1
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Fang S, Wang J, Liu G, Qu B, Chunyu J, Xu W, Xiang J, Li X. DPPA2/4 Promote the Pluripotency and Proliferation of Bovine Extended Pluripotent Stem Cells by Upregulating the PI3K/AKT/GSK3β/β-Catenin Signaling Pathway. Cells 2024; 13:382. [PMID: 38474345 DOI: 10.3390/cells13050382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Developmental pluripotency-associated 2 (DPPA2) and DPPA4 are crucial transcription factors involved in maintaining pluripotency in humans and mice. However, the role of DPPA2/4 in bovine extended pluripotent stem cells (bEPSCs) has not been investigated. In this study, a subset of bEPSC-related differentially expressed genes (DEGs), including DPPA2 and DPPA4, was identified based on multiomics data (ATAC-seq and RNA-seq). Subsequent investigations revealed that double overexpression of DPPA2/4 facilitates the reprogramming of bovine fetal fibroblasts (BFFs) into bEPSCs, whereas knockout of DPPA2/4 in BFFs leads to inefficient reprogramming. DPPA2/4 overexpression and knockdown experiments revealed that the pluripotency and proliferation capability of bEPSCs were maintained by promoting the transition from the G1 phase to the S phase of the cell cycle. By activating the PI3K/AKT/GSK3β/β-catenin pathway in bEPSCs, DPPA2/4 can increase the nuclear accumulation of β-catenin, which further upregulates lymphoid enhancer binding factor 1 (LEF1) transcription factor activity. Moreover, DPPA2/4 can also regulate the expression of LEF1 by directly binding to its promoter region. Overall, our results demonstrate that DPPA2/4 promote the reprogramming of BFFs into bEPSCs while also maintaining the pluripotency and proliferation capability of bEPSCs by regulating the PI3K/AKT/GSK3β/β-catenin pathway and subsequently activating LEF1. These findings expand our understanding of the gene regulatory network involved in bEPSC pluripotency.
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Affiliation(s)
- Shu Fang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Jing Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Guangbo Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Burong Qu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Jian Chunyu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Wenqiang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Jinzhu Xiang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Xueling Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
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2
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Dynamic cytosolic foci of DPPA4 in human pluripotent stem cells. Tissue Cell 2022; 78:101893. [DOI: 10.1016/j.tice.2022.101893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/28/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022]
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3
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Yue H, Yang X, Ji X, Wu X, Li G, Sang N. Time series of transcriptome analysis in entire lung development stages provide insights into the origin of NO 2 related lung diseases. ENVIRONMENT INTERNATIONAL 2022; 168:107454. [PMID: 35963059 DOI: 10.1016/j.envint.2022.107454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Lung growth is a critical window, when exposure to various pollutants can disturb the finely-tuned lung development and enhance risk of long-term structural and functional sequelae of lung. In this study, pregnant C57/6 mice were treated with NO2, and lungs of fetus/offspring were collected at different developmental windows and dynamic lung development was determined. The results showed that maternal NO2 exposure suppressed fetal weight, implying that fetal development can be disturbed. The time-series RNA-seq analysis of lungs showed that maternal NO2 exposure induced significant time-dependent changes in the expression profiles of genes associated with lung vein myocardium development in fetus/offspring. Most of these genes in NO2 exposure group were suppressed at middle gestation and at birth. Our results also indicated that the gene expressions of Nkx2.5 in NO2 exposure were suppressed to 0.27- and 0.44-fold of the corresponding Air group at E13.5 and PND1, and restored at later time points. This indicated that the transcription factor Nkx2.5 played an important role in abnormal lung development in fetus/offspring caused by maternal NO2 exposure. Importantly, gene expressions of lung vein myocardium development were related to transcription factors (TFs) and lung functions, and TFs showed similar trends with lung function. These results provide a comprehensive view of the adverse effects of maternal NO2 exposure on fetal lung development by uncovering molecular targets and related signaling pathways at the transcriptional level.
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Affiliation(s)
- Huifeng Yue
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Xiaowen Yang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Xiaotong Ji
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Xiaoyun Wu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
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4
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Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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5
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Yeh CY, Huang WH, Chen HC, Meir YJJ. Capturing Pluripotency and Beyond. Cells 2021; 10:cells10123558. [PMID: 34944066 PMCID: PMC8700150 DOI: 10.3390/cells10123558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
During the development of a multicellular organism, the specification of different cell lineages originates in a small group of pluripotent cells, the epiblasts, formed in the preimplantation embryo. The pluripotent epiblast is protected from premature differentiation until exposure to inductive cues in strictly controlled spatially and temporally organized patterns guiding fetus formation. Epiblasts cultured in vitro are embryonic stem cells (ESCs), which recapitulate the self-renewal and lineage specification properties of their endogenous counterparts. The characteristics of totipotency, although less understood than pluripotency, are becoming clearer. Recent studies have shown that a minor ESC subpopulation exhibits expanded developmental potential beyond pluripotency, displaying a characteristic reminiscent of two-cell embryo blastomeres (2CLCs). In addition, reprogramming both mouse and human ESCs in defined media can produce expanded/extended pluripotent stem cells (EPSCs) similar to but different from 2CLCs. Further, the molecular roadmaps driving the transition of various potency states have been clarified. These recent key findings will allow us to understand eutherian mammalian development by comparing the underlying differences between potency network components during development. Using the mouse as a paradigm and recent progress in human PSCs, we review the epiblast's identity acquisition during embryogenesis and their ESC counterparts regarding their pluripotent fates and beyond.
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Affiliation(s)
- Chih-Yu Yeh
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Wei-Han Huang
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Hung-Chi Chen
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
| | - Yaa-Jyuhn James Meir
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
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6
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Kubinyecz O, Santos F, Drage D, Reik W, Eckersley-Maslin MA. Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival. Development 2021; 148:273814. [PMID: 34931676 PMCID: PMC8722389 DOI: 10.1242/dev.200191] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/22/2021] [Indexed: 01/20/2023]
Abstract
Zygotic genome activation (ZGA) represents the initiation of transcription following fertilisation. Despite its importance, we know little of the molecular events that initiate mammalian ZGA in vivo. Recent in vitro studies in mouse embryonic stem cells have revealed developmental pluripotency associated 2 and 4 (Dppa2/4) as key regulators of ZGA-associated transcription. However, their roles in initiating ZGA in vivo remain unexplored. We reveal that Dppa2/4 proteins are present in the nucleus at all stages of preimplantation development and associate with mitotic chromatin. We generated conditional single and double maternal knockout mouse models to deplete maternal stores of Dppa2/4. Importantly, Dppa2/4 maternal knockout mice were fertile when mated with wild-type males. Immunofluorescence and transcriptome analyses of two-cell embryos revealed that, although ZGA took place, there were subtle defects in embryos that lacked maternal Dppa2/4. Strikingly, heterozygous offspring that inherited the null allele maternally had higher preweaning lethality than those that inherited the null allele paternally. Together, our results show that although Dppa2/4 are dispensable for ZGA transcription, maternal stores have an important role in offspring survival, potentially via epigenetic priming of developmental genes. Summary: Conditional knockout mouse models reveal maternal stores of Dppa2 and Dppa4 are dispensable for zygotic genome activation, contrasting findings in embryonic stem cells. However, both maternal and zygotic Dppa2/4 are required for development.
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Affiliation(s)
- Oana Kubinyecz
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Fatima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Deborah Drage
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Melanie A Eckersley-Maslin
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.,Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia.,Department of Anatomy and Physiology, University of Melbourne, Victoria 3010, Australia
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7
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Chen Z, Xie Z, Zhang Y. DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and pre-implantation development. Development 2021; 148:273813. [PMID: 34878123 DOI: 10.1242/dev.200178] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022]
Abstract
How maternal factors in oocytes initiate zygotic genome activation (ZGA) remains elusive in mammals, partly due to the challenge of de novo identification of key factors using scarce materials. Two-cell (2C)-like cells have been widely used as an in vitro model in order to understand mouse ZGA and totipotency because of their expression of a group of two-cell embryo-specific genes and their simplicity for genetic manipulation. Recent studies indicate that DPPA2 and DPPA4 are required for establishing the 2C-like state in mouse embryonic stem cells in a DUX-dependent manner. These results suggest that DPPA2 and DPPA4 are essential maternal factors that regulate Dux and ZGA in embryos. By analyzing maternal knockout and maternal-zygotic knockout embryos, we unexpectedly found that DPPA2 and DPPA4 are dispensable for Dux activation, ZGA and pre-implantation development. Our study suggests that 2C-like cells do not fully recapitulate two-cell embryos in terms of regulation of two-cell embryo-specific genes, and, therefore, caution should be taken when studying ZGA and totipotency using 2C-like cells as the model system.
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Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Zhenfei Xie
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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8
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Klein RH, Knoepfler PS. DPPA2, DPPA4, and other DPPA factor epigenomic functions in cell fate and cancer. Stem Cell Reports 2021; 16:2844-2851. [PMID: 34767751 PMCID: PMC8693620 DOI: 10.1016/j.stemcr.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
Many gene networks are shared between pluripotent stem cells and cancer; a concept exemplified by several DPPA factors such as DPPA2 and DPPA4, which are highly and selectively expressed in stem cells but also found to be reactivated in cancer. Despite their striking expression pattern, for many years the function of DPPA2 and DPPA4 remained a mystery; knockout of Dppa2 and Dppa4 did not affect pluripotency, but caused lung and skeletal defects late in development, long after Dppa2 and Dppa4 expression had been turned off. A number of recent papers have further clarified and defined the roles of these important factors, identifying roles in priming the chromatin and maintaining developmental competency through regulating both H3K4me3 and H3K27me3 at bivalent chromatin domains, and acting to remodel chromatin and facilitate reprogramming of somatic cells to induced pluripotency. These findings highlight an important regulatory role for DPPA2 and DPPA4 at the transitional boundary between pluripotency and differentiation and may have relevance to the functions of DPPA2 and 4 in the context of cancer cells as well.
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Affiliation(s)
- Rachel Herndon Klein
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA 95817, USA; Genome Center, University of California, Davis, CA 95616, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA 95817, USA; Genome Center, University of California, Davis, CA 95616, USA.
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9
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Kinisu M, Choi YJ, Cattoglio C, Liu K, Roux de Bezieux H, Valbuena R, Pum N, Dudoit S, Huang H, Xuan Z, Kim SY, He L. Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes. Cell Rep 2021; 37:109982. [PMID: 34758315 PMCID: PMC8711565 DOI: 10.1016/j.celrep.2021.109982] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/30/2021] [Accepted: 10/20/2021] [Indexed: 01/05/2023] Open
Abstract
Early blastomeres of mouse preimplantation embryos exhibit bi-potential cell fate, capable of generating both embryonic and extra-embryonic lineages in blastocysts. Here we identify three major two-cell-stage (2C)-specific endogenous retroviruses (ERVs) as the molecular hallmark of this bi-potential plasticity. Using the long terminal repeats (LTRs) of all three 2C-specific ERVs, we identify Krüppel-like factor 5 (Klf5) as their major upstream regulator. Klf5 is essential for bi-potential cell fate; a single Klf5-overexpressing embryonic stem cell (ESC) generates terminally differentiated embryonic and extra-embryonic lineages in chimeric embryos, and Klf5 directly induces inner cell mass (ICM) and trophectoderm (TE) specification genes. Intriguingly, Klf5 and Klf4 act redundantly during ICM specification, whereas Klf5 deficiency alone impairs TE specification. Klf5 is regulated by multiple 2C-specific transcription factors, particularly Dux, and the Dux/Klf5 axis is evolutionarily conserved. The 2C-specific transcription program converges on Klf5 to establish bi-potential cell fate, enabling a cell state with dual activation of ICM and TE genes. Using multiple 2C-specific ERV cell fate markers, Kinisu et al. identify Klf5 as a key transcription factor that confers a 2C-like developmental potential and activates ICM and TE specification genes. Klf5 and Klf4 act redundantly for ICM and TE specification in mouse preimplantation embryos.
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Affiliation(s)
- Martin Kinisu
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Yong Jin Choi
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Claudia Cattoglio
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ke Liu
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hector Roux de Bezieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raeline Valbuena
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Nicole Pum
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Sandrine Dudoit
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haiyan Huang
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zhenyu Xuan
- Department of Molecular and Cell Biology, University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Sang Yong Kim
- Department of Pathology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA.
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10
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Keeping your options open: insights from Dppa2/4 into how epigenetic priming factors promote cell plasticity. Biochem Soc Trans 2021; 48:2891-2902. [PMID: 33336687 PMCID: PMC7752079 DOI: 10.1042/bst20200873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
The concept of cellular plasticity is particularly apt in early embryonic development, where there is a tug-of-war between the stability and flexibility of cell identity. This balance is controlled in part through epigenetic mechanisms. Epigenetic plasticity dictates how malleable cells are to change by adjusting the potential to initiate new transcriptional programmes. The higher the plasticity of a cell, the more readily it can adapt and change its identity in response to external stimuli such as differentiation cues. Epigenetic plasticity is regulated in part through the action of epigenetic priming factors which establish this permissive epigenetic landscape at genomic regulatory elements to enable future transcriptional changes. Recent studies on the DNA binding proteins Developmental Pluripotency Associated 2 and 4 (Dppa2/4) support their roles as epigenetic priming factors in facilitating cell fate transitions. Here, using Dppa2/4 as a case study, the concept of epigenetic plasticity and molecular mechanism of epigenetic priming factors will be explored. Understanding how epigenetic priming factors function is key not only to improve our understanding of the tight control of development, but also to give insights into how this goes awry in diseases of cell identity, such as cancer.
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11
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Greenberg MVC. Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Front Cell Dev Biol 2021; 8:629068. [PMID: 33490089 PMCID: PMC7817772 DOI: 10.3389/fcell.2020.629068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Vertebrate genomes are marked by notably high levels of 5-cytosine DNA methylation (5meC). The clearest function of DNA methylation among members of the subphylum is repression of potentially deleterious transposable elements (TEs). However, enrichment in the bodies of protein coding genes and pericentromeric heterochromatin indicate an important role for 5meC in those genomic compartments as well. Moreover, DNA methylation plays an important role in silencing of germline-specific genes. Impaired function of major components of DNA methylation machinery results in lethality in fish, amphibians and mammals. Despite such apparent importance, mammals exhibit a dramatic loss and regain of DNA methylation in early embryogenesis prior to implantation, and then again in the cells specified for the germline. In this minireview we will highlight recent studies that shine light on two major aspects of embryonic DNA methylation reprogramming: (1) The mechanism of DNA methylation loss after fertilization and (2) the protection of discrete loci from ectopic DNA methylation deposition during reestablishment. Finally, we will conclude with some extrapolations for the evolutionary underpinnings of such extraordinary events that seemingly put the genome under unnecessary risk during a particularly vulnerable window of development.
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Affiliation(s)
- Maxim V C Greenberg
- Centre National de la Recherche Scientifique, Institut Jacques Monod, Université de Paris, Paris, France
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12
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Li H, Long C, Xiang J, Liang P, Li X, Zuo Y. Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region. Brief Bioinform 2020; 22:6034044. [PMID: 33316032 DOI: 10.1093/bib/bbaa342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022] Open
Abstract
Developmental pluripotency-associated 2 (Dppa2) and developmental pluripotency-associated 4 (Dppa4) as positive drivers were helpful for transcriptional regulation of zygotic genome activation (ZGA). Here, we systematically assessed the cooperative interplay of Dppa2 and Dppa4 in regulating cell pluripotency and found that simultaneous overexpression of Dppa2/4 can make induced pluripotent stem cells closer to embryonic stem cells (ESCs). Compared with other pluripotency transcription factors, Dppa2/4 can regulate majorities of signaling pathways by binding on CG-rich region of proximal promoter (0-500 bp), of which 85% and 77% signaling pathways were significantly activated by Dppa2 and Dppa4, respectively. Notably, Dppa2/4 also can dramatically trigger the decisive signaling pathways for facilitating ZGA, including Hippo, MAPK and TGF-beta signaling pathways and so on. At last, we found alkaline phosphatase, placental-like 2 (Alppl2) was completely silenced when Dppa2 and 4 single- or double-knockout in ESC, which is consistent with Dux. Moreover, Alppl2 was significantly activated in mouse 2-cell embryos and 4-8 cells stage of human embryos, further predicted that Alppl2 was directly regulated by Dppa2/4 as a ZGA candidate driver to facilitate pre-embryonic development.
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Affiliation(s)
- Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jinzhu Xiang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Pengfei Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xueling Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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13
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Eckersley-Maslin MA, Parry A, Blotenburg M, Krueger C, Ito Y, Franklin VNR, Narita M, D'Santos CS, Reik W. Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment. Nat Struct Mol Biol 2020; 27:696-705. [PMID: 32572255 PMCID: PMC7614975 DOI: 10.1038/s41594-020-0443-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022]
Abstract
How the epigenetic landscape is established in development is still being elucidated. Here, we uncover developmental pluripotency associated 2 and 4 (DPPA2/4) as epigenetic priming factors that establish a permissive epigenetic landscape at a subset of developmentally important bivalent promoters characterized by low expression and poised RNA-polymerase. Differentiation assays reveal that Dppa2/4 double knockout mouse embryonic stem cells fail to exit pluripotency and differentiate efficiently. DPPA2/4 bind both H3K4me3-marked and bivalent gene promoters and associate with COMPASS- and Polycomb-bound chromatin. Comparing knockout and inducible knockdown systems, we find that acute depletion of DPPA2/4 results in rapid loss of H3K4me3 from key bivalent genes, while H3K27me3 is initially more stable but lost following extended culture. Consequently, upon DPPA2/4 depletion, these promoters gain DNA methylation and are unable to be activated upon differentiation. Our findings uncover a novel epigenetic priming mechanism at developmental promoters, poising them for future lineage-specific activation.
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Affiliation(s)
| | - Aled Parry
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Marloes Blotenburg
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Wellcome Trust Sanger Institute, Hinxton, UK.
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14
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Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat Struct Mol Biol 2020; 27:706-716. [DOI: 10.1038/s41594-020-0445-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
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15
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Lim PSL, Meshorer E. Dppa2 and Dppa4 safeguard bivalent chromatin in order to establish a pluripotent epigenome. Nat Struct Mol Biol 2020; 27:685-686. [DOI: 10.1038/s41594-020-0453-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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De Iaco A, Verp S, Offner S, Grun D, Trono D. DUX is a non-essential synchronizer of zygotic genome activation. Development 2020; 147:dev.177725. [PMID: 31806660 DOI: 10.1242/dev.177725] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022]
Abstract
Some of the earliest transcripts produced in fertilized human and mouse oocytes code for DUX, a double homeodomain protein that promotes embryonic genome activation (EGA). Deleting Dux by genome editing at the one- to two-cell stage in the mouse impairs EGA and blastocyst maturation. Here, we demonstrate that mice carrying homozygous Dux deletions display markedly reduced expression of DUX target genes and defects in both pre- and post-implantation development, with, notably, a disruption of the pace of the first few cell divisions and significant rates of late embryonic mortality. However, some Dux -/- embryos give rise to viable pups, indicating that DUX is important but not strictly essential for embryogenesis.
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Affiliation(s)
- Alberto De Iaco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sonia Verp
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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17
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Takahashi K, Ross PJ, Sawai K. The necessity of ZSCAN4 for preimplantation development and gene expression of bovine embryos. J Reprod Dev 2019; 65:319-326. [PMID: 31019155 PMCID: PMC6708851 DOI: 10.1262/jrd.2019-039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Zinc finger and SCAN domain containing 4 (Zscan4) is a gene that is specifically expressed during zygotic genome activation (ZGA) in mouse preimplantation embryos, and a
reduction of Zscan4 transcripts leads to developmental failure. In mouse embryonic stem cells (ESCs), Zscan4 is expressed transiently in as little as 1–5%
of the cell population. Zscan4 has also been shown to enhance the efficiency of mouse induced pluripotent stem cells (iPSCs) generation and their quality. Although ZSCAN4
plays important roles in murine embryos and stem cells, its expression and role in bovine embryos is unknown. This study examines ZSCAN4 transcripts in bovine embryos at
various developmental stages and attempts to elucidate the functions of ZSCAN4 during bovine preimplantation development. ZSCAN4 transcripts were found to be upregulated at
the 8- and 16-cell stages. We next attempted ZSCAN4 downregulation in bovine early embryos by RNA interference and evaluated developmental competency and transcripts levels
of genes involved in ZGA and iPSCs generation. Although the bovine embryos injected with ZSCAN4-siRNA could develop to the 8-cell stage, very few were developing beyond the
16-cell stage. PIWIL2 expression was reduced in ZSCAN4 downregulated embryos. It is possible that ZSCAN4 downregulated embryos fail to
regulate gene expression during ZGA. Our results indicate that ZSCAN4 is an important factor for the preimplantation development of bovine embryos.
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Affiliation(s)
- Kazuki Takahashi
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate 020-8550, Japan
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, CA 95616, U. S. A
| | - Ken Sawai
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate 020-8550, Japan.,Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan
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18
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Yan YL, Zhang C, Hao J, Wang XL, Ming J, Mi L, Na J, Hu X, Wang Y. DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program. PLoS Biol 2019; 17:e3000324. [PMID: 31226106 PMCID: PMC6608977 DOI: 10.1371/journal.pbio.3000324] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 07/03/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
The molecular mechanism controlling the zygotic genome activation (ZGA) in mammals remains poorly understood. The 2-cell (2C)-like cells spontaneously emerging from cultures of mouse embryonic stem cells (ESCs) share some key transcriptional and epigenetic programs with 2C-stage embryos. By studying the transition of ESCs into 2C-like cells, we identified developmental pluripotency associated 2 and 4 (Dppa2/4) as important regulators controlling zygotic transcriptional program through directly up-regulating the expression of double homeobox (Dux). In addition, we found that DPPA2 protein is sumoylated and its activity is negatively regulated by small ubiquitin-like modifier (Sumo) E3 ligase protein inhibitor of activated STAT 4 (PIAS4). PIAS4 is down-regulated during ZGA process and during transitioning of ESCs into 2C-like cells. Depleting Pias4 or overexpressing Dppa2/4 is sufficient to activate 2C-like transcriptional program, whereas depleting Dppa2/4 or forced expression of Pias4 or Sumo2-Dppa2 inhibits 2C-like transcriptional program. Furthermore, ectopic expression of Pias4 or Sumo2-Dppa2 impairs early mouse embryo development. In summary, our study identifies key molecular rivals consisting of transcription factors and a Sumo2 E3 ligase that regulate zygotic transcriptional program upstream of Dux.
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Affiliation(s)
- Yao-Long Yan
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chao Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jing Hao
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xue-Lian Wang
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia Ming
- School of Medicine, Tsinghua University, Beijing, China
| | - Li Mi
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Na
- School of Medicine, Tsinghua University, Beijing, China
| | - Xinli Hu
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yangming Wang
- Institute of Molecular Medicine, Peking University, Beijing, China
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19
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Abu-Dawud R, Graffmann N, Ferber S, Wruck W, Adjaye J. Pluripotent stem cells: induction and self-renewal. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0213. [PMID: 29786549 DOI: 10.1098/rstb.2017.0213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 12/21/2022] Open
Abstract
Pluripotent stem cells (PSCs) lie at the heart of modern regenerative medicine due to their properties of unlimited self-renewal in vitro and their ability to differentiate into cell types representative of the three embryonic germ layers-mesoderm, ectoderm and endoderm. The derivation of induced PSCs bypasses ethical concerns associated with the use of human embryonic stem cells and also enables personalized cell-based therapies. To exploit their regenerative potential, it is essential to have a firm understanding of the molecular processes associated with their induction from somatic cells. This understanding serves two purposes: first, to enable efficient, reliable and cost-effective production of excellent quality induced PSCs and, second, to enable the derivation of safe, good manufacturing practice-grade transplantable donor cells. Here, we review the reprogramming process of somatic cells into induced PSCs and associated mechanisms with emphasis on self-renewal, epigenetic control, mitochondrial bioenergetics, sub-states of pluripotency, naive ground state, naive and primed. A meta-analysis identified genes expressed exclusively in the inner cell mass and in the naive but not in the primed pluripotent state. We propose these as additional biomarkers defining naive PSCs.This article is part of the theme issue 'Designer human tissue: coming to a lab near you'.
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Affiliation(s)
- R Abu-Dawud
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Zahrawi Street, Riyadh 11211, Saudi Arabia
| | - N Graffmann
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich-Heine-Universität Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - S Ferber
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich-Heine-Universität Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - W Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich-Heine-Universität Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - J Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich-Heine-Universität Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
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20
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De Iaco A, Coudray A, Duc J, Trono D. DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells. EMBO Rep 2019; 20:embr.201847382. [PMID: 30948459 PMCID: PMC6500978 DOI: 10.15252/embr.201847382] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
After fertilization of the transcriptionally silent oocyte, expression from both parental chromosomes is launched through zygotic genome activation (ZGA), occurring in the mouse at the 2‐cell (2C) stage. Among the first elements to be transcribed are the Dux gene, the product of which induces a wide array of ZGA genes, and a subset of evolutionary recent LINE‐1 retrotransposons that regulate chromatin accessibility in the early embryo. The maternally inherited factors that activate Dux and LINE‐1 transcription have so far remained unknown. Mouse embryonic stem cells (mESCs) recapitulate some aspects of ZGA in culture, owing to their ability to cycle through a 2C‐like stage when Dux, its target genes, and LINE‐1 integrants are expressed. Here, we identify the paralog proteins DPPA2 and DPPA4 as necessary for the activation of Dux and LINE‐1 expression in mESCs. Since their encoding RNAs are maternally transmitted to the zygote, it is likely that these factors are important upstream mediators of murine ZGA.
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Affiliation(s)
- Alberto De Iaco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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21
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Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell 2019; 176:816-830.e18. [PMID: 30595451 PMCID: PMC6546437 DOI: 10.1016/j.cell.2018.11.036] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Marco Michalski
- Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nicolas P Holcomb
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jesse L Turner
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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22
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Eckersley-Maslin M, Alda-Catalinas C, Blotenburg M, Kreibich E, Krueger C, Reik W. Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program. Genes Dev 2019; 33:194-208. [PMID: 30692203 PMCID: PMC6362816 DOI: 10.1101/gad.321174.118] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2023]
Abstract
In this study, Eckersley-Maslin et al. investigated the upstream maternal factors that initiate zygotic genome activation (ZGA) in either a Dux-dependent (a transcription factor expressed in the minor wave of ZGA) or Dux-independent manner. They performed a candidate-based overexpression screen, identifying developmental pluripotency-associated 2 (Dppa2) and Dppa4 as positive regulators of 2C-like cells and transcription of ZGA genes, and their results suggest that Dppa2/4 binding to the Dux promoter leads to Dux up-regulation and activation of the 2C-like transcriptional program, which is subsequently reinforced by Zscan4c. The molecular regulation of zygotic genome activation (ZGA) in mammals remains an exciting area of research. Primed mouse embryonic stem cells contain a rare subset of “2C-like” cells that are epigenetically and transcriptionally similar to the two-cell embryo and thus represent an in vitro approximation for studying ZGA transcription regulation. Recently, the transcription factor Dux, expressed in the minor wave of ZGA, was described to activate many downstream ZGA transcripts. However, it remains unknown what upstream maternal factors initiate ZGA in either a Dux-dependent or Dux-independent manner. Here we performed a candidate-based overexpression screen, identifying, among others, developmental pluripotency-associated 2 (Dppa2) and Dppa4 as positive regulators of 2C-like cells and transcription of ZGA genes. In the germline, promoter DNA demethylation coincides with expression of Dppa2 and Dppa4, which remain expressed until embryonic day 7.5 (E7.5), when their promoters are remethylated. Furthermore, Dppa2 and Dppa4 are also expressed during induced pluripotent stem cell (iPSC) reprogramming at the time that 2C-like transcription transiently peaks. Through a combination of overexpression, knockdown, knockout, and rescue experiments together with transcriptional analyses, we show that Dppa2 and Dppa4 directly regulate the 2C-like cell population and associated transcripts, including Dux and the Zscan4 cluster. Importantly, we teased apart the molecular hierarchy in which the 2C-like transcriptional program is initiated and stabilized. Dppa2 and Dppa4 require Dux to initiate 2C-like transcription, suggesting that they act upstream by directly regulating Dux. Supporting this, ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) analysis revealed that Dppa2 and Dppa4 bind to the Dux promoter and gene body and drive its expression. Zscan4c is also able to induce 2C-like cells in wild-type cells but, in contrast to Dux, can no longer do so in Dppa2/4 double-knockout cells, suggesting that it may act to stabilize rather than drive the transcriptional network. Our findings suggest a model in which Dppa2/4 binding to the Dux promoter leads to Dux up-regulation and activation of the 2C-like transcriptional program, which is subsequently reinforced by Zscan4c.
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Affiliation(s)
| | | | - Marloes Blotenburg
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Elisa Kreibich
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Christel Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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23
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Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports 2019; 10:627-641. [PMID: 29358085 PMCID: PMC5830946 DOI: 10.1016/j.stemcr.2017.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
The heterochromatin protein 1 (HP1) family is involved in various functions with maintenance of chromatin structure. During murine somatic cell reprogramming, we find that early depletion of HP1γ reduces the generation of induced pluripotent stem cells, while late depletion enhances the process, with a concomitant change from a centromeric to nucleoplasmic localization and elongation-associated histone H3.3 enrichment. Depletion of heterochromatin anchoring protein SENP7 increased reprogramming efficiency to a similar extent as HP1γ, indicating the importance of HP1γ release from chromatin for pluripotency acquisition. HP1γ interacted with OCT4 and DPPA4 in HP1α and HP1β knockouts and in H3K9 methylation depleted H3K9M embryonic stem cell (ESC) lines. HP1α and HP1γ complexes in ESCs differed in association with histones, the histone chaperone CAF1 complex, and specific components of chromatin-modifying complexes such as DPY30, implying distinct functional contributions. Taken together, our results reveal the complex contribution of the HP1 proteins to pluripotency. Release of HP1γ from anchoring by Senp7 increases reprogramming efficiency HP1γ switches enrichment from histone H1 to histone H3.3 in pluripotent cells HP1γ interacts with OCT4 and DPPA4 independent of HP1α, HP1β, and H3K9 methylation Proteomic characterization of HP1 protein family in pluripotent cells
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Affiliation(s)
- Nur Zafirah Zaidan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kolin J Walker
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jaime E Brown
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA.
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24
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Mochizuki K, Tando Y, Sekinaka T, Otsuka K, Hayashi Y, Kobayashi H, Kamio A, Ito-Matsuoka Y, Takehara A, Kono T, Osumi N, Matsui Y. SETDB1 is essential for mouse primordial germ cell fate determination by ensuring BMP signaling. Development 2018; 145:dev.164160. [PMID: 30446626 DOI: 10.1242/dev.164160] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/12/2018] [Indexed: 02/04/2023]
Abstract
In mouse embryos, primordial germ cells (PGCs) are fate-determined from epiblast cells. Signaling pathways involved in PGC formation have been identified, but their epigenetic mechanisms remain poorly understood. Here, we show that the histone methyltransferase SETDB1 is an epigenetic regulator of PGC fate determination. Setdb1-deficient embryos exhibit drastic reduction of nascent PGCs. Dppa2, Otx2 and Utf1 are de-repressed whereas mesoderm development-related genes, including BMP4 signaling-related genes, are downregulated by Setdb1 knockdown during PGC-like cell (PGCLC) induction. In addition, binding of SETDB1 is observed at the flanking regions of Dppa2, Otx2 and Utf1 in cell aggregates containing PGCLCs, and trimethylation of lysine 9 of histone H3 is reduced by Setdb1 knockdown at those regions. Furthermore, DPPA2, OTX2 and UTF1 binding is increased in genes encoding BMP4 signaling-related proteins, including SMAD1. Finally, overexpression of Dppa2, Otx2 and Utf1 in cell aggregates containing PGCLCs results in the repression of BMP4 signaling-related genes and PGC determinant genes. We propose that the localization of SETDB1 to Dppa2, Otx2 and Utf1, and subsequent repression of their expression, are crucial for PGC determination by ensuring BMP4 signaling.
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Affiliation(s)
- Kentaro Mochizuki
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan.,Center for Environmental Conservation and Research Safety, Tohoku University, Sendai, Miyagi 980-8577, Japan.,Department of Germ Cell Development, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan.,Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Yukiko Tando
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tamotsu Sekinaka
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Germ Cell Development, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Kei Otsuka
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Yohei Hayashi
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Germ Cell Development, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Asuka Kamio
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yumi Ito-Matsuoka
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Asuka Takehara
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tomohiro Kono
- Department of BioScience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi 980-8575, Japan .,Department of Germ Cell Development, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan.,Center for Regulatory Epigenome and Diseases, Tohoku University School of Medicine, Sendai, Miyagi 980-8575, Japan
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Hernandez C, Wang Z, Ramazanov B, Tang Y, Mehta S, Dambrot C, Lee YW, Tessema K, Kumar I, Astudillo M, Neubert TA, Guo S, Ivanova NB. Dppa2/4 Facilitate Epigenetic Remodeling during Reprogramming to Pluripotency. Cell Stem Cell 2018; 23:396-411.e8. [PMID: 30146411 PMCID: PMC6128737 DOI: 10.1016/j.stem.2018.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 06/04/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
Abstract
As somatic cells are converted into induced pluripotent stem cells (iPSCs), their chromatin is remodeled to a pluripotent configuration with unique euchromatin-to-heterochromatin ratios, DNA methylation patterns, and enhancer and promoter status. The molecular machinery underlying this process is largely unknown. Here, we show that embryonic stem cell (ESC)-specific factors Dppa2 and Dppa4 play a key role in resetting the epigenome to a pluripotent state. They are induced in reprogramming intermediates, function as a heterodimer, and are required for efficient reprogramming of mouse and human cells. When co-expressed with Oct4, Klf4, Sox2, and Myc (OKSM) factors, Dppa2/4 yield reprogramming efficiencies that exceed 80% and accelerate reprogramming kinetics, generating iPSCs in 2 to 4 days. When bound to chromatin, Dppa2/4 initiate global chromatin decompaction via the DNA damage response pathway and contribute to downregulation of somatic genes and activation of ESC enhancers, all of which enables an efficient transition to pluripotency. Our work provides critical insights into how the epigenome is remodeled during acquisition of pluripotency.
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Affiliation(s)
- Charles Hernandez
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Zheng Wang
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Bulat Ramazanov
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Yin Tang
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Sameet Mehta
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Cheryl Dambrot
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Yu-Wei Lee
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Kaleab Tessema
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Ishan Kumar
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Michael Astudillo
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Shangqin Guo
- Yale Stem Cell Center, Yale University, New Haven, CT, USA; Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Natalia B Ivanova
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA.
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26
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Klein RH, Tung PY, Somanath P, Fehling HJ, Knoepfler PS. Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer. Stem Cell Res 2018; 31:83-94. [PMID: 30031967 PMCID: PMC6133722 DOI: 10.1016/j.scr.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental pluripotency associated factor 4 (Dppa4) is a highly specific marker of pluripotent cells, and is also overexpressed in certain cancers, but its function in either of these contexts is poorly understood. In this study, we use ChIP-Seq to identify Dppa4 binding genome-wide in three distinct cell types: mouse embryonic stem cells (mESC), embryonal carcinoma cells, and 3T3 fibroblasts ectopically expressing Dppa4. We find a core set of Dppa4 binding sites shared across cell types, and also a substantial number of sites unique to each cell type. Across cell types Dppa4 shows a preference for binding to regions with active chromatin signatures, and can influence chromatin modifications at target genes. In 3T3 fibroblasts with enforced Dppa4 expression, Dppa4 represses the cell cycle inhibitor Cdkn2c and activates Ets family transcription factor Etv4, leading to alterations in the cell cycle that likely contribute to the oncogenic phenotype. Dppa4 also directly regulates Etv4 in mESC but represses it in this context, and binds with Oct4 to a set of shared targets that are largely independent of Sox2 and Nanog, indicating that Dppa4 functions independently of the core pluripotency network in stem cells. Together these data provide novel insights into Dppa4 function in both pluripotent and oncogenic contexts.
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Affiliation(s)
- Rachel Herndon Klein
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Po-Yuan Tung
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Priyanka Somanath
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | | | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States.
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27
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Somanath P, Bush KM, Knoepfler PS. ERBB3-Binding Protein 1 (EBP1) Is a Novel Developmental Pluripotency-Associated-4 (DPPA4) Cofactor in Human Pluripotent Cells. Stem Cells 2018; 36:671-682. [PMID: 29327467 DOI: 10.1002/stem.2776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 12/04/2017] [Accepted: 12/09/2017] [Indexed: 12/31/2022]
Abstract
Developmental Pluripotency-Associated-4 (DPPA4) is one of the few core pluripotency genes lacking clearly defined molecular and cellular functions. Here, we used a proteomics screening approach of human embryonic stem cell (hESC) nuclear extract to determine DPPA4 molecular functions through identification of novel cofactors. Unexpectedly, the signaling molecule ERBB3-binding protein 1 (EBP1) was the strongest candidate binding partner for DPPA4 in hESC. EBP1 is a growth factor signaling mediator present in two isoforms, p48 and p42. The two isoforms generally have opposing functions, however their roles in pluripotent cells have not been established. We found that DPPA4 preferentially binds p48 in pluripotent and NTERA-2 cells, but this interaction is largely absent in non-pluripotent cells and is reduced with differentiation. The DPPA4-EBP1 interaction is mediated at least in part in DPPA4 by the highly conserved SAF-A/B, Acinus and PIAS (SAP) domain. Functionally, we found that DPPA4 transcriptional repressive function in reporter assays is significantly increased by specific p48 knockdown, an effect that was abolished with an interaction-deficient DPPA4 ΔSAP mutant. Thus, DPPA4 and EBP1 may cooperate in transcriptional functions through their physical association in a pluripotent cell specific context. Our study identifies EBP1 as a novel pluripotency cofactor and provides insight into potential mechanisms used by DPPA4 in regulating pluripotency through its association with EBP1. Stem Cells 2018;36:671-682.
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Affiliation(s)
- Priyanka Somanath
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
| | - Kelly M Bush
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
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28
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Sone M, Morone N, Nakamura T, Tanaka A, Okita K, Woltjen K, Nakagawa M, Heuser JE, Yamada Y, Yamanaka S, Yamamoto T. Hybrid Cellular Metabolism Coordinated by Zic3 and Esrrb Synergistically Enhances Induction of Naive Pluripotency. Cell Metab 2017; 25:1103-1117.e6. [PMID: 28467928 DOI: 10.1016/j.cmet.2017.04.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/06/2017] [Accepted: 04/15/2017] [Indexed: 01/05/2023]
Abstract
Naive pluripotent stem cells (PSCs) utilize both glycolysis and oxidative phosphorylation (OXPHOS) to satisfy their metabolic demands. However, it is unclear how somatic cells acquire this hybrid energy metabolism during reprogramming toward naive pluripotency. Here, we show that when transduced with Oct4, Sox2, and Klf4 (OSK) into murine fibroblasts, Zic3 and Esrrb synergistically enhance the reprogramming efficiency by regulating cellular metabolic pathways. These two transcription factors (TFs) cooperatively activate glycolytic metabolism independently of hypoxia inducible factors (HIFs). In contrast, the regulatory modes of the TFs on OXPHOS are antagonistic: Zic3 represses OXPHOS, whereas Esrrb activates it. Therefore, when introduced with Zic3, Esrrb restores OXPHOS activity, which is essential for efficient reprogramming. In addition, Esrrb-mediated OXPHOS activation is critical for the conversion of primed PSCs into the naive state. Our study suggests that the combinatorial function of TFs achieves an appropriate balance of metabolic pathways to induce naive PSCs.
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Affiliation(s)
- Masamitsu Sone
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Nobuhiro Morone
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; MRC Toxicology Unit, University of Leicester, Leicester, LE1 9HN, UK
| | - Tomonori Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keisuke Okita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Masato Nakagawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - John E Heuser
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiro Yamada
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; AMED-CREST, AMED 1-7-1 Otemach, Chiyodaku, Tokyo, 100-0004, Japan.
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29
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Engelen E, Brandsma JH, Moen MJ, Signorile L, Dekkers DHW, Demmers J, Kockx CEM, Ozgür Z, van IJcken WFJ, van den Berg DLC, Poot RA. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Nat Commun 2015; 6:7155. [PMID: 25990348 PMCID: PMC4455091 DOI: 10.1038/ncomms8155] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 04/13/2015] [Indexed: 12/27/2022] Open
Abstract
The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type.
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Affiliation(s)
- Erik Engelen
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Johannes H Brandsma
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Maaike J Moen
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Luca Signorile
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Christel E M Kockx
- Center for Biomics, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Zehila Ozgür
- Center for Biomics, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | | | - Debbie L C van den Berg
- 1] Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands [2] Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Raymond A Poot
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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30
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Tung PY, Varlakhanova NV, Knoepfler PS. Identification of DPPA4 and DPPA2 as a novel family of pluripotency-related oncogenes. Stem Cells 2014; 31:2330-42. [PMID: 23963736 DOI: 10.1002/stem.1526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/07/2013] [Accepted: 07/07/2013] [Indexed: 11/07/2022]
Abstract
In order to identify novel pluripotency-related oncogenes, an expression screen for oncogenic foci-inducing genes within a retroviral human embryonic stem cell cDNA library was conducted. From this screen, we identified not only known oncogenes but also intriguingly the key pluripotency factor, DPPA4 (developmental pluripotency-associated four) that encodes a DNA binding SAP domain-containing protein. DPPA4 has not been previously identified as an oncogene but is highly expressed in embryonal carcinomas, pluripotent germ cell tumors, and other cancers. DPPA4 is also mutated in some cancers. In direct transformation assays, we validated that DPPA4 is an oncogene in both mouse 3T3 cells and immortalized human dermal fibroblasts. Overexpression of DPPA4 generates oncogenic foci (sarcoma cells) and causes anchorage-independent growth. The in vitro transformed cells also give rise to tumors in immunodeficient mice. Furthermore, functional analyses indicate that both the DNA-binding SAP domain and the histone-binding C-terminal domain are critical for the oncogenic transformation activity of DPPA4. Downregulation of DPPA4 in E14 mouse embryonic stem cells and P19 mouse embryonic carcinoma cells causes decreased cell proliferation in each case. In addition, DPPA4 overexpression induces cell proliferation through genes related to regulation of G1/S transition. Interestingly, we observed similar findings for family member DPPA2. Thus, we have identified a new family of pluripotency-related oncogenes consisting of DPPA2 and DPPA4. Our findings have important implications for stem cell biology and tumorigenesis.
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Affiliation(s)
- Po-Yuan Tung
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, California, USA; University of California Davis Genome Center, University of California Davis, Davis, California, USA; UC Davis Comprehensive Cancer Center, Shriners Hospital For Children Northern California, Sacramento, California, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, California, USA
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31
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Abstract
Maintenance of nuclear architecture is crucial for gene regulation, cell proliferation and tissue development. However, during every open mitosis and meiosis, chromosomes are exposed to cytoskeletal forces until they are fully reassembled into mature nuclei. Here we discuss our recent study of nuclear assembly in Xenopus egg extracts, where we showed that the DNA binding protein Developmental pluripotency associated 2 (Dppa2) directly inhibits microtubule polymerization during nuclear formation, and that this is essential for normal nuclear shape and replication. We explore mechanisms by which microtubule dynamics could regulate nuclear formation and morphology, and discuss the importance of both spatial and temporal regulation of microtubules in this process. Moreover, expression of Dppa2 is limited to the early embryo and pluripotent tissues, and we highlight the specific demands of mitosis in these often rapidly dividing cells, in which telophase nuclear assembly must be expedited and may facilitate developmental changes in nuclear architecture.
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Affiliation(s)
- John Z Xue
- Laboratory of Chromosome and Cell Biology; The Rockefeller University; New York, NY USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology; The Rockefeller University; New York, NY USA
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32
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White SN, Mousel MR, Herrmann-Hoesing LM, Reynolds JO, Leymaster KA, Neibergs HL, Lewis GS, Knowles DP. Genome-wide association identifies multiple genomic regions associated with susceptibility to and control of ovine lentivirus. PLoS One 2012; 7:e47829. [PMID: 23082221 PMCID: PMC3474742 DOI: 10.1371/journal.pone.0047829] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/17/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Like human immunodeficiency virus (HIV), ovine lentivirus (OvLV) is macrophage-tropic and causes lifelong infection. OvLV infects one quarter of U.S. sheep and induces pneumonia and body condition wasting. There is no vaccine to prevent OvLV infection and no cost-effective treatment for infected animals. However, breed differences in prevalence and proviral concentration have indicated a genetic basis for susceptibility to OvLV. A recent study identified TMEM154 variants in OvLV susceptibility. The objective here was to identify additional loci associated with odds and/or control of OvLV infection. METHODOLOGY/PRINCIPAL FINDINGS This genome-wide association study (GWAS) included 964 sheep from Rambouillet, Polypay, and Columbia breeds with serological status and proviral concentration phenotypes. Analytic models accounted for breed and age, as well as genotype. This approach identified TMEM154 (nominal P=9.2×10(-7); empirical P=0.13), provided 12 additional genomic regions associated with odds of infection, and provided 13 regions associated with control of infection (all nominal P<1 × 10(-5)). Rapid decline of linkage disequilibrium with distance suggested many regions included few genes each. Genes in regions associated with odds of infection included DPPA2/DPPA4 (empirical P=0.006), and SYTL3 (P=0.051). Genes in regions associated with control of infection included a zinc finger cluster (ZNF192, ZSCAN16, ZNF389, and ZNF165; P=0.001), C19orf42/TMEM38A (P=0.047), and DLGAP1 (P=0.092). CONCLUSIONS/SIGNIFICANCE These associations provide targets for mutation discovery in sheep susceptibility to OvLV. Aside from TMEM154, these genes have not been associated previously with lentiviral infection in any species, to our knowledge. Further, data from other species suggest functional hypotheses for future testing of these genes in OvLV and other lentiviral infections. Specifically, SYTL3 binds and may regulate RAB27A, which is required for enveloped virus assembly of human cytomegalovirus. Zinc finger transcription factors have been associated with positive selection for repression of retroviral replication. DLGAP1 binds and may regulate DLG1, a known regulator of HIV infectivity.
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Affiliation(s)
- Stephen N White
- Animal Disease Research Unit, Agricultural Research Service, U. S. Department of Agriculture, Pullman, Washington, USA.
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33
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Watabe T. Roles of Dppa2 in the regulation of the present status and future of pluripotent stem cells. J Biochem 2012; 152:1-3. [DOI: 10.1093/jb/mvs057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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