915634 PMCID: PMC5593605 DOI: 10.18632/oncotarget.18072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/25/2017] [Indexed: 11/25/2022] Open
Abstract
DNA methylation have crucial roles in regulating the expression of developmental genes during mammalian pre-implantation embryonic development (PED). However, the DNA methylation dynamic pattern of long noncoding RNA (lncRNA) genes, one type of epigenetic regulators, in human PED have not yet been demonstrated. Here, we performed a comprehensive analysis of lncRNA genes in human PED based on public reduced representation bisulphite sequencing (RRBS) data. We observed that both lncRNA and protein-coding genes complete the major demethylation wave at the 2-cell stage, whereas the promoters of lncRNA genes show higher methylation level than protein-coding genes during PED. Similar methylation distribution was observed across the transcription start sites (TSS) of lncRNA and protein-coding genes, contrary to previous observations in tissues. Besides, not only the gamete-specific differentially methylated regions (G-DMRs) but also the embryonic developmental-specific DMRs (D-DMRs) showed more paternal bias, especially in promoter regions in lncRNA genes. Moreover, coding-non-coding gene co-expression network analysis of genes containing D-DMRs suggested that lncRNA genes involved in PED are associated with gene expression regulation through several means, such as mRNA splicing, translational regulation and mRNA catabolic. This firstly provides study provides the methylation profiles of lncRNA genes in human PED and improves the understanding of lncRNA genes involvement in human PED.
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Affiliation(s)
- Jingyu Li
- Chongqing Reproductive and Genetics Institute, Chongqing 400013, China
| | - Wei Han
- Chongqing Reproductive and Genetics Institute, Chongqing 400013, China
| | - Xiaoli Shen
- Chongqing Reproductive and Genetics Institute, Chongqing 400013, China
| | - Shubiao Han
- Chongqing Reproductive and Genetics Institute, Chongqing 400013, China
| | - Hong Ye
- Chongqing Reproductive and Genetics Institute, Chongqing 400013, China
| | - Guoning Huang
- Chongqing Reproductive and Genetics Institute, Chongqing 400013, China
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113
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De Iaco A, Planet E, Coluccio A, Verp S, Duc J, Trono D. DUX-family transcription factors regulate zygotic genome activation in placental mammals. Nat Genet 2017; 49:941-945. [PMID: 28459456 PMCID: PMC5446900 DOI: 10.1038/ng.3858] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/07/2017] [Indexed: 12/22/2022]
Abstract
In animal embryos, transcription is mostly silent for several cell divisions, until the release of the first major wave of embryonic transcripts through so-called zygotic genome activation (ZGA). Maternally provided ZGA-triggering factors have been identified in Drosophila melanogaster and Danio rerio, but their mammalian homologs are still undefined. Here, we provide evidence that the DUX family of transcription factors is essential to this process in mice and potentially in humans. First, human DUX4 and mouse Dux are both expressed before ZGA in their respective species. Second, both orthologous proteins bind the promoters of ZGA-associated genes and activate their transcription. Third, Dux knockout in mouse embryonic stem cells (mESCs) prevents the cells from cycling through a 2-cell-like state. Finally, zygotic depletion of Dux leads to impaired early embryonic development and defective ZGA. We conclude that DUX-family proteins are key inducers of zygotic genome activation in placental mammals.
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Affiliation(s)
- Alberto De Iaco
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Coluccio
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sonia Verp
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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114
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McCoy RC. Mosaicism in Preimplantation Human Embryos: When Chromosomal Abnormalities Are the Norm. Trends Genet 2017; 33:448-463. [PMID: 28457629 DOI: 10.1016/j.tig.2017.04.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/15/2022]
Abstract
Along with errors in meiosis, mitotic errors during post-zygotic cell division contribute to pervasive aneuploidy in human embryos. Relatively little is known, however, about the genesis of these errors or their fitness consequences. Rapid technological advances are helping to close this gap, revealing diverse molecular mechanisms contributing to mitotic error. These include altered cell cycle checkpoints, aberrations of the centrosome, and failed chromatid cohesion, mirroring findings from cancer biology. Recent studies are challenging the idea that mitotic error is abnormal, emphasizing that the fitness impacts of mosaicism depend on its scope and severity. In light of these findings, technical and philosophical limitations of various screening approaches are discussed, along with avenues for future research.
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Affiliation(s)
- Rajiv C McCoy
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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115
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Gao F, Niu Y, Sun YE, Lu H, Chen Y, Li S, Kang Y, Luo Y, Si C, Yu J, Li C, Sun N, Si W, Wang H, Ji W, Tan T. De novo DNA methylation during monkey pre-implantation embryogenesis. Cell Res 2017; 27:526-539. [PMID: 28233770 PMCID: PMC5385613 DOI: 10.1038/cr.2017.25] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/01/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022] Open
Abstract
Critical epigenetic regulation of primate embryogenesis entails DNA methylome changes. Here we report genome-wide composition, patterning, and stage-specific dynamics of DNA methylation in pre-implantation rhesus monkey embryos as well as male and female gametes studied using an optimized tagmentation-based whole-genome bisulfite sequencing method. We show that upon fertilization, both paternal and maternal genomes undergo active DNA demethylation, and genome-wide de novo DNA methylation is also initiated in the same period. By the 8-cell stage, remethylation becomes more pronounced than demethylation, resulting in an increase in global DNA methylation. Promoters of genes associated with oxidative phosphorylation are preferentially remethylated at the 8-cell stage, suggesting that this mode of energy metabolism may not be favored. Unlike in rodents, X chromosome inactivation is not observed during monkey pre-implantation development. Our study provides the first comprehensive illustration of the 'wax and wane' phases of DNA methylation dynamics. Most importantly, our DNA methyltransferase loss-of-function analysis indicates that DNA methylation influences early monkey embryogenesis.
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Affiliation(s)
- Fei Gao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yuyu Niu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Yi Eve Sun
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Translational Stem Cell Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China
- Department of Psychiatry and Biobehavioral Sciences, UCLA Medical School, Los Angeles, CA 90095, USA
| | - Hanlin Lu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yongchang Chen
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Siguang Li
- Translational Stem Cell Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China
| | - Yu Kang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Yuping Luo
- Translational Stem Cell Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China
| | - Chenyang Si
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Juehua Yu
- Department of Psychiatry and Biobehavioral Sciences, UCLA Medical School, Los Angeles, CA 90095, USA
| | - Chang Li
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Nianqin Sun
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Wei Si
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Hong Wang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
| | - Tao Tan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan 650500, China
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116
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Ge SX. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics 2017; 18:200. [PMID: 28231763 PMCID: PMC5324221 DOI: 10.1186/s12864-017-3566-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study the complex gene regulation in mouse pre-implantation development (PD). RESULTS Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time. CONCLUSIONS Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.
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Affiliation(s)
- Steven Xijin Ge
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD, 57110, USA.
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117
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Wang X, Liu D, He D, Suo S, Xia X, He X, Han JDJ, Zheng P. Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos. Genome Res 2017; 27:567-579. [PMID: 28223401 PMCID: PMC5378175 DOI: 10.1101/gr.198044.115] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 02/10/2017] [Indexed: 12/31/2022]
Abstract
Preimplantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA), and cell-fate commitment. The molecular basis of these processes remains obscure in primates in which there is a high rate of embryo wastage. Thus, understanding the factors involved in genome reprogramming and ZGA might help reproductive success during this susceptible period of early development and generate induced pluripotent stem cells with greater efficiency. Moreover, explaining the molecular basis responsible for embryo wastage in primates will greatly expand our knowledge of species evolution. By using RNA-seq in single and pooled oocytes and embryos, we defined the transcriptome throughout preimplantation development in rhesus monkey. In comparison to archival human and mouse data, we found that the transcriptome dynamics of monkey oocytes and embryos were very similar to those of human but very different from those of mouse. We identified several classes of maternal and zygotic genes, whose expression peaks were highly correlated with the time frames of genome reprogramming, ZGA, and cell-fate commitment, respectively. Importantly, comparison of the ZGA-related network modules among the three species revealed less robust surveillance of genomic instability in primate oocytes and embryos than in rodents, particularly in the pathways of DNA damage signaling and homology-directed DNA double-strand break repair. This study highlights the utility of monkey models to better understand the molecular basis for genome reprogramming, ZGA, and genomic stability surveillance in human early embryogenesis and may provide insights for improved homologous recombination-mediated gene editing in monkey.
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Affiliation(s)
- Xinyi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Denghui Liu
- 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.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dajian He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, 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.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian Xia
- 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.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiechao He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - 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
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
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118
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Hasley A, Chavez S, Danilchik M, Wühr M, Pelegri F. Vertebrate Embryonic Cleavage Pattern Determination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:117-171. [PMID: 27975272 PMCID: PMC6500441 DOI: 10.1007/978-3-319-46095-6_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pattern of the earliest cell divisions in a vertebrate embryo lays the groundwork for later developmental events such as gastrulation, organogenesis, and overall body plan establishment. Understanding these early cleavage patterns and the mechanisms that create them is thus crucial for the study of vertebrate development. This chapter describes the early cleavage stages for species representing ray-finned fish, amphibians, birds, reptiles, mammals, and proto-vertebrate ascidians and summarizes current understanding of the mechanisms that govern these patterns. The nearly universal influence of cell shape on orientation and positioning of spindles and cleavage furrows and the mechanisms that mediate this influence are discussed. We discuss in particular models of aster and spindle centering and orientation in large embryonic blastomeres that rely on asymmetric internal pulling forces generated by the cleavage furrow for the previous cell cycle. Also explored are mechanisms that integrate cell division given the limited supply of cellular building blocks in the egg and several-fold changes of cell size during early development, as well as cytoskeletal specializations specific to early blastomeres including processes leading to blastomere cohesion. Finally, we discuss evolutionary conclusions beginning to emerge from the contemporary analysis of the phylogenetic distributions of cleavage patterns. In sum, this chapter seeks to summarize our current understanding of vertebrate early embryonic cleavage patterns and their control and evolution.
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Affiliation(s)
- Andrew Hasley
- Laboratory of Genetics, University of Wisconsin-Madison, Genetics/Biotech Addition, Room 2424, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Shawn Chavez
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Department of Physiology & Pharmacology, Oregon Heath & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Department of Obstetrics & Gynecology, Oregon Heath & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Michael Danilchik
- Department of Integrative Biosciences, L499, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Martin Wühr
- Department of Molecular Biology & The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Icahn Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Genetics/Biotech Addition, Room 2424, 425-G Henry Mall, Madison, WI, 53706, USA.
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119
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Kirkegaard K, Dyrlund TF, Ingerslev HJ. Clinical Application of Methods to Select In VitroFertilized Embryos. Hum Reprod 2016. [DOI: 10.1002/9781118849613.ch7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Kirstine Kirkegaard
- Department of Medical Biochemistry; Aarhus University Hospital; Aarhus Denmark
| | - Thomas F. Dyrlund
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus Denmark
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120
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Tedeschi G, Albani E, Borroni EM, Parini V, Brucculeri AM, Maffioli E, Negri A, Nonnis S, Maccarrone M, Levi-Setti PE. Proteomic profile of maternal-aged blastocoel fluid suggests a novel role for ubiquitin system in blastocyst quality. J Assist Reprod Genet 2016; 34:225-238. [PMID: 27924460 DOI: 10.1007/s10815-016-0842-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The etiology of maternal aging, a common cause of female factor infertility and a rate-limiting step in vitro fertilization (IVF) success, remains still unclear. Proteomic changes responsible for the impaired successful pregnancy outcome after IVF with aged blastocysts have not been yet evaluated. The objective of this prospective study was to employ proteomic techniques and bioinformatic tools to enlight differences at the protein level in blastocoel fluid of aged and younger woman. METHODS Protein composition of human blastocoel fluid isolated by micromanipulation from 46 blastocysts of women aged <37 years (group A) and 29 of women aged ≥37 years (group B) have been identified by a shotgun proteomic approach based on high-resolution nano-liquid chromatography electrospray-ionization-tandem mass spectrometry (nLC-ESI-MS/MS) using label free for the relative quantification of their expression levels. RESULTS The proteomic analysis leads to the identification and quantification of 148 proteins; 132 and 116 proteins were identified in groups A and B, respectively. Interestingly, the identified proteins are mainly involved in processes aimed at fine tuning embryo implantation and development. Among the 100 proteins commonly expressed in both groups, 17 proteins are upregulated and 44 downregulated in group B compared to group A. Overall, the analysis identified 33 proteins, which were increased or present only in B while 76 were decreased in B or present only in A. CONCLUSIONS Data revealed that maternal aging mainly affects blastocyst survival and implantation through unbalancing the equilibrium of the ubiquitin system known to play a crucial role in fine-tuning several aspects required to ensure successful pregnancy outcome.
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Affiliation(s)
- Gabriella Tedeschi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy.,Fondazione Filarete, 20139, Milan, Italy
| | - Elena Albani
- Humanitas Fertility Center, Department of Gynecology, Division of Gynecology and Reproductive Medicine, Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Elena Monica Borroni
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy.
| | - Valentina Parini
- Humanitas Fertility Center, Department of Gynecology, Division of Gynecology and Reproductive Medicine, Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Anna Maria Brucculeri
- Humanitas Fertility Center, Department of Gynecology, Division of Gynecology and Reproductive Medicine, Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | | | - Armando Negri
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Simona Nonnis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Mauro Maccarrone
- Department of Medicine, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128, Rome, Italy
| | - Paolo Emanuele Levi-Setti
- Humanitas Fertility Center, Department of Gynecology, Division of Gynecology and Reproductive Medicine, Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
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121
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Li J, Gao Z, Wang X, Liu H, Zhang Y, Liu Z. Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development. Sci Rep 2016; 6:38333. [PMID: 27922056 PMCID: PMC5138625 DOI: 10.1038/srep38333] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species. By weighted co-expression network analysis, we identified 5 developmental stages specific co-expression modules. Gene ontology enrichment analysis of these specific co-expression modules suggested that many lincRNAs are associated with cell cycle regulation, transcription and metabolism to regulate the process of zygotic genome activation. Futhermore, we identified hub lincRNAs in each co-expression modules, and found two lincRNAs TCONS_00166370 and TCONS_00020255 may play a vital role in porcine PED. This study systematically analyze lincRNAs in pig and provides the first catalog of lincRNAs that might function as gene regulatory factors of porcine PED.
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Affiliation(s)
- Jingyu Li
- College of Life Science, North-east Agricultural University, Harbin, 150030, China.,Chong Qing Reproductive and Genetics Institute, Chongqing Obstetrics and Gynecology Hospital, 64 Jing Tang ST, Yu Zhong District, Chongqing, 400013, China
| | - Zhengling Gao
- College of Life Science, North-east Agricultural University, Harbin, 150030, China
| | - Xingyu Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China
| | - Zhonghua Liu
- College of Life Science, North-east Agricultural University, Harbin, 150030, China
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122
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Liu L. Linking Telomere Regulation to Stem Cell Pluripotency. Trends Genet 2016; 33:16-33. [PMID: 27889084 DOI: 10.1016/j.tig.2016.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/18/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022]
Abstract
Embryonic stem cells (ESCs), somatic cell nuclear transfer ESCs, and induced pluripotent stem cells (iPSCs) represent the most studied group of PSCs. Unlimited self-renewal without incurring chromosomal instability and pluripotency are essential for the potential use of PSCs in regenerative therapy. Telomere length maintenance is critical for the unlimited self-renewal, pluripotency, and chromosomal stability of PSCs. While telomerase has a primary role in telomere maintenance, alternative lengthening of telomere pathways involving recombination and epigenetic modifications are also required for telomere length regulation, notably in mouse PSCs. Telomere rejuvenation is part of epigenetic reprogramming to pluripotency. Insights into telomere reprogramming and maintenance in PSCs may have implications for understanding of aging and tumorigenesis. Here, I discuss the link between telomere elongation and homeostasis to the acquisition and maintenance of stem cell pluripotency, and their regulatory mechanisms by epigenetic modifications.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin 300071, China.
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123
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Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genet 2016; 12:e1006427. [PMID: 27835649 PMCID: PMC5106035 DOI: 10.1371/journal.pgen.1006427] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Thousands of regions in gametes have opposing methylation profiles that are largely resolved during the post-fertilization epigenetic reprogramming. However some specific sequences associated with imprinted loci survive this demethylation process. Here we present the data describing the fate of germline-derived methylation in humans. With the exception of a few known paternally methylated germline differentially methylated regions (DMRs) associated with known imprinted domains, we demonstrate that sperm-derived methylation is reprogrammed by the blastocyst stage of development. In contrast a large number of oocyte-derived methylation differences survive to the blastocyst stage and uniquely persist as transiently methylated DMRs only in the placenta. Furthermore, we demonstrate that this phenomenon is exclusive to primates, since no placenta-specific maternal methylation was observed in mouse. Utilizing single cell RNA-seq datasets from human preimplantation embryos we show that following embryonic genome activation the maternally methylated transient DMRs can orchestrate imprinted expression. However despite showing widespread imprinted expression of genes in placenta, allele-specific transcriptional profiling revealed that not all placenta-specific DMRs coordinate imprinted expression and that this maternal methylation may be absent in a minority of samples, suggestive of polymorphic imprinted methylation. Differences in gamete DNA methylation is subject to genome-wide reprogramming during preimplantation development to establish an embryo with an epigenetic state compatible with totipotency. DNA sequences associated with imprinted differentially methylated regions (DMRs) are largely protected from this process, retaining their parent-of-origin epigenetic marks. By comparing the methylation profiles of human oocytes, sperm, blastocysts and various somatic tissues including placenta, we observe hundreds of CpG island sequences that maintain methylation on their maternal allele in blastocysts and placenta indicative of incomplete reprogramming. In some cases this maternal methylation influence transcription of nearby genes, revealing transient imprinting in embryos after genome-activation and in placenta. Strikingly, these placenta-specific DMRs are polymorphic between placenta samples with a minority of samples being robustly unmethylated on both alleles.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Franck Court
- Laboratoire GReD, CNRS, UMR6293, Clermont-Ferrand, France
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Isabel Iglesias-Platas
- Neonatal service, Hospital Sant Joan de Déu, BCNatal Hospital Sant Joan de Déu i Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Maria Eugenia Poo-Llanillo
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institute of Research and Advanced Studies, (ICREA), Passeig de Lluís Companys, Barcelona, Spain
- Centro Nacional de Analisis Genomico (CRG-CNAG), Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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124
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Freour T, Vassena R. Transcriptomics analysis and human preimplantation development. J Proteomics 2016; 162:135-140. [PMID: 27765633 DOI: 10.1016/j.jprot.2016.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/25/2016] [Accepted: 10/14/2016] [Indexed: 12/12/2022]
Abstract
The study of oocyte and preimplantation embryo biology has been regarded with great curiosity throughout scientific history, but it is not until the development of robust methods for in vitro observation and manipulation of animal gametes that developmental biology has flourished as a discipline. By far the biggest technical challenge in studying transcription in oocytes and early embryo has been the necessity of developing techniques that retain a high level of accuracy when starting from small amount of material. The objective of this narrative review is to summarize the knowledge gained about the embryonic preimplantation period in the human species from transcriptomics experiments, and to discuss technical limitations and solutions to the study of transcriptomics in these samples. SIGNIFICANCE In this review we identify key critical issues in performing transcriptomics experiments during the human preimplantation period, and identifying possible ways to overcome them. This, combined with a description of clinical perspectives and the definition of future avenues for research will provide useful for future research.
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Affiliation(s)
- Thomas Freour
- Clinica EUGIN, Barcelona, Spain; Service de médecine et biologie de la reproduction, CHU de Nantes, Nantes, France; Faculté de médecine, Université de Nantes, Nantes, France; INSERM UMR1064, Nantes, France
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125
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Zimmerlin L, Park TS, Huo JS, Verma K, Pather SR, Talbot CC, Agarwal J, Steppan D, Zhang YW, Considine M, Guo H, Zhong X, Gutierrez C, Cope L, Canto-Soler MV, Friedman AD, Baylin SB, Zambidis ET. Tankyrase inhibition promotes a stable human naïve pluripotent state with improved functionality. Development 2016; 143:4368-4380. [PMID: 27660325 DOI: 10.1242/dev.138982] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/11/2016] [Indexed: 01/04/2023]
Abstract
The derivation and maintenance of human pluripotent stem cells (hPSCs) in stable naïve pluripotent states has a wide impact in human developmental biology. However, hPSCs are unstable in classical naïve mouse embryonic stem cell (ESC) WNT and MEK/ERK signal inhibition (2i) culture. We show that a broad repertoire of conventional hESC and transgene-independent human induced pluripotent stem cell (hiPSC) lines could be reverted to stable human preimplantation inner cell mass (ICM)-like naïve states with only WNT, MEK/ERK, and tankyrase inhibition (LIF-3i). LIF-3i-reverted hPSCs retained normal karyotypes and genomic imprints, and attained defining mouse ESC-like functional features, including high clonal self-renewal, independence from MEK/ERK signaling, dependence on JAK/STAT3 and BMP4 signaling, and naïve-specific transcriptional and epigenetic configurations. Tankyrase inhibition promoted a stable acquisition of a human preimplantation ICM-like ground state via modulation of WNT signaling, and was most efficacious in efficiently reprogrammed conventional hiPSCs. Importantly, naïve reversion of a broad repertoire of conventional hiPSCs reduced lineage-primed gene expression and significantly improved their multilineage differentiation capacities. Stable naïve hPSCs with reduced genetic variability and improved functional pluripotency will have great utility in regenerative medicine and human disease modeling.
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Affiliation(s)
- Ludovic Zimmerlin
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Tea Soon Park
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Jeffrey S Huo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Karan Verma
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Sarshan R Pather
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences at Johns Hopkins, Baltimore, MD 21205, USA
| | - Jasmin Agarwal
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Diana Steppan
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Yang W Zhang
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Michael Considine
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Hong Guo
- Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Xiufeng Zhong
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christian Gutierrez
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Leslie Cope
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - M Valeria Canto-Soler
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Stephen B Baylin
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA .,Division of Pediatric Oncology, Baltimore, MD 21205, USA
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Huntriss J, Lu J, Hemmings K, Bayne R, Anderson R, Rutherford A, Balen A, Elder K, Picton HM. Isolation and expression of the human gametocyte-specific factor 1 gene (GTSF1) in fetal ovary, oocytes, and preimplantation embryos. J Assist Reprod Genet 2016; 34:23-31. [PMID: 27646122 PMCID: PMC5330970 DOI: 10.1007/s10815-016-0795-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/16/2016] [Indexed: 01/23/2023] Open
Abstract
Purpose Gametocyte-specific factor 1 has been shown in other species to be required for the silencing of retrotransposons via the Piwi-interacting RNA (piRNA) pathway. In this study, we aimed to isolate and assess expression of transcripts of the gametocyte-specific factor 1 (GTSF1) gene in the human female germline and in preimplantation embryos. Methods Complementary DNA (cDNA) libraries from human fetal ovaries and testes, human oocytes and preimplantation embryos and ovarian follicles isolated from an adult ovarian cortex biopsy were used to as templates for PCR, cloning and sequencing, and real time PCR experiments of GTSF1 expression. Results GTSF1 cDNA clones that covered the entire coding region were isolated from human oocytes and preimplantation embryos. GTSF1 mRNA expression was detected in archived cDNAs from staged human ovarian follicles, germinal vesicle (GV) stage oocytes, metaphase II oocytes, and morula and blastocyst stage preimplantation embryos. Within the adult female germline, expression was highest in GV oocytes. GTSF1 mRNA expression was also assessed in human fetal ovary and was observed to increase during gestation, from 8 to 21 weeks, during which time oogonia enter meiosis and primordial follicle formation first occurs. In human fetal testis, GTSF1 expression also increased from 8 to 19 weeks. Conclusions To our knowledge, this report is the first to describe the expression of the human GTSF1 gene in human gametes and preimplantation embryos. Electronic supplementary material The online version of this article (doi:10.1007/s10815-016-0795-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Huntriss
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK.
| | - Jianping Lu
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Karen Hemmings
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Rosemary Bayne
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Richard Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Anthony Rutherford
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Adam Balen
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Kay Elder
- Bourn Hall Clinic, Cambridge, CB23 2TN, UK
| | - Helen M Picton
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
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127
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Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State. Cell Stem Cell 2016; 19:476-490. [PMID: 27618217 DOI: 10.1016/j.stem.2016.08.008] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 04/25/2016] [Accepted: 08/09/2016] [Indexed: 12/17/2022]
Abstract
The rate of glycolytic metabolism changes during differentiation of human embryonic stem cells (hESCs) and reprogramming of somatic cells to pluripotency. However, the functional contribution of glycolytic metabolism to the pluripotent state is unclear. Here we show that naive hESCs exhibit increased glycolytic flux, MYC transcriptional activity, and nuclear N-MYC localization relative to primed hESCs. This status is consistent with the inner cell mass of human blastocysts, where MYC transcriptional activity is higher than in primed hESCs and nuclear N-MYC levels are elevated. Reduction of glycolysis decreases self-renewal of naive hESCs and feeder-free primed hESCs, but not primed hESCs grown in feeder-supported conditions. Reduction of glycolysis in feeder-free primed hESCs also enhances neural specification. These findings reveal associations between glycolytic metabolism and human naive pluripotency and differences in the metabolism of feeder-/feeder-free cultured hESCs. They may also suggest methods for regulating self-renewal and initial cell fate specification of hESCs.
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128
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Petropoulos S, Panula SP, Schell JP, Lanner F. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development. J Intern Med 2016; 280:252-64. [PMID: 27046137 DOI: 10.1111/joim.12493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early human development is a dynamic, heterogeneous, complex and multidimensional process. During the first week, the single-cell zygote undergoes eight to nine rounds of cell division generating the multicellular blastocyst, which consists of hundreds of cells forming spatially organized embryonic and extra-embryonic tissues. At the level of transcription, degradation of maternal RNA commences at around the two-cell stage, coinciding with embryonic genome activation. Although numerous efforts have recently focused on delineating this process in humans, many questions still remain as thorough investigation has been limited by ethical issues, scarce availability of human embryos and the presence of minute amounts of DNA and RNA. In vitro cultures of embryonic stem cells provide some insight into early human development, but such studies have been confounded by analysis on a population level failing to appreciate cellular heterogeneity. Recent technical developments in single-cell RNA sequencing have provided a novel and powerful tool to explore the early human embryo in a systematic manner. In this review, we will discuss the advantages and disadvantages of the techniques utilized to specifically investigate human development and consider how the technology has yielded new insights into pre-implantation development, embryonic stem cells and the establishment of the germ line.
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Affiliation(s)
- S Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - S P Panula
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - J P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - F Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
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129
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Sunde A, Brison D, Dumoulin J, Harper J, Lundin K, Magli MC, Van den Abbeel E, Veiga A. Time to take human embryo culture seriously. Hum Reprod 2016; 31:2174-82. [PMID: 27554442 DOI: 10.1093/humrep/dew157] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
STUDY QUESTION Is it important that end-users know the composition of human embryo culture media? SUMMARY ANSWER We argue that there is as strong case for full transparency concerning the composition of embryo culture media intended for human use. WHAT IS KNOWN ALREADY Published data suggest that the composition of embryo culture media may influence the phenotype of the offspring. STUDY DESIGN, SIZE, DURATION A review of the literature was carried out. PARTICIPANTS/MATERIALS, SETTING, METHODS Data concerning the potential effects on embryo development of culture media were assessed and recommendations for users made. MAIN RESULTS AND THE ROLE OF CHANCE The safety of ART procedures, especially with respect to the health of the offspring, is of major importance. There are reports from the literature indicating a possible effect of culture conditions, including culture media, on embryo and fetal development. Since the introduction of commercially available culture media, there has been a rapid development of different formulations, often not fully documented, disclosed or justified. There is now evidence that the environment the early embryo is exposed to can cause reprogramming of embryonic growth leading to alterations in fetal growth trajectory, birthweight, childhood growth and long-term disease including Type II diabetes and cardiovascular problems. The mechanism for this is likely to be epigenetic changes during the preimplantation period of development. In the present paper the ESHRE working group on culture media summarizes the present knowledge of potential effects on embryo development related to culture media, and makes recommendations. LIMITATIONS, REASONS FOR CAUTION There is still a need for large prospective randomized trials to further elucidate the link between the composition of embryo culture media used and the phenotype of the offspring. We do not presently know if the phenotypic changes induced by in vitro embryo culture represent a problem for long-term health of the offspring. WIDER IMPLICATIONS OF THE FINDINGS Published data indicate that there is a strong case for demanding full transparency concerning the compositions of and the scientific rationale behind the composition of embryo culture media. STUDY FUNDING/COMPETING INTERESTS This work was funded by The European Society for Human Reproduction and Embryology. No competing interests to declare.
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Affiliation(s)
- Arne Sunde
- Department of Obstetrics and Gynaecology, St. Olav's University Hospital in Trondheim, Trondheim, Norway
| | - Daniel Brison
- Department of Reproductive Medicine, St Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - John Dumoulin
- Department of Obstetrics and Gynaecology, IVF Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joyce Harper
- Embryology, IVF and reproductive genetics group, Institute for Women's Health, University College London, London, UK
| | - Kersti Lundin
- Reproductive Medicine, Sahlgrenska University Hospital, Göteborg, Sweden
| | | | | | - Anna Veiga
- Reproductive Medicine Service, Hospital Universitari Dexeus, Barcelona, Spain
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130
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Petrussa L, Van de Velde H, De Rycke M. Similar kinetics for 5-methylcytosine and 5-hydroxymethylcytosine during human preimplantation development in vitro. Mol Reprod Dev 2016; 83:594-605. [PMID: 27163211 DOI: 10.1002/mrd.22656] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/07/2016] [Indexed: 12/22/2022]
Abstract
After fertilization, the mammalian embryo undergoes epigenetic reprogramming with genome-wide DNA demethylation and subsequent remethylation. Oxidation of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) was suggested to be an intermediate step in the DNA demethylation pathway. Other evidence, such as the stability of 5hmC in specific tissues, suggests that 5hmC constitutes a new epigenetic modification with its own biological function. Since few studies have been conducted on human material compared to animal models and species-specific epigenetic differences have been reported, we studied global DNA methylation and hydroxymethylation patterns in human in vitro preimplantation embryos using immunocytochemistry, comparing these patterns in good-quality and abnormally developing embryos. Our data showed that DNA methylation and hydroxymethylation modifications co-exist. 5mC and 5hmC signals were found in oocytes and in paternal and maternal pronuclei of zygotes, present in non-reciprocal patterns-which contrasts published data for the mouse. These two epigenetic modifications are present between Days 1 and 7 of in vitro development, with 5mC levels declining over cell divisions without noticeable remethylation during this period. A main decline in 5mC and 5hmC occurred as the embryo progressed from compaction to the blastocyst stage. No difference in (hydroxy)methylation was found between the inner cell mass and trophectoderm. When comparing normally and abnormally developing embryos, DNA (hydroxy)methylation reprogramming was abnormal in poor-quality embryos, especially during the first cleavages. Mol. Reprod. Dev. 83: 594-605, 2016 © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Laetitia Petrussa
- Department of Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, Belgium
| | - Hilde Van de Velde
- Department of Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, Belgium.,Centre for Reproductive Medicine (CRM), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, Brussels, Belgium
| | - Martine De Rycke
- Department of Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, Belgium.,Centre for Medical Genetics (CMG), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, Brussels, Belgium
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131
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Abstract
Reproduction across mammalian species is conserved with a general pattern of fertilization followed by nascent embryo development in transcriptional silence for a variable length of time, a series of cleavage divisions that occur without growth in size of the embryo, compaction to form a morula, and production of a blastocyst. Following blastocyst formation, the embryo may implant immediately or after substantial differentiation of the epiblast and hypoblast layers. In this chapter, the shared and unique properties of several species, commonly used in studies of reproduction and embryology, are outlined.
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Affiliation(s)
| | - L Prezzoto
- Agricultural Research Centers, Montana State University, Bozeman, MT, United States
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132
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Martínez M, Obradors A, Vernaeve V, Santaló J, Vassena R. Oocyte vitrification does not affect early developmental timings after intracytoplasmic sperm injection for women younger than 30 years old. Mol Reprod Dev 2016; 83:624-9. [PMID: 27283498 DOI: 10.1002/mrd.22667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/04/2016] [Indexed: 11/06/2022]
Abstract
Oocyte vitrification causes a temporary disassembly of the metaphase plate and spindle, which needs time to recover after warming. As a consequence, early post-fertilization events-such as timing of second polar body extrusion-might be altered, with unknown effects on preimplantation development, timing to pronuclear breakdown, and timing of cleavages. The aim of this study was to evaluate if differences exist among these events when comparing embryos obtained from fresh-donated versus vitrified/warmed oocytes from young women. We performed a prospective study with 201 embryos from 100 fresh and 101 vitrified/warmed oocytes that were subsequently fertilized by intracytoplasmic sperm injection. Kaplan-Meier curves of each time period were generated, in which we observed that median developmental times did not differ between embryos from fresh versus vitrified/warmed oocytes among all the metrics assessed. Thus, for young women without fertility problems, no differences exist between the timing of early developmental milestones in embryos derived from fresh or vitrified oocytes, and vitrification does not affect the preimplantation development of the resulting embryos. Mol. Reprod. Dev. 83: 624-629, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | | | - Josep Santaló
- Departamento de Biología Celular, Fisiología e Immunología, Universidad Autónoma de Barcelona, Barcelona, Spain
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133
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Dang Y, Yan L, Hu B, Fan X, Ren Y, Li R, Lian Y, Yan J, Li Q, Zhang Y, Li M, Ren X, Huang J, Wu Y, Liu P, Wen L, Zhang C, Huang Y, Tang F, Qiao J. Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biol 2016; 17:130. [PMID: 27315811 PMCID: PMC4911693 DOI: 10.1186/s13059-016-0991-3] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 05/24/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND PolyA- RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of materials. In particular, circular RNA (circRNA), a novel type of polyA- RNA, has not been characterized during human pre-implantation development. RESULTS We systematically analyze polyA+ messenger RNAs (mRNAs) and polyA- RNAs in individual human oocytes and pre-implantation embryos using SUPeR-seq. We de novo identify 10,032 circRNAs from 2974 hosting genes. Most of these circRNAs are developmentally stage-specific and dynamically regulated. Many of them are maternally expressed, implying their potentially important regulatory functions in oogenesis and the formation of totipotent zygotes. Comparison between human and mouse embryos reveals both high conservation and clear distinction between these two species. Human pre-implantation embryos generate more types of circRNA compared with mouse embryos and this is associated with a striking increase of the length of the circRNA flanking introns in humans. We also perform RNA de novo assembly and identify novel transcript units, many of which are potentially novel long non-coding RNAs. CONCLUSIONS This study reports the first analysis of the whole transcriptome comprising both polyA+ mRNAs and polyA- RNAs including circRNAs during human pre-implantation development. It provides an invaluable resource for analyzing the unique function and complex regulatory mechanisms of circRNAs during this process.
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Affiliation(s)
- Yujiao Dang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Liying Yan
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Boqiang Hu
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Xiaoying Fan
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Yixin Ren
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Rong Li
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Ying Lian
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Jie Yan
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Qingqing Li
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Yan Zhang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Min Li
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Xiulian Ren
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Jin Huang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Yuqi Wu
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Ping Liu
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Lu Wen
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Chen Zhang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Yanyi Huang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing, 100191, China.
| | - Jie Qiao
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.
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134
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Munch EM, Sparks AE, Gonzalez Bosquet J, Christenson LK, Devor EJ, Van Voorhis BJ. Differentially expressed genes in preimplantation human embryos: potential candidate genes for blastocyst formation and implantation. J Assist Reprod Genet 2016; 33:1017-25. [PMID: 27241529 PMCID: PMC4974233 DOI: 10.1007/s10815-016-0745-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/19/2016] [Indexed: 11/30/2022] Open
Abstract
Purpose The aim of this study was to determine which genes and gene pathways are differentially expressed when comparing human blastocysts with cleavage-stage embryos. Methods We individually assessed gene expression in preimplantation human embryos at cleavage (n = 3) and blastocyst (n = 3) stages. Gene expression patterns were then validated in publically available datasets and then independently validated in vitro with additional human embryos using TaqMan gene expression assays. Immunolocalization studies were conducted to identify protein expression in intact blastocyst-stage embryos. Results Compared to cleavage-stage embryos, blastocyst-stage embryos differentially expressed 51 genes (p < 0.001), with overrepresentation in amoebiasis pathways and pathways in cancer. Of these 51 genes, 21 were found to be independently validated in a separate, publically available dataset, with a substantial agreement with our initial findings (κ = 0.8). In an independent set of cleavage- and blastocyst-stage embryos, we validated that six of eight tested genes were differentially expressed (p < 0.05) by RT-qPCR. Immunofluorescence studies documented the presence of two studied proteins in the trophectoderm of blastocyst-stage embryos. Conclusions Differentially expressed genes may be implicated in the invasion and proliferation of the early embryo. Our research highlights specific genes that may be further studied for their role in the implantation process and additionally raises questions about localized gene and/or protein expression in the trophectoderm, which could affect protocols for, and interpretation of, trophectoderm biopsies performed in in vitro fertilization cycles. Electronic supplementary material The online version of this article (doi:10.1007/s10815-016-0745-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erika M Munch
- Department of Obstetrics and Gynecology, The University of Iowa Carver College of Medicine, 200 Hawkins Drive, PFP 31330, Iowa City, IA, 52242, USA.
| | - Amy E Sparks
- Department of Obstetrics and Gynecology, The University of Iowa Carver College of Medicine, 200 Hawkins Drive, PFP 31330, Iowa City, IA, 52242, USA
| | - Jesus Gonzalez Bosquet
- Department of Obstetrics and Gynecology, The University of Iowa Carver College of Medicine, 200 Hawkins Drive, PFP 31330, Iowa City, IA, 52242, USA
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Eric J Devor
- Department of Obstetrics and Gynecology, The University of Iowa Carver College of Medicine, 200 Hawkins Drive, PFP 31330, Iowa City, IA, 52242, USA
| | - Bradley J Van Voorhis
- Department of Obstetrics and Gynecology, The University of Iowa Carver College of Medicine, 200 Hawkins Drive, PFP 31330, Iowa City, IA, 52242, USA
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135
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Escribá MJ, Escrich L, Galiana Y, Grau N, Galán A, Pellicer A. Kinetics of the early development of uniparental human haploid embryos. Fertil Steril 2016; 105:1360-1368.e1. [DOI: 10.1016/j.fertnstert.2015.12.139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 12/18/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
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136
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Men NT, Kikuchi K, Furusawa T, Dang-Nguyen TQ, Nakai M, Fukuda A, Noguchi J, Kaneko H, Viet Linh N, Xuan Nguyen B, Tajima A. Expression of DNA repair genes in porcine oocytes before and after fertilization by ICSI using freeze-dried sperm. Anim Sci J 2016; 87:1325-1333. [PMID: 26988944 DOI: 10.1111/asj.12554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/04/2015] [Accepted: 08/19/2015] [Indexed: 11/30/2022]
Abstract
Boar sperm freeze-dried with trehalose showed a protective effect against sperm DNA fragmentation. However, normal fertilization and embryonic development were not improved. Damaged sperm may activate maternal DNA repair genes when injected into oocytes. Therefore, we investigated the expression profile of some DNA repair genes in porcine oocytes after intra-cytoplasmic sperm injection. First, the expression levels of MGMT, UDG, XPC, MSH2, XRCC6 and RAD51 genes that are concerned with different types of DNA repair were examined in in vitro mature (IVM) oocytes injected with ejaculated sperm, or freeze-dried sperm with or without trehalose. Quantitative reverse transcription polymerase chain reaction revealed that expression of six DNA repair genes in the oocytes at 4 h after injection did not differ among the four groups. Next, we investigated the gene expression levels of these genes at different stages of maturation. The relative expression levels of UDG and XPC were significantly up-regulated in mature oocytes compared with earlier stages. Furthermore, there was an increased tendency in relative expression of MSH2 and RAD51. These results suggested two possible mechanisms that messenger RNA of DNA repair genes are either accumulated during IVM to be ready for fertilization or increased expression levels of DNA repair genes in oocytes caused by suboptimal IVM conditions.
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Affiliation(s)
- Nguyen Thi Men
- Division of Animal Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan. .,Laboratory of Embryo Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| | - Kazuhiro Kikuchi
- Division of Animal Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Tadashi Furusawa
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | | | - Michiko Nakai
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Atsunori Fukuda
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Junko Noguchi
- Division of Animal Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Hiroyuki Kaneko
- Division of Animal Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Nguyen Viet Linh
- Laboratory of Embryo Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Bui Xuan Nguyen
- Laboratory of Embryo Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Atsushi Tajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Wang J, Singh M, Sun C, Besser D, Prigione A, Ivics Z, Hurst LD, Izsvák Z. Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression. Nat Protoc 2016; 11:327-46. [PMID: 26797457 DOI: 10.1038/nprot.2016.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability to derive and stably maintain ground-state human pluripotent stem cells (hPSCs) that resemble the cells seen in vivo in the inner cell mass has the potential to be an invaluable tool for researchers developing stem cell-based therapies. To date, derivation of human naive-like pluripotent stem cell lines has been limited to a small number of lineages, and their long-term culturing remains problematic. We describe a protocol for genetic and phenotypic tagging, selecting and maintaining naive-like hPSCs. We tag hPSCs by GFP, expressed by the long terminal repeat (LTR7) of HERVH endogenous retrovirus. This simple and efficient protocol has been reproduced with multiple hPSC lines, including embryonic and induced pluripotent stem cells, and it takes ∼6 weeks. By using the reporter, homogeneous hPSC cultures can be derived, characterized and maintained for the long term by repeated re-sorting and re-plating steps. The HERVH-expressing cells have a similar, but nonidentical, expression pattern to other naive-like cells, suggesting that alternative pluripotent states might exist.
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Affiliation(s)
- Jichang Wang
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Manvendra Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Chuanbo Sun
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Daniel Besser
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Division of Medical Biotechnology, Langen, Germany
| | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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Floor SN, Doudna JA. Tunable protein synthesis by transcript isoforms in human cells. eLife 2016; 5:e10921. [PMID: 26735365 DOI: 10.7554/elife.10921.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/05/2016] [Indexed: 05/25/2023] Open
Abstract
Eukaryotic genes generate multiple RNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5' and 3' untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5' untranslated regions exert robust translational control between cell lines, while 3' untranslated regions can confer cell type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels.
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Affiliation(s)
- Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States
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139
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Floor SN, Doudna JA. Tunable protein synthesis by transcript isoforms in human cells. eLife 2016; 5. [PMID: 26735365 PMCID: PMC4764583 DOI: 10.7554/elife.10921] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/05/2016] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic genes generate multiple RNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5′ and 3′ untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5′ untranslated regions exert robust translational control between cell lines, while 3′ untranslated regions can confer cell type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels. DOI:http://dx.doi.org/10.7554/eLife.10921.001 To produce a protein, a gene’s DNA is first copied to make molecules of messenger RNA (mRNA). The mRNAs pass through a molecular machine known as the ribosome, which translates the genetic code to make a protein. Not all of an mRNA is translated to make a protein; the “untranslated” regions play crucial roles in regulating how much of the protein is produced. In animals, plants and other eukaryotes, many mRNAs are made up of small pieces that are “spliced” together. During this process, proteins are deposited on the mRNA to mark the splice junctions, which are then cleared when the mRNA is translated. Many different mRNAs can be produced from the same gene by splicing different combinations of RNA pieces. Each of these mRNA “isoforms” can, in principle, contain a unique set of features that control its translation. Hence each mRNA isoform can be translated differently so that different amounts of the corresponding protein product are produced. However, the relationship between the variety of isoforms and the control of translation is complex and not well understood. To address these questions, Floor and Doudna measured the translation of over 60,000 mRNA isoforms made from almost 14,000 human genes. The experiments show that untranslated regions at the end of the mRNA (known as the 3′ end) strongly influence translation, even if the protein coding regions remain the same. Furthermore, the data showed that mRNAs with more splice junctions are translated better, implying an mRNA has some sort of memory of how many junctions it had even after the protein markers have been cleared. Next, Floor and Doudna inserted regulatory sequences from differently translated isoforms into an unrelated “reporter” gene. This dramatically changed the amount of protein produced from the reporter gene, in a manner predicted by the earlier experiments. Untranslated regions at the beginning of the mRNAs (known as the 5′ end) controlled the amount of protein produced from the reporter consistently across different types of cells from the body. On the other hand, the 3′ regions can tune the level of protein production in particular types of cells. Floor and Doudna’s findings demonstrate that differences between mRNA isoforms of a gene can have a big effect on the level of protein production. Changes in the types of mRNA made from a gene are often associated with human diseases, and these findings suggest one reason why. Additionally, the ability to engineer translation of an mRNA using the data is likely to aid the development of mRNA-based therapies. DOI:http://dx.doi.org/10.7554/eLife.10921.002
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Affiliation(s)
- Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, California, United States
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141
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Sun Y, Gu R, Lu X, Zhao S, Feng Y. Vitrification of in vitro matured oocytes diminishes embryo development potential before but not after embryo genomic activation. J Assist Reprod Genet 2015; 33:231-6. [PMID: 26685678 DOI: 10.1007/s10815-015-0637-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/09/2015] [Indexed: 11/29/2022] Open
Abstract
PURPOSE The aim of this study is to evaluate the impact of oocyte vitrification on embryo development potential and to assess the chromosome abnormalities of blastocysts derived from fresh/vitrified-warmed oocytes to assure the safety of the oocyte cryopreservation technique. METHODS In vitro matured oocytes derived from immature oocytes were retrieved from small follicles during IVF/intracytoplasmic sperm injection (ICSI) cycles were randomly divided into a fresh and vitrified-warmed groups. After intracytoplasmic sperm injection, the fertilization rate, embryo quality, and developmental status were compared between the two groups. Blastocysts derived from both groups were analyzed using the copy number variation (CNV)-seq technique to evaluate DNA abnormalities. RESULTS The fertilization rate with ICSI and the cleavage rate were similar between the two groups. Among the vitrified-warmed group, there was a lower incidence of usable embryos on day 3 (16.42 vs. 28.57 %; P < 0.05) and a lower incidence of blastocysts (7.46 vs. 17.86 %; P < 0.05). However, the proportions of embryos that developed to blastocysts from the day 3 available embryos were similar between the two groups (62.5 vs. 45.45 %; P > 0.05). In the day 3 embryos, the proportion of >5 cell embryos in the fresh group was markedly higher than in the vitrified-warmed group (41.67 vs. 21.64 %; P < 0.05), and the proportion of embryos with ≧50 % fragments was not significantly different between the two groups (39.29 vs. 43.28 %; P > 0.05). The result of CNV-seq demonstrated that there was no difference in chromosomal abnormalities between the two groups (20 vs. 20 %). CONCLUSIONS Oocyte vitrification and the warming procedure diminished the embryo development potential before day 3, when embryo genomic activation started. The day 3 usable embryos derived from vitrified-warmed oocytes had the same potential for developing into blastocysts. Vitrification and the warming procedure did not increase the chromosome abnormalities of the blastocysts. Oocyte vitrification is a safe technique for those patients who have no other options, although the oocyte efficiency may be diminished after the vitrified-warmed procedure.
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Affiliation(s)
- Yijuan Sun
- Reproductive Medical Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Ji Ai Genetics & IVF Institute, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, China
| | - Ruihuan Gu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, China
| | - Xiaowei Lu
- Reproductive Medical Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shen Zhao
- Reproductive Medical Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Feng
- Reproductive Medical Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Mantikou E, Jonker MJ, Wong KM, van Montfoort APA, de Jong M, Breit TM, Repping S, Mastenbroek S. Factors affecting the gene expression of in vitro cultured human preimplantation embryos. Hum Reprod 2015; 31:298-311. [PMID: 26677958 DOI: 10.1093/humrep/dev306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/20/2015] [Indexed: 01/20/2023] Open
Abstract
STUDY QUESTION What is the relative effect of common environmental and biological factors on transcriptome changes during human preimplantation development? SUMMARY ANSWER Developmental stage and maternal age had a larger effect on the global gene expression profile of human preimplantation embryos than the culture medium or oxygen concentration used in in vitro culture. WHAT IS KNOWN ALREADY Studies on mouse and bovine embryos have shown that different conditions in the in vitro culture of embryos can lead to changes in transcriptome profiles. For humans, an effect of developmental stage on the transcriptome profile of embryos has been demonstrated, but studies on the effect of maternal age or culture conditions are lacking. STUDY DESIGN, SIZE, DURATION Donated, good quality, day 4 cryopreserved human preimplantation embryos (N = 89) were randomized to be cultured in one of two culture media (G5 medium or HTF medium) and one of two oxygen concentrations (5% or 20%), with stratification for maternal age. Next to these variables, developmental stage after culture was taken into account in the analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS Embryos that developed to morula or blastocyst stage during these 2 days whose amplified mRNA passed our quality control criteria for microarray hybridization were individually examined for genome-wide gene expression (N = 37). MAIN RESULTS AND THE ROLE OF CHANCE Based on the number of differentially expressed genes (DEGs), developmental stage (3519 DEGs) and maternal age (1258 DEGs) had a larger effect on the global gene expression profile of human preimplantation embryos than either tested culture medium (596 DEGs) or oxygen concentration (492 DEGs) used during in vitro culture. Interactions between the factors were found, indicating that culture conditions might have a different effect depending on the developmental stage or the maternal age of the embryos. Affected pathways included metabolism, cell cycle processes and oxidative phosphorylation. LIMITATIONS, REASONS FOR CAUTION Culture of embryos for only 2 days might have limited the effect on global gene expression by the investigated culture conditions. Earlier stages of development (Day 0 until Day 4) were not analyzed and these embryos might respond differently to the experimental conditions. The freezing and thawing procedures might have had an effect on gene expression. RT-PCR validation was not performed due to scarcity of the material. WIDER IMPLICATIONS OF THE FINDINGS Our results show that when studying gene expression in single human preimplantation embryos under various experimental conditions, one should take into account the confounding effect of biological variables, such as developmental stage and maternal age. This makes these experiments different from gene expression experiments where these variables can be tightly controlled, for example when using cell lines. STUDY FUNDING/COMPETING INTERESTS This study received no external funding and there were no competing interests.
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Affiliation(s)
- E Mantikou
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences, Faculty of Science (FNWI), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - M J Jonker
- MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences, Faculty of Science (FNWI), University of Amsterdam, 1090 GE Amsterdam, The Netherlands Netherlands Bioinformatics Center (NBIC), 6525 GA Nijmegen, The Netherlands
| | - K M Wong
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - A P A van Montfoort
- Department of Obstetrics and Gynaecology, GROW school for Oncology and Developmental Biology, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
| | - M de Jong
- MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences, Faculty of Science (FNWI), University of Amsterdam, 1090 GE Amsterdam, The Netherlands Present address: GenomeScan B.V., Plesmanlaan 1d, 2333BZ Leiden, The Netherlands
| | - T M Breit
- MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences, Faculty of Science (FNWI), University of Amsterdam, 1090 GE Amsterdam, The Netherlands Netherlands Bioinformatics Center (NBIC), 6525 GA Nijmegen, The Netherlands
| | - S Repping
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - S Mastenbroek
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Ajduk A, Zernicka-Goetz M. Polarity and cell division orientation in the cleavage embryo: from worm to human. Mol Hum Reprod 2015; 22:691-703. [PMID: 26660321 PMCID: PMC5062000 DOI: 10.1093/molehr/gav068] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/25/2015] [Indexed: 01/01/2023] Open
Abstract
Cleavage is a period after fertilization, when a 1-cell embryo starts developing into a multicellular organism. Due to a series of mitotic divisions, the large volume of a fertilized egg is divided into numerous smaller, nucleated cells—blastomeres. Embryos of different phyla divide according to different patterns, but molecular mechanism of these early divisions remains surprisingly conserved. In the present paper, we describe how polarity cues, cytoskeleton and cell-to-cell communication interact with each other to regulate orientation of the early embryonic division planes in model animals such as Caenorhabditis elegans, Drosophila and mouse. We focus particularly on the Par pathway and the actin-driven cytoplasmic flows that accompany it. We also describe a unique interplay between Par proteins and the Hippo pathway in cleavage mammalian embryos. Moreover, we discuss the potential meaning of polarity, cytoplasmic dynamics and cell-to-cell communication as quality biomarkers of human embryos.
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Affiliation(s)
- Anna Ajduk
- Department of Embryology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
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MicroRNAs: From Female Fertility, Germ Cells, and Stem Cells to Cancer in Humans. Stem Cells Int 2015; 2016:3984937. [PMID: 26664407 PMCID: PMC4655303 DOI: 10.1155/2016/3984937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/19/2015] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs are a family of naturally occurring small noncoding RNA molecules that play an important regulatory role in gene expression. They are suggested to regulate a large proportion of protein encoding genes by mediating the translational suppression and posttranscriptional control of gene expression. Recent findings show that microRNAs are emerging as important regulators of cellular differentiation and dedifferentiation, and are deeply involved in developmental processes including human preimplantation development. They keep a balance between pluripotency and differentiation in the embryo and embryonic stem cells. Moreover, it became evident that dysregulation of microRNA expression may play a fundamental role in progression and dissemination of different cancers including ovarian cancer. The interest is still increased by the discovery of exosomes, that is, cell-derived vesicles, which can carry different proteins but also microRNAs between different cells and are involved in cell-to-cell communication. MicroRNAs, together with exosomes, have a great potential to be used for prognosis, therapy, and biomarkers of different diseases including infertility. The aim of this review paper is to summarize the existent knowledge on microRNAs related to female fertility and cancer: from primordial germ cells and ovarian function, germinal stem cells, oocytes, and embryos to embryonic stem cells.
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Zdravkovic T, Nazor KL, Larocque N, Gormley M, Donne M, Hunkapillar N, Giritharan G, Bernstein HS, Wei G, Hebrok M, Zeng X, Genbacev O, Mattis A, McMaster MT, Krtolica A, Valbuena D, Simón C, Laurent LC, Loring JF, Fisher SJ. Human stem cells from single blastomeres reveal pathways of embryonic or trophoblast fate specification. Development 2015; 142:4010-25. [PMID: 26483210 PMCID: PMC4712832 DOI: 10.1242/dev.122846] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 10/05/2015] [Indexed: 01/04/2023]
Abstract
Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines (designated UCSFB1-10) from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple. Compared with numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns that were, in part, indicative of trophoblast competence. At a transcriptional level, UCSFB lines from different embryos were often more closely related than those from the same embryo. As predicted by the transcriptomic data, immunolocalization of EOMES, T brachyury, GDF15 and active β-catenin revealed differential expression among blastomeres of 8- to 10-cell human embryos. The UCSFB lines formed derivatives of the three germ layers and CDX2-positive progeny, from which we derived the first human trophoblast stem cell line. Our data suggest heterogeneity among early-stage blastomeres and that the UCSFB lines have unique properties, indicative of a more immature state than conventional lines.
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Affiliation(s)
- Tamara Zdravkovic
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kristopher L Nazor
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas Larocque
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Gormley
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Donne
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nathan Hunkapillar
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Harold S Bernstein
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Grace Wei
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Xianmin Zeng
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Olga Genbacev
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Aras Mattis
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michael T McMaster
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Diana Valbuena
- Fundación Instituto Valenciano de Infertilidad (IVI), Parc Científic Universitat de València, 46980, Valencia, Spain
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad (IVI), Parc Científic Universitat de València, 46980, Valencia, Spain
| | - Louise C Laurent
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Susan J Fisher
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
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Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:896176. [PMID: 26543497 PMCID: PMC4620428 DOI: 10.1155/2015/896176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 06/15/2015] [Indexed: 12/20/2022]
Abstract
High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO) studies. EVO-DEVO studies focus on the evolutionary pressure affecting the morphogenesis of development and previous works have been conducted to illustrate the most conserved stages during embryonic development. Old measurements of these studies are based on the morphological similarity from macro view and new technology enables the micro detection of similarity in molecular mechanism. Evolutionary model of embryo development, which includes the "funnel-like" model and the "hourglass" model, has been evaluated by combination of these new comparative transcriptomic methods with prior comparative genomic information. Although the technology has promoted the EVO-DEVO studies into a new era, technological and material limitation still exist and further investigations require more subtle study design and procedure.
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147
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Carbone L, Chavez SL. Mammalian pre-implantation chromosomal instability: species comparison, evolutionary considerations, and pathological correlations. Syst Biol Reprod Med 2015; 61:321-35. [PMID: 26366555 DOI: 10.3109/19396368.2015.1073406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pre-implantation embryo development in mammals begins at fertilization with the migration and fusion of the maternal and paternal pro-nuclei, followed by the degradation of inherited factors involved in germ cell specification and the activation of embryonic genes required for subsequent cell divisions, compaction, and blastulation. The majority of studies on early embryogenesis have been conducted in the mouse or non-mammalian species, often requiring extrapolation of the findings to human development. Given both conserved similarities and species-specific differences, however, even comparison between closely related mammalian species may be challenging as certain aspects, including susceptibility to chromosomal aberrations, varies considerably across mammals. Moreover, most human embryo studies are limited to patient samples obtained from in vitro fertilization (IVF) clinics and donated for research, which are generally of poorer quality and produced with germ cells that may be sub-optimal. Recent technical advances in genetic, epigenetic, chromosomal, and time-lapse imaging analyses of high quality whole human embryos have greatly improved our understanding of early human embryogenesis, particularly at the single embryo and cell level. This review summarizes the major characteristics of mammalian pre-implantation development from a chromosomal perspective, in addition to discussing the technological achievements that have recently been developed to obtain this data. We also discuss potential translation to clinical applications in reproductive medicine and conclude by examining the broader implications of these findings for the evolution of mammalian species and cancer pathology in somatic cells.
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Affiliation(s)
- Lucia Carbone
- a Division of Neuroscience , Oregon National Primate Research Center .,b Department of Behavioral Neuroscience .,c Department of Molecular & Medical Genetics .,d Bioinformatics & Computational Biology, Oregon Health & Science University
| | - Shawn L Chavez
- e Division of Reproductive & Developmental Sciences , Oregon National Primate Research Center .,f Department of Obstetrics & Gynecology , and.,g Department of Physiology & Pharmacology , Oregon Health & Science University , Portland , Oregon , USA
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148
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Uysal F, Akkoyunlu G, Ozturk S. Dynamic expression of DNA methyltransferases (DNMTs) in oocytes and early embryos. Biochimie 2015; 116:103-13. [PMID: 26143007 DOI: 10.1016/j.biochi.2015.06.019] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/26/2015] [Indexed: 11/26/2022]
Abstract
Epigenetic mechanisms play critical roles in oogenesis and early embryo development in mammals. One of these epigenetic mechanisms, DNA methylation is accomplished through the activities of DNA methyltransferases (DNMTs), which are responsible for adding a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinuclotide sites. Five DNMT enzymes have been identified in mammals including DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L. They function in two different methylation processes: maintenance and de novo. For maintenance methylation, DNMT1 preferentially transfers methyl groups to the hemi-methylated DNA strands following DNA replication. However, for de novo methylation activities both DNMT3A and DNMT3B function in the methylation of the unmodified cytosine residues. Although DNMT3L indirectly contributes to de novo methylation process, DNMT2 enables the methylation of the cytosine 38 in the anticodon loop of aspartic acid transfer RNA and does not methylate DNA. In this review article, we have evaluated and discussed the existing published studies to characterize the spatial and temporal expression patterns of the DNMTs in mouse, bovine and human oocytes and early embryos. We have also reviewed the effects of in vitro culture conditions (serum abundance and glucose concentration), aging, superovulation, vitrification, and somatic cell nuclear transfer technology on the dynamics of DNMTs.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey.
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149
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Amano T, Jeffries E, Amano M, Ko AC, Yu H, Ko MSH. Correction of Down syndrome and Edwards syndrome aneuploidies in human cell cultures. DNA Res 2015; 22:331-42. [PMID: 26324424 PMCID: PMC4596399 DOI: 10.1093/dnares/dsv016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/24/2015] [Indexed: 12/26/2022] Open
Abstract
Aneuploidy, an abnormal number of chromosomes, has previously been considered irremediable. Here, we report findings that euploid cells increased among cultured aneuploid cells after exposure to the protein ZSCAN4, encoded by a mammalian-specific gene that is ordinarily expressed in preimplantation embryos and occasionally in stem cells. For footprint-free delivery of ZSCAN4 to cells, we developed ZSCAN4 synthetic mRNAs and Sendai virus vectors that encode human ZSCAN4. Applying the ZSCAN4 biologics to established cultures of mouse embryonic stem cells, most of which had become aneuploid and polyploid, dramatically increased the number of euploid cells within a few days. We then tested the biologics on non-immortalized primary human fibroblast cells derived from four individuals with Down syndrome—the most frequent autosomal trisomy of chromosome 21. Within weeks after ZSCAN4 application to the cells in culture, fluorescent in situ hybridization with a chromosome 21-specific probe detected the emergence of up to 24% of cells with only two rather than three copies. High-resolution G-banded chromosomes further showed up to 40% of cells with a normal karyotype. These findings were confirmed by whole-exome sequencing. Similar results were obtained for cells with the trisomy 18 of Edwards syndrome. Thus a direct, efficient correction of aneuploidy in human fibroblast cells seems possible in vitro using human ZSCAN4.
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Affiliation(s)
- Tomokazu Amano
- Elixirgen, LLC, Science + Technology Park at Johns Hopkins, 855 N Wolfe Street, Suite 621, Baltimore MD 21205-1511, USA
| | - Emiko Jeffries
- Elixirgen, LLC, Science + Technology Park at Johns Hopkins, 855 N Wolfe Street, Suite 621, Baltimore MD 21205-1511, USA
| | - Misa Amano
- Elixirgen, LLC, Science + Technology Park at Johns Hopkins, 855 N Wolfe Street, Suite 621, Baltimore MD 21205-1511, USA
| | - Akihiro C Ko
- Elixirgen, LLC, Science + Technology Park at Johns Hopkins, 855 N Wolfe Street, Suite 621, Baltimore MD 21205-1511, USA
| | - Hong Yu
- Elixirgen, LLC, Science + Technology Park at Johns Hopkins, 855 N Wolfe Street, Suite 621, Baltimore MD 21205-1511, USA
| | - Minoru S H Ko
- Elixirgen, LLC, Science + Technology Park at Johns Hopkins, 855 N Wolfe Street, Suite 621, Baltimore MD 21205-1511, USA Department of Systems Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160, Japan
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150
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Akiyama T, Xin L, Oda M, Sharov AA, Amano M, Piao Y, Cadet JS, Dudekula DB, Qian Y, Wang W, Ko SBH, Ko MSH. Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 2015; 22:307-18. [PMID: 26324425 PMCID: PMC4596397 DOI: 10.1093/dnares/dsv013] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/24/2015] [Indexed: 01/06/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochromatin.
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Affiliation(s)
- Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Li Xin
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mayumi Oda
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Alexei A Sharov
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Misa Amano
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - J Scotty Cadet
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yong Qian
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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