1
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Ulfig A, Jakob U. Redox heterogeneity in mouse embryonic stem cells individualizes cell fate decisions. Dev Cell 2024; 59:2118-2133.e8. [PMID: 39106861 PMCID: PMC11338707 DOI: 10.1016/j.devcel.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/23/2024] [Accepted: 07/09/2024] [Indexed: 08/09/2024]
Abstract
Pluripotent embryonic stem cells (ESCs) can develop into any cell type in the body. Yet, the regulatory mechanisms that govern cell fate decisions during embryogenesis remain largely unknown. We now demonstrate that mouse ESCs (mESCs) display large natural variations in mitochondrial reactive oxygen species (mitoROS) levels that individualize their nuclear redox state, H3K4me3 landscape, and cell fate. While mESCs with high mitoROS levels (mitoROSHIGH) differentiate toward mesendoderm and form the primitive streak during gastrulation, mESCs, which generate less ROS, choose the alternative neuroectodermal fate. Temporal studies demonstrated that mesendodermal (ME) specification of mitoROSHIGH mESCs is mediated by a Nrf2-controlled switch in the nuclear redox state, triggered by the accumulation of redox-sensitive H3K4me3 marks, and executed by a hitherto unknown ROS-dependent activation process of the Wnt signaling pathway. In summary, our study explains how ESC heterogeneity is generated and used by individual cells to decide between distinct cellular fates.
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Affiliation(s)
- Agnes Ulfig
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Zhang C, Shan Y, Lin H, Zhang Y, Xing Q, Zhu J, Zhou T, Lin A, Chen Q, Wang J, Pan G. HBO1 determines SMAD action in pluripotency and mesendoderm specification. Nucleic Acids Res 2024; 52:4935-4949. [PMID: 38421638 PMCID: PMC11109972 DOI: 10.1093/nar/gkae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/11/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
TGF-β signaling family plays an essential role to regulate fate decisions in pluripotency and lineage specification. How the action of TGF-β family signaling is intrinsically executed remains not fully elucidated. Here, we show that HBO1, a MYST histone acetyltransferase (HAT) is an essential cell intrinsic determinant for TGF-β signaling in human embryonic stem cells (hESCs). HBO1-/- hESCs fail to response to TGF-β signaling to maintain pluripotency and spontaneously differentiate into neuroectoderm. Moreover, HBO1 deficient hESCs show complete defect in mesendoderm specification in BMP4-triggered gastruloids or teratomas. Molecularly, HBO1 interacts with SMAD4 and co-binds the open chromatin labeled by H3K14ac and H3K4me3 in undifferentiated hESCs. Upon differentiation, HBO1/SMAD4 co-bind and maintain the mesoderm genes in BMP4-triggered mesoderm cells while lose chromatin occupancy in neural cells induced by dual-SMAD inhibition. Our data reveal an essential role of HBO1, a chromatin factor to determine the action of SMAD in both human pluripotency and mesendoderm specification.
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Affiliation(s)
- Cong Zhang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Yongli Shan
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Huaisong Lin
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Yanqi Zhang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Qi Xing
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Jinmin Zhu
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Tiancheng Zhou
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Aiping Lin
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Qianyu Chen
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Junwei Wang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Guangjin Pan
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
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3
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Shen Z, Wu Y, Manna A, Yi C, Cairns BR, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. Genes Dev 2024; 38:308-321. [PMID: 38719541 PMCID: PMC11146590 DOI: 10.1101/gad.351411.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we used domain swapping and mutagenesis to study Oct4's reprogramming ability, identifying a redox-sensitive DNA binding domain, cysteine residue (Cys48), as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1 C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs) but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression, and aberrant differentiation. Pou5f1 C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1 C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yifan Wu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Asit Manna
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Chongil Yi
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mahesh B Chandrasekharan
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA;
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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4
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Shen Z, Wu Y, Mana A, Yi C, Cairns B, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.21.529404. [PMID: 36865286 PMCID: PMC9980064 DOI: 10.1101/2023.02.21.529404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we use domain swapping and mutagenesis to study Oct4s reprogramming ability, identifying a redox-sensitive DNA binding domain cysteine residue (Cys48) as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs), but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression and aberrant differentiation. Pou5f1C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
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5
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Terzi Cizmecioglu N. Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024. [PMID: 38231346 DOI: 10.1007/5584_2023_794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation. The various roles of H3K4 methylation are interpreted by dedicated chromatin reader proteins, linking this modification to broader molecular and cellular phenotypes. In this review, we discuss the regulation of different levels of H3K4 methylation, their distinct accumulation pattern, and downstream molecular roles with an early embryogenesis perspective.
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6
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Liu C, Sun L, Tan Y, Wang Q, Luo T, Li C, Yao N, Xie Y, Yi X, Zhu Y, Guo T, Ji J. USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and noncatalytic activities. SCIENCE ADVANCES 2023; 9:eade3888. [PMID: 37196079 DOI: 10.1126/sciadv.ade3888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 04/12/2023] [Indexed: 05/19/2023]
Abstract
USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function that shapes the transcriptional network in mouse embryonic stem cells (mESCs) remains poorly understood. We report that USP7 maintains mESC identity through both catalytic activity-dependent and -independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 levels and derepresses lineage differentiation genes thereby compromising mESC pluripotency. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant Polycomb repressive complex 1 and contributes to Polycomb chromatin-mediated repression of ME lineage genes in a catalytic activity-dependent manner. USP7 deficiency in its deubiquitination function is able to maintain RYBP binding to chromatin for repressing primitive endoderm-associated genes. Our study demonstrates that USP7 harbors both catalytic and noncatalytic activities to repress different lineage differentiation genes, thereby revealing a previously unrecognized role in controlling gene expression for maintaining mESC identity.
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Affiliation(s)
- Chao Liu
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China
| | - Lingang Sun
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yijun Tan
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qi Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tao Luo
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chenlu Li
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Nan Yao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Center for Infectious Disease Research, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Yuting Xie
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Center for Infectious Disease Research, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Xiao Yi
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Center for Infectious Disease Research, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Yi Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Center for Infectious Disease Research, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Center for Infectious Disease Research, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Junfeng Ji
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Institute of Hematology, Zhejiang University, Hangzhou 310058, China
- Department of Geriatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- Eye Center, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, Zhejiang 310009, China
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Bu S, Lau SSY, Yong WL, Zhang H, Thiagarajan S, Bashirullah A, Yu F. Polycomb group genes are required for neuronal pruning in Drosophila. BMC Biol 2023; 21:33. [PMID: 36793038 PMCID: PMC9933400 DOI: 10.1186/s12915-023-01534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Pruning that selectively eliminates unnecessary or incorrect neurites is required for proper wiring of the mature nervous system. During Drosophila metamorphosis, dendritic arbourization sensory neurons (ddaCs) and mushroom body (MB) γ neurons can selectively prune their larval dendrites and/or axons in response to the steroid hormone ecdysone. An ecdysone-induced transcriptional cascade plays a key role in initiating neuronal pruning. However, how downstream components of ecdysone signalling are induced remains not entirely understood. RESULTS Here, we identify that Scm, a component of Polycomb group (PcG) complexes, is required for dendrite pruning of ddaC neurons. We show that two PcG complexes, PRC1 and PRC2, are important for dendrite pruning. Interestingly, depletion of PRC1 strongly enhances ectopic expression of Abdominal B (Abd-B) and Sex combs reduced, whereas loss of PRC2 causes mild upregulation of Ultrabithorax and Abdominal A in ddaC neurons. Among these Hox genes, overexpression of Abd-B causes the most severe pruning defects, suggesting its dominant effect. Knockdown of the core PRC1 component Polyhomeotic (Ph) or Abd-B overexpression selectively downregulates Mical expression, thereby inhibiting ecdysone signalling. Finally, Ph is also required for axon pruning and Abd-B silencing in MB γ neurons, indicating a conserved function of PRC1 in two types of pruning. CONCLUSIONS This study demonstrates important roles of PcG and Hox genes in regulating ecdysone signalling and neuronal pruning in Drosophila. Moreover, our findings suggest a non-canonical and PRC2-independent role of PRC1 in Hox gene silencing during neuronal pruning.
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Affiliation(s)
- Shufeng Bu
- grid.4280.e0000 0001 2180 6431Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Samuel Song Yuan Lau
- grid.4280.e0000 0001 2180 6431Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - Wei Lin Yong
- grid.4280.e0000 0001 2180 6431Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - Heng Zhang
- grid.4280.e0000 0001 2180 6431Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - Sasinthiran Thiagarajan
- grid.4280.e0000 0001 2180 6431Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Arash Bashirullah
- grid.14003.360000 0001 2167 3675Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222 USA
| | - Fengwei Yu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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8
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Zhang C, Lin H, Zhang Y, Xing Q, Zhang J, Zhang D, Liu Y, Chen Q, Zhou T, Wang J, Shan Y, Pan G. BRPF1 bridges H3K4me3 and H3K23ac in human embryonic stem cells and is essential to pluripotency. iScience 2023; 26:105939. [PMID: 36711238 PMCID: PMC9874078 DOI: 10.1016/j.isci.2023.105939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 10/04/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
Post-translational modifications (PTMs) on histones play essential roles in cell fate decisions during development. However, how these PTMs are recognized and coordinated remains to be fully illuminated. Here, we show that BRPF1, a multi-histone binding module protein, is essential for pluripotency in human embryonic stem cells (ESCs). BRPF1, H3K4me3, and H3K23ac substantially co-occupy the open chromatin and stemness genes in hESCs. BRPF1 deletion impairs H3K23ac in hESCs and leads to closed chromatin accessibility on stemness genes and hESC differentiation as well. Deletion of the N terminal or PHD-zinc knuckle-PHD (PZP) module in BRPF1 completely impairs its functions in hESCs while PWWP module deletion partially impacts the function. In sum, we reveal BRPF1, the multi-histone binding module protein that bridges the crosstalk between different histone modifications in hESCs to maintain pluripotency.
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Affiliation(s)
- Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Huaisong Lin
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qi Xing
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Di Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yancai Liu
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Junwei Wang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Corresponding author
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Key Lab for Rare & Uncommon Diseases of Shandong Province, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong 250117, China,Corresponding author
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9
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Retention of ERK in the cytoplasm mediates the pluripotency of embryonic stem cells. Stem Cell Reports 2022; 18:305-318. [PMID: 36563690 PMCID: PMC9860118 DOI: 10.1016/j.stemcr.2022.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 12/24/2022] Open
Abstract
The dynamic subcellular localization of ERK1/2 plays an important role in regulating cell fate. Differentiation of mouse embryonic stem cells (mESCs) involves inductive stimulation of ERK1/2, and therefore, inhibitors of the ERK cascade are used to maintain pluripotency. Interestingly, we found that in pluripotent mESCs, ERK1/2 do not translocate to the nucleus either before or after stimulation. This inhibition of nuclear translocation may be dependent on a lack of stimulated ERK1/2 interaction with importin7 rather than a lack of ERK1/2 phosphorylation activating translocation. At late stages of naive-to-primed transition, the action of the translocating machinery is restored, leading to elevation in ERK1/2-importin7 interaction and their nuclear translocation. Importantly, forcing ERK2 into the naive cells' nuclei accelerates their early differentiation, while prevention of the translocation restores stem cells' pluripotency. These results indicate that prevention of nuclear ERK1/2 translocation serves as a safety mechanism for keeping pluripotency of mESCs.
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10
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Shao W, Ning W, Liu C, Zou Y, Yao Y, Kang J, Cao Z. Histone Methyltransferase SETD2 Is Required for Porcine Early Embryonic Development. Animals (Basel) 2022; 12:ani12172226. [PMID: 36077946 PMCID: PMC9454584 DOI: 10.3390/ani12172226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Normal early embryonic development is important for ensuring sow fertility. Low quality of in vitro production embryos severely limits extensive application of porcine embryo engineering technologies in animal agriculture and the biomedicine field. Histone H3K36 methyltransferase SETD2 reportedly regulates oocyte maturation and preimplantation embryonic development in mice. However, the specific substrate and function of SETD2 in porcine early embryonic development remains unclear. Here, we show that SETD2 preferentially catalyzes H3K36me3 in porcine early embryos. SETD2 knockdown severely impeded blastocyst cavitation and perturbed normal allocation of inner cell mass and trophectoderm. SETD2 knockdown caused the apoptosis of cells within blastocysts. Therefore, SETD2 is essential for porcine early embryonic development. These findings provide a better understanding of porcine early embryonic development and lay a potential basis for improving the quality of porcine in vitro production embryos. Abstract SET domain-containing 2 (SETD2) is a methyltransferase that can catalyze the di- and tri-methylation of lysine 36 on histone H3 (H3K36me2/me3). SETD2 frequently mediates H3K36me3 modification to regulate both oocyte maturation and preimplantation embryonic development in mice. However, the specific substrate and function of SETD2 in porcine early embryonic development are still unclear. In this study, SETD2 preferentially catalyzed H3K36me3 to regulate porcine early embryonic development. SETD2 mRNA is dynamically expressed during early embryonic development. Functional studies using an RNA interference (RNAi) approach revealed that the expression levels of SETD2 mRNA were effectively knocked down by siRNA microinjection. Immunofluorescence analysis indicated that SETD2 knockdown (KD) did not affect H3K36me2 modification but significantly reduced H3K36me3 levels, suggesting a preferential H3K36me3 recognition of SETD2 in porcine embryos. Furthermore, SETD2 KD significantly reduced blastocyst rate and disrupted allocation between inner cell mass (ICM) and trophectoderm (TE) lineage. The expression levels of key genes important for specification of the first two lineages apparently decreased in SETD2 KD blastocysts. SETD2 KD markedly increased the apoptotic percentage of cells within embryos and altered the expression of pro- and anti-apoptotic genes. Therefore, our data indicate that SETD2 is essential for porcine early embryonic development.
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Affiliation(s)
| | | | | | | | | | | | - Zubing Cao
- Correspondence: ; Tel.: +86-551-6578-6537
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11
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Lien YC, Lu XM, Won KJ, Wang PZ, Osei-Bonsu W, Simmons RA. The Transcriptome and Epigenome Reveal Novel Changes in Transcription Regulation During Pancreatic Rat Islet Maturation. Endocrinology 2021; 162:6360893. [PMID: 34467975 PMCID: PMC8455347 DOI: 10.1210/endocr/bqab181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 01/03/2023]
Abstract
Islet function is critical for normal glucose homeostasis. Unlike adult β cells, fetal and neonatal islets are more proliferative and have decreased insulin secretion in response to stimuli. However, the underlying mechanisms governing functional maturity of islets have not been completely elucidated. Pancreatic islets comprise different cell types. The microenvironment of islets and interactions between these cell types are critical for β-cell development and maturation. Thus, the study of intact islets is optimal to identify novel molecular mechanisms controlling islet functional development. Transcriptomes and genome-wide histone landscapes of H3K4me3, H3K27me3, and H3K27Ac from intact islets isolated from 2- and 10-week-old Sprague-Dawley rats were integrated to elucidate genes and pathways modulating islet development, as well as the contribution of epigenetic regulation. A total of 4489 differentially expressed genes were identified; 2289 and 2200 of them were up- and down-regulated in 10-week islets, respectively. Ingenuity Pathway Analysis revealed critical pathways regulating functional maturation of islets, including nutrient sensing, neuronal function, immune function, cell replication, and extracellular matrix. Furthermore, we identified significant changes in enrichment of H3K4me3, H3K27me3, and H3K27Ac marks, which correlated with expression changes of genes critical for islet function. These histone marks were enriched at critical transcription factor-binding motifs, such as Hoxa9, C/EBP-β, Gata1, Foxo1, E2f1, E2f3, and Mafb. In addition, our chromatin immunoprecipitation sequencing data revealed multiple potential bivalent genes whose poised states changed with maturation. Collectively, our current study identified critical novel pathways for mature islet function and suggested a role for histone modifications in regulating islet development and maturation.
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Affiliation(s)
- Yu-Chin Lien
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xueqing Maggie Lu
- Institute for Biomedical Informatics, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Paul Zhiping Wang
- Institute for Biomedical Informatics, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wendy Osei-Bonsu
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Correspondence: Rebecca A. Simmons, MD, BRB II/III, 13th Floor, Rm 1308, 421 Curie Blvd, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Ferreira RS, Assis RIF, Feltran GDS, do Rosário Palma IC, Françoso BG, Zambuzzi WF, Andia DC, da Silva RA. Genome-wide DNA (hydroxy) methylation reveals the individual epigenetic landscape importance on osteogenic phenotype acquisition in periodontal ligament cells. J Periodontol 2021; 93:435-448. [PMID: 34291826 DOI: 10.1002/jper.21-0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 06/09/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Mesenchymal cells' biology has been an important investigative tool to maximize bone regeneration through tissue engineering. Here we used mesenchymal cells from periodontal ligament (PDLCs) with high (h-) and low (l-) osteogenic potential, isolated from different donors, to investigate the impact of the individual epigenetic and transcriptional profiles on the osteogenic potential. METHODS Genome-wide and gene-specific DNA (hydroxy) methylation, mRNA expression and immunofluorescence analysis were carried out in h- and l-PDLCs at DMEM (non-induced to osteogenesis) and OM (induced-3rd and 10th days of osteogenic differentiation) groups in vitro. RESULTS Genome-wide results showed distinct epigenetic profile among PDLCs with most of the differences on 10th day of OM; DMEMs showed higher concentrations (xOM) of differentially methylated probes in gene body, intronic and open sea (3rd day), increasing this concentration in TSS200 and island regions, at 10 days. At basal levels, h- and l-PDLCs showed different transcriptional profiles; l-PDLCs demonstrated higher levels of NANOG/OCT4/SOX2, BAPX1, DNMT3A, TET1/3, and lower levels of RUNX2 transcripts, confirmed by NANOG/OCT4 and RUNX2 immunofluorescence. After osteogenic induction, the distinct transcriptional profile of multipotentiality genes was maintained among PDLCs. In l-PDLCs, the anti-correlation between DNA methylation and gene expression in RUNX2 and NANOG indicates methylation could play a role in modulating both transcripts. CONCLUSIONS Epigenetic and transcriptional distinct profiles detected at basal levels among PDLCs were maintained after osteogenic induction. We cannot discard the existence of a complex that represses osteogenesis, suggesting the individual donors' characteristics have significant impact on the osteogenic phenotype acquisition.
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Affiliation(s)
- Rogério S Ferreira
- School of Dentistry, Health Science Institute, Paulista University, São Paulo, Brazil
| | - Rahyza I F Assis
- Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | - Geórgia da S Feltran
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | | | - Beatriz G Françoso
- School of Dentistry, Health Science Institute, Paulista University, São Paulo, Brazil
| | - Willian F Zambuzzi
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Denise C Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo, Brazil
| | - Rodrigo A da Silva
- Department of Dentistry, University of Taubaté, Taubaté, Brazil.,Program in Environmental and Experimental Pathology, Paulista University, São Paulo, Brazil
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13
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Liu J, Liu S, Han L, Sheng Y, Zhang Y, Kim IM, Wan J, Yang L. LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells. Development 2021; 148:268341. [PMID: 34027990 PMCID: PMC8276986 DOI: 10.1242/dev.199628] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
Polycomb repressive complex 2 (PRC2) deposits H3K27me3 on chromatin to silence transcription. PRC2 broadly interacts with RNAs. Currently, the role of the RNA-PRC2 interaction in human cardiogenesis remains elusive. Here, we found that human-specific heart brake lncRNA 1 (HBL1) interacted with two PRC2 subunits, JARID2 and EED, in human pluripotent stem cells (hPSCs). Loss of JARID2, EED or HBL1 significantly enhanced cardiac differentiation from hPSCs. HBL1 depletion disrupted genome-wide PRC2 occupancy and H3K27me3 chromatin modification on essential cardiogenic genes, and broadly enhanced cardiogenic gene transcription in undifferentiated hPSCs and later-on differentiation. In addition, ChIP-seq revealed reduced EED occupancy on 62 overlapped cardiogenic genes in HBL1−/− and JARID2−/− hPSCs, indicating that the epigenetic state of cardiogenic genes was determined by HBL1 and JARID2 at pluripotency stage. Furthermore, after cardiac development occurs, the cytosolic and nuclear fractions of HBL1 could crosstalk via a conserved ‘microRNA-1-JARID2’ axis to modulate cardiogenic gene transcription. Overall, our findings delineate the indispensable role of HBL1 in guiding PRC2 function during early human cardiogenesis, and expand the mechanistic scope of lncRNA(s) that cytosolic and nuclear portions of HBL1 could coordinate to orchestrate human cardiogenesis. Summary: This study reveals the indispensable role of the lncRNA HBL1 in guiding PRC2 function during early human cardiogenesis, and uncovers the crosstalk of the cytosolic and nuclear regions of HBL1 to orchestrate human cardiac development.
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Affiliation(s)
- Juli Liu
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lei Han
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yi Sheng
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yucheng Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Il-Man Kim
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lei Yang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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14
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Terzi Cizmecioglu N, Huang J, Keskin EG, Wang X, Esen I, Chen F, Orkin SH. ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit. J Biol Chem 2021; 295:17738-17751. [PMID: 33454011 DOI: 10.1074/jbc.ra120.015534] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/13/2020] [Indexed: 11/06/2022] Open
Abstract
Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies have focused on epigenetic factors that affect embryonic stem cells (ESC) self-renewal and pluripotency. However, the contribution of chromatin to lineage decisions at the exit from pluripotency has not been as extensively studied. Using a pooled epigenetic shRNA screen strategy, we identified chromatin-related factors critical for differentiation toward mesodermal and endodermal lineages. Here we reveal a critical role for the chromatin protein, ARID4B. Arid4b-deficient mESCs are similar to WT mESCs in the expression of pluripotency factors and their self-renewal. However, ARID4B loss results in defects in up-regulation of the meso/endodermal gene expression program. It was previously shown that Arid4b resides in a complex with SIN3A and HDACS 1 and 2. We identified a physical and functional interaction of ARID4B with HDAC1 rather than HDAC2, suggesting functionally distinct Sin3a subcomplexes might regulate cell fate decisions Finally, we observed that ARID4B deficiency leads to increased H3K27me3 and a reduced H3K27Ac level in key developmental gene loci, whereas a subset of genomic regions gain H3K27Ac marks. Our results demonstrate that epigenetic control through ARID4B plays a key role in the execution of lineage-specific gene expression programs at pluripotency exit.
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Affiliation(s)
- Nihal Terzi Cizmecioglu
- Department of Biological Sciences, Faculty of Arts and Sciences, Middle East Technical University, Ankara, Turkey.
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian China
| | - Ezgi G Keskin
- Department of Biological Sciences, Faculty of Arts and Sciences, Middle East Technical University, Ankara, Turkey
| | - Xiaofeng Wang
- Geisel School of Medicine, Dartmouth University, Hanover, New Hampshire USA
| | - Idil Esen
- Howard Hughes Medical Institute, Dana Farber/Boston Children's Cancer and Blood Disorders Center, Dept. of Pediatrics, Harvard Medical School, Boston, Massachusetts USA
| | - Fei Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian China
| | - Stuart H Orkin
- Howard Hughes Medical Institute, Dana Farber/Boston Children's Cancer and Blood Disorders Center, Dept. of Pediatrics, Harvard Medical School, Boston, Massachusetts USA.
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15
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Niu C, Wang S, Guo J, Wei X, Jia M, Chen Z, Gong W, Qin Y, Wang X, Zhi X, Lu M, Chen S, Gu M, Zhang J, Han JDJ, Lan F, Meng D. BACH1 recruits NANOG and histone H3 lysine 4 methyltransferase MLL/SET1 complexes to regulate enhancer-promoter activity and maintains pluripotency. Nucleic Acids Res 2021; 49:1972-1986. [PMID: 33503260 PMCID: PMC7913776 DOI: 10.1093/nar/gkab034] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 01/12/2023] Open
Abstract
Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a transcription factor BACH1, which directly interacts with OCT4/SOX2/NANOG (OSN) and MLL/SET1 methyltransferase complexes and maintains pluripotency in mouse ESCs (mESCs). BTB domain and bZIP domain of BACH1 are required for these interactions and pluripotency maintenance. Loss of BACH1 reduced the interaction between NANOG and MLL1/SET1 complexes, and decreased their occupancy on chromatin, and further decreased H3 lysine 4 trimethylation (H3K4me3) level on gene promoters and (super-) enhancers, leading to decreased enhancer activity and transcription activity, especially on stemness-related genes. Moreover, BACH1 recruited NANOG through chromatin looping and regulated remote NANOG binding, fine-tuning enhancer-promoter activity and gene expression. Collectively, these observations suggest that BACH1 maintains pluripotency in ESCs by recruiting NANOG and MLL/SET1 complexes to chromatin and maintaining the trimethylated state of H3K4 and enhancer-promoter activity, especially on stemness-related genes.
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Affiliation(s)
- Cong Niu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Siqing Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jieyu Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiangxiang Wei
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mengping Jia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhaoxiong Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Wenxuan Gong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Qin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xinhong Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiuling Zhi
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Meng Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Sifeng Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mingxia Gu
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jianyi Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Fei Lan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dan Meng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Muñoa-Hoyos I, Halsall JA, Araolaza M, Ward C, Garcia I, Urizar-Arenaza I, Gianzo M, Garcia P, Turner B, Subirán N. Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs. Clin Epigenetics 2020; 12:170. [PMID: 33168052 PMCID: PMC7654014 DOI: 10.1186/s13148-020-00955-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Environmentally induced epigenetic changes can lead to health problems or disease, but the mechanisms involved remain unclear. Morphine can pass through the placental barrier leading to abnormal embryo development. However, the mechanism by which morphine causes these effects and how they sometimes persist into adulthood is not well known. To unravel the morphine-induced chromatin alterations involved in aberrant embryo development, we explored the role of the H3K27me3/PRC2 repressive complex in gene expression and its transmission across cellular generations in response to morphine. Results Using mouse embryonic stem cells as a model system, we found that chronic morphine treatment induces a global downregulation of the histone modification H3K27me3. Conversely, ChIP-Seq showed a remarkable increase in H3K27me3 levels at specific genomic sites, particularly promoters, disrupting selective target genes related to embryo development, cell cycle and metabolism. Through a self-regulatory mechanism, morphine downregulated the transcription of PRC2 components responsible for H3K27me3 by enriching high H3K27me3 levels at the promoter region. Downregulation of PRC2 components persisted for at least 48 h (4 cell cycles) following morphine removal, though promoter H3K27me3 levels returned to control levels.
Conclusions Morphine induces targeting of the PRC2 complex to selected promoters, including those of PRC2 components, leading to characteristic changes in gene expression and a global reduction in H3K27me3. Following morphine removal, enhanced promoter H3K27me3 levels revert to normal sooner than global H3K27me3 or PRC2 component transcript levels. We suggest that H3K27me3 is involved in initiating morphine-induced changes in gene expression, but not in their maintenance. Graphic abstract Model of Polycomb repressive complex 2 (PRC2) and H3K27me3 alterations induced by chronic morphine exposure. Morphine induces H3K27me3 enrichment at promoters of genes encoding core members of the PRC2 complex and is associated with their transcriptional downregulation.![]()
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Affiliation(s)
- Iraia Muñoa-Hoyos
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,Innovation in Assisted Reproduction Group, Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - John A Halsall
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Manu Araolaza
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain
| | - Carl Ward
- Stem Cell Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Idoia Garcia
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,Biodonostia Health Research Institute, 2009 San Sebastian, Gipuzkoa, Spain
| | - Itziar Urizar-Arenaza
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,Innovation in Assisted Reproduction Group, Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Marta Gianzo
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain
| | - Paloma Garcia
- Stem Cell Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Bryan Turner
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Nerea Subirán
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain. .,Innovation in Assisted Reproduction Group, Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain.
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17
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Oh S, Boo K, Kim J, Baek SA, Jeon Y, You J, Lee H, Choi HJ, Park D, Lee JM, Baek SH. The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes. Nucleic Acids Res 2020; 48:9037-9052. [PMID: 32735658 PMCID: PMC7498345 DOI: 10.1093/nar/gkaa626] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.
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Affiliation(s)
- Sungryong Oh
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyungjin Boo
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jaebeom Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seon Ah Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Jeon
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Junghyun You
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, South Korea
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
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18
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Garland W, Comet I, Wu M, Radzisheuskaya A, Rib L, Vitting-Seerup K, Lloret-Llinares M, Sandelin A, Helin K, Jensen TH. A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2. Cell Rep 2020; 29:1800-1811.e6. [PMID: 31722198 PMCID: PMC6856724 DOI: 10.1016/j.celrep.2019.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/28/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) constitute an essential cellular niche sustained by epigenomic and transcriptional regulation. Any role of post-transcriptional processes remains less explored. Here, we identify a link between nuclear RNA levels, regulated by the poly(A) RNA exosome targeting (PAXT) connection, and transcriptional control by the polycomb repressive complex 2 (PRC2). Knockout of the PAXT component ZFC3H1 impairs mouse ESC differentiation. In addition to the upregulation of bona fide PAXT substrates, Zfc3h1−/− cells abnormally express developmental genes usually repressed by PRC2. Such de-repression is paralleled by decreased PRC2 binding to chromatin and low PRC2-directed H3K27 methylation. PRC2 complex stability is compromised in Zfc3h1−/− cells with elevated levels of unspecific RNA bound to PRC2 components. We propose that excess RNA hampers PRC2 function through its sequestration from DNA. Our results highlight the importance of balancing nuclear RNA levels and demonstrate the capacity of bulk RNA to regulate chromatin-associated proteins. Depletion of ZFC3H1 in mouse ESCs results in differentiation defects PRC2 target genes are deregulated in Zfc3h1−/− cells Chromatin binding of PRC2 and H3K27me3 is reduced in Zfc3h1−/− cells Increased binding of RNA impairs PRC2 complex stability
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Itys Comet
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Aliaksandra Radzisheuskaya
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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19
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Li W, Karwacki-Neisius V, Ma C, Tan L, Shi Y, Wu F, Shi YG. Nono deficiency compromises TET1 chromatin association and impedes neuronal differentiation of mouse embryonic stem cells. Nucleic Acids Res 2020; 48:4827-4838. [PMID: 32286661 PMCID: PMC7229820 DOI: 10.1093/nar/gkaa213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 03/19/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
NONO is a DNA/RNA-binding protein, which plays a critical regulatory role during cell stage transitions of mouse embryonic stem cells (mESCs). However, its function in neuronal lineage commitment and the molecular mechanisms of its action in such processes are largely unknown. Here we report that NONO plays a key role during neuronal differentiation of mESCs. Nono deletion impedes neuronal lineage commitment largely due to a failure of up-regulation of specific genes critical for neuronal differentiation. Many of the NONO regulated genes are also DNA demethylase TET1 targeted genes. Importantly, re-introducing wild type NONO to the Nono KO cells, not only restores the normal expression of the majority of NONO/TET1 coregulated genes but also rescues the defective neuronal differentiation of Nono-deficient mESCs. Mechanistically, our data shows that NONO directly interacts with TET1 via its DNA binding domain and recruits TET1 to genomic loci to regulate 5-hydroxymethylcytosine levels. Nono deletion leads to a significant dissociation of TET1 from chromatin and dysregulation of DNA hydroxymethylation of neuronal genes. Taken together, our findings reveal a key role and an epigenetic mechanism of action of NONO in regulation of TET1-targeted neuronal genes, offering new functional and mechanistic understanding of NONO in stem cell functions, lineage commitment and specification.
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Affiliation(s)
- Wenjing Li
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Violetta Karwacki-Neisius
- Division of Newborn Medicine and Program in Epigenetics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Chun Ma
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Li Tan
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yang Shi
- Division of Newborn Medicine and Program in Epigenetics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Feizhen Wu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yujiang Geno Shi
- Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
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20
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Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194609. [PMID: 32730897 DOI: 10.1016/j.bbagrm.2020.194609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
A wealth of biochemical and cellular data, accumulated over several years by multiple groups, has provided a great degree of insight into the molecular mechanisms of actions of GCN5 and PCAF in gene activation. Studies of these lysine acetyltransferases (KATs) in vitro, in cultured cells, have revealed general mechanisms for their recruitment by sequence-specific binding factors and their molecular functions as transcriptional co-activators. Genetic studies indicate that GCN5 and PCAF are involved in multiple developmental processes in vertebrates, yet our understanding of their molecular functions in these contexts remains somewhat rudimentary. Understanding the functions of GCN5/PCAF in developmental processes provides clues to the roles of these KATs in disease states. Here we will review what is currently known about the developmental roles of GCN5 and PCAF, as well as emerging role of these KATs in oncogenesis.
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Affiliation(s)
- Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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21
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Zhu Y, Yan Z, Tang Z, Li W. Novel Approaches to Profile Functional Long Noncoding RNAs Associated with Stem Cell Pluripotency. Curr Genomics 2020; 21:37-45. [PMID: 32655297 PMCID: PMC7324891 DOI: 10.2174/1389202921666200210142840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/17/2020] [Accepted: 01/31/2020] [Indexed: 12/11/2022] Open
Abstract
The pluripotent state of stem cells depends on the complicated network orchestrated by thousands of factors and genes. Long noncoding RNAs (lncRNAs) are a class of RNA longer than 200 nt without a protein-coding function. Single-cell sequencing studies have identified hundreds of lncRNAs with dynamic changes in somatic cell reprogramming. Accumulating evidence suggests that they participate in the initiation of reprogramming, maintenance of pluripotency, and developmental processes by cis and/or trans mechanisms. In particular, they may interact with proteins, RNAs, and chromatin modifier complexes to form an intricate pluripotency-associated network. In this review, we focus on recent progress in approaches to profiling functional lncRNAs in somatic cell reprogramming and cell differentiation.
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Affiliation(s)
- Yanbo Zhu
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Zi Yan
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Ze Tang
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Wei Li
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
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22
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Zhang Y, Chan HL, Garcia-Martinez L, Karl DL, Weich N, Slingerland JM, Verdun RE, Morey L. Estrogen induces dynamic ERα and RING1B recruitment to control gene and enhancer activities in luminal breast cancer. SCIENCE ADVANCES 2020; 6:eaaz7249. [PMID: 32548262 PMCID: PMC7274770 DOI: 10.1126/sciadv.aaz7249] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/02/2020] [Indexed: 05/04/2023]
Abstract
RING1B, a core Polycomb repressive complex 1 subunit, is a histone H2A ubiquitin ligase essential for development. RING1B is overexpressed in patients with luminal breast cancer (BC) and recruited to actively transcribed genes and enhancers co-occupied by the estrogen receptor α (ERα). Whether ERα-induced transcriptional programs are mediated by RING1B is not understood. We show that prolonged estrogen administration induces transcriptional output and chromatin landscape fluctuations. RING1B loss impairs full estrogen-mediated gene expression and chromatin accessibility for key BC transcription factors. These effects were mediated, in part, by RING1B enzymatic activity and nucleosome binding functions. RING1B is recruited in a cyclic manner to ERα, FOXA1, and GRHL2 cobound sites and regulates estrogen-induced enhancers and ERα recruitment. Last, ChIP exo revealed multiple binding events of these factors at single-nucleotide resolution, including RING1B occupancy approximately 10 base pairs around ERα bound sites. We propose RING1B as a key regulator of the dynamic, liganded-ERα transcriptional regulatory circuit in luminal BC.
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Affiliation(s)
- Yusheng Zhang
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ho Lam Chan
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Liliana Garcia-Martinez
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Daniel L. Karl
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Natalia Weich
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joyce M. Slingerland
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Braman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ramiro E. Verdun
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
- Corresponding author.
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23
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Troiano A, Pacelli C, Ruggieri V, Scrima R, Addeo M, Agriesti F, Lucci V, Cavaliere G, Mollica MP, Caterino M, Ruoppolo M, Paladino S, Sarnataro D, Visconte F, Tucci F, Lopriore P, Calabrò V, Capitanio N, Piccoli C, Falco G. ZSCAN4 + mouse embryonic stem cells have an oxidative and flexible metabolic profile. EMBO Rep 2020; 21:e48942. [PMID: 32424995 DOI: 10.15252/embr.201948942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
Cultured mouse embryonic stem cells are a heterogeneous population with diverse differentiation potential. In particular, the subpopulation marked by Zscan4 expression has high stem cell potency and shares with 2 cell stage preimplantation embryos both genetic and epigenetic mechanisms that orchestrate zygotic genome activation. Although embryonic de novo genome activation is known to rely on metabolites, a more extensive metabolic characterization is missing. Here we analyze the Zscan4+ mouse stem cell metabolic phenotype associated with pluripotency maintenance and cell reprogramming. We show that Zscan4+ cells have an oxidative and adaptable metabolism, which, on one hand, fuels a high bioenergetic demand and, on the other hand, provides intermediate metabolites for epigenetic reprogramming. Our findings enhance our understanding of the metastable Zscan4+ stem cell state with potential applications in regenerative medicine.
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Affiliation(s)
- Annaelena Troiano
- Department of Biology, University of Naples Federico II, Naples, Italy.,Istituto di Ricerche Genetiche Gaetano Salvatore Biogem Scarl, Ariano Irpino, Italy
| | - Consiglia Pacelli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Vitalba Ruggieri
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Rosella Scrima
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Martina Addeo
- Department of Biology, University of Naples Federico II, Naples, Italy.,Istituto di Ricerche Genetiche Gaetano Salvatore Biogem Scarl, Ariano Irpino, Italy
| | - Francesca Agriesti
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Valeria Lucci
- Department of Biology, University of Naples Federico II, Naples, Italy.,IEOS-CNR, Institute of Experimental Endocrinology and Oncology "G. Salvatore" - National Research Council, Naples, Italy
| | - Gina Cavaliere
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Francesco Tucci
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Piervito Lopriore
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Viola Calabrò
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Claudia Piccoli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Geppino Falco
- Department of Biology, University of Naples Federico II, Naples, Italy.,Istituto di Ricerche Genetiche Gaetano Salvatore Biogem Scarl, Ariano Irpino, Italy.,IEOS-CNR, Institute of Experimental Endocrinology and Oncology "G. Salvatore" - National Research Council, Naples, Italy
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24
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Asenjo HG, Gallardo A, López-Onieva L, Tejada I, Martorell-Marugán J, Carmona-Sáez P, Landeira D. Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells. SCIENCE ADVANCES 2020; 6:eaay4768. [PMID: 32181346 PMCID: PMC7056320 DOI: 10.1126/sciadv.aay4768] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/11/2019] [Indexed: 05/31/2023]
Abstract
When self-renewing pluripotent cells receive a differentiation signal, ongoing cell duplication needs to be coordinated with entry into a differentiation program. Accordingly, transcriptional activation of lineage specifier genes and cell differentiation is confined to the G1 phase of the cell cycle by unknown mechanisms. We found that Polycomb repressive complex 2 (PRC2) subunits are differentially recruited to lineage specifier gene promoters across cell cycle in mouse embryonic stem cells (mESCs). Jarid2 and the catalytic subunit Ezh2 are markedly accumulated at target promoters during S and G2 phases, while the transcriptionally activating subunits EPOP and EloB are enriched during G1 phase. Fluctuations in the recruitment of PRC2 subunits promote changes in RNA synthesis and RNA polymerase II binding that are compromised in Jarid2 -/- mESCs. Overall, we show that differential recruitment of PRC2 subunits across cell cycle enables the establishment of a chromatin state that facilitates the induction of cell differentiation in G1 phase.
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Affiliation(s)
- Helena G. Asenjo
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Amador Gallardo
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Lourdes López-Onieva
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
| | - Irene Tejada
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Jordi Martorell-Marugán
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Atrys Health S.A., Barcelona, Spain
| | - Pedro Carmona-Sáez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
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25
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Daer R, Hamna F, Barrett CM, Haynes KA. Site-directed targeting of transcriptional activation-associated proteins to repressed chromatin restores CRISPR activity. APL Bioeng 2020; 4:016102. [PMID: 31967103 PMCID: PMC6960031 DOI: 10.1063/1.5127302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
Previously, we used an inducible, transgenic polycomb chromatin system to demonstrate that closed, transcriptionally silenced chromatin reduces Cas9 editing. Here, we investigated strategies to enhance Cas9 editing efficiency by artificially perturbing closed chromatin. We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. We also tested DNA-binding, transiently expressed activation-associated proteins (AAPs) that are known to support an open, transcriptionally active chromatin state. When cells that carried a polycomb-repressed transgene (luciferase) were treated with UNC1999 or the AAP fusion Gal4P65, we observed loss of histone 3 lysine 27 trimethylation (H3K27me3), a silencing-associated chromatin feature, at the transgene. Only Gal4P65 treatment showed full restoration of luciferase expression. Cas9 activity, determined by insertion deletion mutations, was restored in Gal4P65-expressing cells, while no CRISPR enhancement was observed with UNC1999 treatment. CRISPR activity was also restored by other Gal4-AAP fusions that did not activate luciferase expression. Our results demonstrate the use of DNA-binding, activator-associated fusion proteins as an effective method to enhance Cas9 editing within polycomb-repressed chromatin.
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Affiliation(s)
- René Daer
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, USA
| | - Fatima Hamna
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, USA
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26
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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Abstract
The first crucial step in the developmental program occurs during pre-implantation, the time after the oocyte has been fertilized and before the embryo implants in the uterus. This period represents a vulnerable window as the epigenome undergoes dynamic changes in DNA methylation profiles. Alterations in the early embryonic reprogramming wave can impair DNA methylation patterns and induce permanent changes to the developmental program, leading to the onset of adverse health outcomes in offspring. Although there is an increasing body of evidence indicating that harmful exposures during pre-implantation embryo development can trigger lasting epigenetic alterations in offspring, the mechanisms are still not fully understood. Since physiological or pathological changes in DNA methylation can occur as a response to environmental cues, proper environmental milieu plays a critical role in the success of embryonic development. In this review, we depict the mechanisms behind the embryonic epigenetic reprogramming of DNA methylation and highlight how maternal environmental stressors (e.g., alcohol, heat stress, nutrient availability) during pre-implantation and assisted reproductive technology procedures affect development and DNA methylation marks.
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Affiliation(s)
- Mélanie Breton-Larrivée
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada
| | - Elizabeth Elder
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada
| | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada.,Department of Obstetrics & Gynecology, Université de Montréal, Research Center of the CHU Sainte-Justine, Montréal, Canada
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28
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Dhaliwal NK, Abatti LE, Mitchell JA. KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control. Genes Dev 2019; 33:1069-1082. [PMID: 31221664 PMCID: PMC6672055 DOI: 10.1101/gad.324319.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/13/2019] [Indexed: 12/14/2022]
Abstract
Embryonic stem (ES) cells are regulated by a network of transcription factors that maintain the pluripotent state. Differentiation relies on down-regulation of pluripotency transcription factors disrupting this network. While investigating transcriptional regulation of the pluripotency transcription factor Kruppel-like factor 4 (Klf4), we observed that homozygous deletion of distal enhancers caused a 17-fold decrease in Klf4 transcript but surprisingly decreased protein levels by less than twofold, indicating that posttranscriptional control of KLF4 protein overrides transcriptional control. The lack of sensitivity of KLF4 to transcription is due to high protein stability (half-life >24 h). This stability is context-dependent and is disrupted during differentiation, as evidenced by a shift to a half-life of <2 h. KLF4 protein stability is maintained through interaction with other pluripotency transcription factors (NANOG, SOX2, and STAT3) that together facilitate association of KLF4 with RNA polymerase II. In addition, the KLF4 DNA-binding and transactivation domains are required for optimal KLF4 protein stability. Posttranslational modification of KLF4 destabilizes the protein as cells exit the pluripotent state, and mutations that prevent this destabilization also prevent differentiation. These data indicate that the core pluripotency transcription factors are integrated by posttranslational mechanisms to maintain the pluripotent state and identify mutations that increase KLF4 protein stability while maintaining transcription factor function.
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Affiliation(s)
- Navroop K Dhaliwal
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontaria M5S3G5, Canada
| | - Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontaria M5S3G5, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontaria M5S3G5, Canada
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29
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Lu W, Yu J, Shi F, Zhang J, Huang R, Yin S, Songyang Z, Huang J. The long non-coding RNA Snhg3 is essential for mouse embryonic stem cell self-renewal and pluripotency. Stem Cell Res Ther 2019; 10:157. [PMID: 31151411 PMCID: PMC6545032 DOI: 10.1186/s13287-019-1270-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/08/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
Background Small nucleolar RNA host gene 3 (Snhg3) is a long non-coding RNA (lncRNA) that was shown to participate in the tumorigenesis of certain cancers. However, little is known about its role in embryonic stem cells (ESCs). Methods Here, we investigated the role of Snhg3 in mouse ESCs (mESCs) through both loss-of-function (knockdown) and gain-of-function (overexpression) approaches. Alkaline phosphatase staining, secondary colony formation, propidium iodide staining, western blotting, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to access self-renewal capacity, whereas immunofluorescence, qRT-PCR, and embryoid body formation were performed to examine pluripotency. In addition, the effect of Snhg3 on mouse embryonic development was determined based on the morphological changes, blastocyst rate, and altered pluripotency marker (Nanog, Oct4) expression. Moreover, the relationship between Snhg3 and key pluripotency factors was evaluated by chromatin immunoprecipitation qPCR, qRT-PCR, subcellular fractionation, and RNA immunoprecipitation. Finally, RNA pull-down and mass spectrometry were applied to explore the potential interacting proteins of Snhg3 in mESCs. Results We demonstrated that Snhg3 is essential for self-renewal and pluripotency maintenance in mESCs. In addition, Snhg3 knockdown disrupted mouse early embryo development. Mechanistically, Snhg3 formed a positive feedback network with Nanog and Oct4, and 126 Snhg3-interacting proteins were identified in mESCs. Conclusions Snhg3 is essential for mESC self-renewal and pluripotency, as well as mouse early embryo development. Electronic supplementary material The online version of this article (10.1186/s13287-019-1270-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weisi Lu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Jianping Yu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fengtao Shi
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, V5Z 4E8, Canada
| | - Jianing Zhang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rui Huang
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shanshan Yin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhou Songyang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China. .,MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Junjiu Huang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China. .,MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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30
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Chan HL, Morey L. Emerging Roles for Polycomb-Group Proteins in Stem Cells and Cancer. Trends Biochem Sci 2019; 44:688-700. [PMID: 31085088 DOI: 10.1016/j.tibs.2019.04.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 02/07/2023]
Abstract
Polycomb-group (PcG) complexes are multiprotein, evolutionarily conserved epigenetic machineries that regulate stem cell fate decisions and development, and are also implicated in cancer and other maladies. The PcG machinery can be divided into two major complexes: Polycomb repressive complex 1 and 2 (PRC1 and PRC2). Traditionally, PcG complexes have been associated with maintenance of gene repression mainly via histone-modifying activities. However, during the last years, increasing evidence indicates that the PcG complexes can also positively regulate gene transcription and modify non-histone substrates in multiple biological processes, cellular stages, and cancers. In this review, we will illustrate recent findings in PcG-mediated gene regulation, with special focus on the recently described non-classical functions of PcG complexes in stem cells and cancer.
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Affiliation(s)
- Ho Lam Chan
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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31
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Allen SR, Wright A. Stem cell therapy for knee osteoarthritis: a narrative review of a rapidly evolving treatment with implications for physical therapy management. PHYSICAL THERAPY REVIEWS 2019. [DOI: 10.1080/10833196.2019.1585674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sophie Ruth Allen
- School of Physiotherapy and Exercise Science, Curtin University, Perth, Western Australia, Australia
| | - Anthony Wright
- School of Physiotherapy and Exercise Science, Curtin University, Perth, Western Australia, Australia
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32
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Loubiere V, Martinez AM, Cavalli G. Cell Fate and Developmental Regulation Dynamics by Polycomb Proteins and 3D Genome Architecture. Bioessays 2019; 41:e1800222. [PMID: 30793782 DOI: 10.1002/bies.201800222] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/22/2018] [Indexed: 12/14/2022]
Abstract
Targeted transitions in chromatin states at thousands of genes are essential drivers of eukaryotic development. Therefore, understanding the in vivo dynamics of epigenetic regulators is crucial for deciphering the mechanisms underpinning cell fate decisions. This review illustrates how, in addition to its cell memory function, the Polycomb group of transcriptional regulators orchestrates temporal, cell and tissue-specific expression of master genes during development. These highly sophisticated developmental transitions are dependent on the context- and tissue-specific assembly of the different types of Polycomb Group (PcG) complexes, which regulates their targeting and/or activities on chromatin. Here, an overview is provided of how PcG complexes function at multiple scales to regulate transcription, local chromatin environment, and higher order structures that support normal differentiation and are perturbed in tumorigenesis.
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Affiliation(s)
- Vincent Loubiere
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
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33
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Yu M, Wei Y, Xu K, Liu S, Ma L, Pei Y, Hu Y, Liu Z, Zhang X, Wang B, Mu Y, Li K. EGFR deficiency leads to impaired self-renewal and pluripotency of mouse embryonic stem cells. PeerJ 2019; 7:e6314. [PMID: 30713819 PMCID: PMC6357870 DOI: 10.7717/peerj.6314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022] Open
Abstract
Background Self-renewal and pluripotency are considered as unwavering features of embryonic stem cells (ESCs). How ESCs regulate the self-renewal and differentiation is a central question in development and regenerative medicine research. Epidermal growth factor receptor (EGFR) was identified as a critical regulator in embryonic development, but its role in the maintenance of ESCs is poorly understood. Methods Here, EGFR was disrupted by its specific inhibitor AG1478 in mouse ESCs (mESCs), and its self-renewal and pluripotency were characterized according to their proliferation, expression of pluripotency markers, embryoid body (EB) formation, and mRNA expression patterns. We also used another EGFR inhibitor (gefitinib) and RNA interference assay to rule out the possibility of non-specific effects of AG1478. Results EGFR inhibition by AG1478 treatment in mESCs markedly reduced cell proliferation, caused cell cycle arrest at G0/G1 phase, and altered protein expressions of the cell cycle regulatory genes (CDK2 (decreased 11.3%) and proliferating cell nuclear antigen (decreased 25.2%)). The immunoreactivities and protein expression of pluripotency factors (OCT4 (decreased 26.9%)) also dramatically decreased, while the differentiation related genes (GATA4 (increased 1.6-fold)) were up-regulated in mESCs after EGFR inhibition. Meanwhile, EGFR inhibition in mESCs disrupted EB formation, indicating its impaired pluripotency. Additionally, the effects observed by EGFR inhibition with another inhibitor gefitinib and siRNA were consistent with those observed by AG1478 treatment in mESCs. These effects were manifested in the decreased expression of proliferative and pluripotency-related genes and the increased expression of genes involved in differentiation. Moreover, RNA-seq analysis displayed that transcript profiling was changed significantly after EGFR inhibition by AG1478. A large number of differentially expressed genes were involved in cell cycle, apoptotic process, epigenetic modification, and metabolic process, which were related to self-renewal and pluripotency, confirming that EGFR deficiency impaired self-renewal and pluripotency in mESCs. Conclusions Taken together, our results demonstrated the importance of EGFR in guarding the stemness of mESCs.
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Affiliation(s)
- Miaoying Yu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Science, Shangrao Normal University, Shangrao, Jiangxi, China
| | - Yinghui Wei
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shasha Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Yangli Pei
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanqing Hu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiguo Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingyuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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34
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van Nocker S. Hybrids without hybridization-can it revolutionize horticulture? HORTICULTURE RESEARCH 2018; 5:76. [PMID: 30588321 PMCID: PMC6303291 DOI: 10.1038/s41438-018-0113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
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35
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The Impact of Epigenetic Signatures on Amniotic Fluid Stem Cell Fate. Stem Cells Int 2018; 2018:4274518. [PMID: 30627172 PMCID: PMC6304862 DOI: 10.1155/2018/4274518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications play a significant role in determining the fate of stem cells and in directing the differentiation into multiple lineages. Current evidence indicates that mechanisms involved in chromatin regulation are essential for maintaining stable cell identities. There is a tight correlation among DNA methylation, histone modifications, and small noncoding RNAs during the epigenetic control of stem cells' differentiation; however, to date, the precise mechanism is still not clear. In this context, amniotic fluid stem cells (AFSCs) represent an interesting model due to their unique features and the possible advantages of their use in regenerative medicine. Recent studies have elucidated epigenetic profiles involved in AFSCs' lineage commitment and differentiation. In order to use these cells effectively for therapeutic purposes, it is necessary to understand the basis of multiple-lineage potential and elaborate in detail how cell fate decisions are made and memorized. The present review summarizes the most recent findings on epigenetic mechanisms of AFSCs with a focus on DNA methylation, histone modifications, and microRNAs (miRNAs) and addresses how their unique signatures contribute to lineage-specific differentiation.
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36
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Boroviak T, Stirparo GG, Dietmann S, Hernando-Herraez I, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P. Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development. Development 2018; 145:145/21/dev167833. [PMID: 30413530 PMCID: PMC6240320 DOI: 10.1242/dev.167833] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022]
Abstract
The mouse embryo is the canonical model for mammalian preimplantation development. Recent advances in single cell profiling allow detailed analysis of embryogenesis in other eutherian species, including human, to distinguish conserved from divergent regulatory programs and signalling pathways in the rodent paradigm. Here, we identify and compare transcriptional features of human, marmoset and mouse embryos by single cell RNA-seq. Zygotic genome activation correlates with the presence of polycomb repressive complexes in all three species, while ribosome biogenesis emerges as a predominant attribute in primate embryos, supporting prolonged translation of maternally deposited RNAs. We find that transposable element expression signatures are species, stage and lineage specific. The pluripotency network in the primate epiblast lacks certain regulators that are operative in mouse, but encompasses WNT components and genes associated with trophoblast specification. Sequential activation of GATA6, SOX17 and GATA4 markers of primitive endoderm identity is conserved in primates. Unexpectedly, OTX2 is also associated with primitive endoderm specification in human and non-human primate blastocysts. Our cross-species analysis demarcates both conserved and primate-specific features of preimplantation development, and underscores the molecular adaptability of early mammalian embryogenesis. Highlighted Article: Analysis of stage-matched, single-cell gene expression data from three mammalian species reveals conserved and primate-specific regulation of early embryogenesis and lineage specification.
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Affiliation(s)
- Thorsten Boroviak
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | - Giuliano G Stirparo
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | | | - Hisham Mohammed
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Erika Sasaki
- Central Institute for Experimental Animals, Department of Applied Developmental Biology, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | - Paul Bertone
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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37
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Promoter bivalency favors an open chromatin architecture in embryonic stem cells. Nat Genet 2018; 50:1452-1462. [PMID: 30224650 DOI: 10.1038/s41588-018-0218-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 08/01/2018] [Indexed: 11/08/2022]
Abstract
In embryonic stem cells (ESCs), developmental gene promoters are characterized by their bivalent chromatin state, with simultaneous modification by MLL2 and Polycomb complexes. Although essential for embryogenesis, bivalency is functionally not well understood. Here, we show that MLL2 plays a central role in ESC genome organization. We generate a catalog of bona fide bivalent genes in ESCs and demonstrate that loss of MLL2 leads to increased Polycomb occupancy. Consequently, promoters lose accessibility, long-range interactions are redistributed, and ESCs fail to differentiate. We pose that bivalency balances accessibility and long-range connectivity of promoters, allowing developmental gene expression to be properly modulated.
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38
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Gunasekara C, Zhang K, Deng W, Brown L, Wei H. TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction. Nucleic Acids Res 2018; 46:e67. [PMID: 29579312 PMCID: PMC6009660 DOI: 10.1093/nar/gky210] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 12/20/2022] Open
Abstract
Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene mutual interaction (TGMI) for identifying these regulators using high-throughput gene expression data. It first calculated the regulatory interactions among triple gene blocks (two pathway genes and one transcription factor (TF)), using conditional mutual information, and then identifies significantly interacted triple genes using a newly identified novel mutual interaction measure (MIM), which was substantiated to reflect strengths of regulatory interactions within each triple gene block. The TGMI calculated the MIM for each triple gene block and then examined its statistical significance using bootstrap. Finally, the frequencies of all TFs present in all significantly interacted triple gene blocks were calculated and ranked. We showed that the TFs with higher frequencies were usually genuine pathway regulators upon evaluating multiple pathways in plants, animals and yeast. Comparison of TGMI with several other algorithms demonstrated its higher accuracy. Therefore, TGMI will be a valuable tool that can help biologists to identify regulators of metabolic pathways and biological processes from the exploded high-throughput gene expression data in public repositories.
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Affiliation(s)
- Chathura Gunasekara
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Program of Computational Science and Engineering, Michigan Technological University, MI 49931, USA
| | - Kui Zhang
- Department of Mathematical Sciences Michigan Technological University, Houghton, MI 49931, USA
| | - Wenping Deng
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Laura Brown
- Department of Computer Science, Michigan Technological University, MI 49931, USA
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Program of Computational Science and Engineering, Michigan Technological University, MI 49931, USA
- Department of Computer Science, Michigan Technological University, MI 49931, USA
- Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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Papatsenko D, Waghray A, Lemischka IR. Feedback control of pluripotency in embryonic stem cells: Signaling, transcription and epigenetics. Stem Cell Res 2018; 29:180-188. [DOI: 10.1016/j.scr.2018.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 02/06/2018] [Accepted: 02/16/2018] [Indexed: 12/19/2022] Open
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40
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Tu J, Tian G, Cheung HH, Wei W, Lee TL. Gas5 is an essential lncRNA regulator for self-renewal and pluripotency of mouse embryonic stem cells and induced pluripotent stem cells. Stem Cell Res Ther 2018; 9:71. [PMID: 29562912 PMCID: PMC5863440 DOI: 10.1186/s13287-018-0813-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The regulatory role of long noncoding RNAs (lncRNAs) have been partially proved in embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). METHODS In the current study, we investigated mouse ESC (mESC) self-renewal, differentiation, and proliferation in vitro by knocking down a lncRNA, growth arrest specific 5 (Gas5). A series of related indicators were examined by cell counting kit-8 (CCK-8) assay, quantitative reverse-transcription polymerase chain reaction (qRT-PCR), Western blot, alkaline phosphatase staining, propidium iodide (PI) staining, Annexin V staining, competition growth assay, immunofluorescence, and chromatin immunoprecipitation (ChIP)-qPCR. An in vivo teratoma formation assay was also performed to validate the in vitro results. qRT-PCR, fluorescence-activated cell sorting (FACS), alkaline phosphatase staining, and immunofluorescence were used to evaluate the role of Gas5 during mouse iPSC reprogramming. The regulatory axis of Dicer-miR291a-cMyc-Gas5 and the relationship between Gas5 and Tet/5hmC in mESCs was examined by qRT-PCR, Dot blot, and Western blot. RESULTS We identified that Gas5 was required for self-renewal and pluripotency of mESCs and iPSCs. Gas5 formed a positive feedback network with a group of key pluripotent modulators (Sox2, Oct4, Nanog, Tcl1, Esrrb, and Tet1) in mESCs. Knockdown of Gas5 promoted endodermal differentiation of mESCs and impaired the efficiency of iPSC reprogramming. In addition, Gas5 was regulated by the Dicer-miR291a-cMyc axis and was involved in the DNA demethylation process in mESCs. CONCLUSIONS Taken together, our results suggest that the lncRNA Gas5 plays an important role in modulating self-renewal and pluripotency of mESCs as well as iPSC reprogramming.
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Affiliation(s)
- Jiajie Tu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Medical University, 81# Meishan Road, Hefei, Anhui China
| | - Geng Tian
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, N.T 622A Hong Kong, Special Administrative Region of China
| | - Hoi-Hung Cheung
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, N.T 622A Hong Kong, Special Administrative Region of China
| | - Wei Wei
- Institute of Clinical Pharmacology, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Medical University, 81# Meishan Road, Hefei, Anhui China
| | - Tin-lap Lee
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, N.T 622A Hong Kong, Special Administrative Region of China
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41
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Marasca F, Bodega B, Orlando V. How Polycomb-Mediated Cell Memory Deals With a Changing Environment. Bioessays 2018. [DOI: 10.1002/bies.201700137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Federica Marasca
- Istituto Nazionale di Genetica Molecolare (INGM) “Romeo and Enrica Invernizzi”; Milan 20122 Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare (INGM) “Romeo and Enrica Invernizzi”; Milan 20122 Italy
| | - Valerio Orlando
- King Abdullah University of Science and Technology (KAUST); Environmental Epigenetics Research Program; Biological and Environmental Sciences and Engineering Division; Thuwal 23955-6900 Saudi Arabia
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43
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Cell Polarity-Dependent Regulation of Cell Allocation and the First Lineage Specification in the Preimplantation Mouse Embryo. Curr Top Dev Biol 2018; 128:11-35. [DOI: 10.1016/bs.ctdb.2017.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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44
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Kasulanati S, Venkatesan V. Understanding pluripotency under folic acid deficiency using embryonic stem cells as an in vitro model. Med Hypotheses 2017; 111:24-26. [PMID: 29406990 DOI: 10.1016/j.mehy.2017.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/06/2017] [Accepted: 12/13/2017] [Indexed: 02/07/2023]
Abstract
Innumerable studies have been carried out by people to trace out those elements, find out the mechanisms that are vital to the maintenance of stemness. Amongst them, the one which is gaining importance in the recent past is the metabolism of stem cells, especially One carbon metabolism. Being associated directly or indirectly, with DNA and Histone methylation, One carbon metabolism has an important role to play as far as epigenetic regulation of stemness is concerned. Folic acid being a methyl donor, forms an important component of One Carbon metabolism, and thus its availability has a significant effect on the methylation reactions. The present hypothesis says, using embryonic stem cells grown in vitro as a model system, one can study how deficiency of Folate during pre implantation embryonic development influence the self renewal as well as pluripotency of stem cells, from the perspective of One carbon metabolism and epigenetic mechanisms. Findings from such a study can possibly provide an explanation for the observed intra uterine growth retardation seen under maternal micronutrient deficiency.
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Affiliation(s)
- Sowmya Kasulanati
- Biochemistry/Stem Cell Research, National Institute of Nutrition (ICMR), Jamai Osmania P.O, Tarnaka, Hyderabad, Telangana 500007, India
| | - Vijayalakshmi Venkatesan
- Biochemistry/Stem Cell Research, National Institute of Nutrition (ICMR), Jamai Osmania P.O, Tarnaka, Hyderabad, Telangana 500007, India.
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45
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Negrón-Pérez VM, Zhang Y, Hansen PJ. Single-cell gene expression of the bovine blastocyst. Reproduction 2017; 154:627-644. [PMID: 28814615 PMCID: PMC5630521 DOI: 10.1530/rep-17-0345] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/03/2017] [Accepted: 08/16/2017] [Indexed: 12/22/2022]
Abstract
The first two differentiation events in the embryo result in three cell types - epiblast, trophectoderm (TE) and hypoblast. The purpose here was to identify molecular markers for each cell type in the bovine and evaluate the differences in gene expression among individual cells of each lineage. The cDNA from 67 individual cells of dissociated blastocysts was used to determine transcript abundance for 93 genes implicated as cell lineage markers in other species or potentially involved in developmental processes. Clustering analysis indicated that the cells belonged to two major populations (clades A and B) with two subpopulations of clade A and four of clade B. Use of lineage-specific markers from other species indicated that the two subpopulations of clade A represented epiblast and hypoblast respectively while the four subpopulations of clade B were TE. Among the genes upregulated in epiblast were AJAP1, DNMT3A, FGF4, H2AFZ, KDM2B, NANOG, POU5F1, SAV1 and SLIT2 Genes overexpressed in hypoblast included ALPL, FGFR2, FN1, GATA6, GJA1, HDAC1, MBNL3, PDGFRA and SOX17, while genes overexpressed in all four TE populations were ACTA2, CDX2, CYP11A1, GATA2, GATA3, IFNT, KRT8, RAC1 and SFN The subpopulations of TE varied among each other for multiple genes including the prototypical TE marker IFNT. New markers for each cell type in the bovine blastocyst were identified. Results also indicate heterogeneity in gene expression among TE cells. Further studies are needed to confirm whether subpopulations of TE cells represent different stages in the development of a committed TE phenotype.
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Affiliation(s)
- Verónica M. Negrón-Pérez
- Department of Animal Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Yanping Zhang
- Gene Expression and Genotyping Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Peter J. Hansen
- Department of Animal Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville, Florida, USA
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46
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Zhao W, Huang Y, Zhang J, Liu M, Ji H, Wang C, Cao N, Li C, Xia Y, Jiang Q, Qin J. Polycomb group RING finger proteins 3/5 activate transcription via an interaction with the pluripotency factor Tex10 in embryonic stem cells. J Biol Chem 2017; 292:21527-21537. [PMID: 29054931 DOI: 10.1074/jbc.m117.804054] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/11/2017] [Indexed: 11/06/2022] Open
Abstract
Polycomb group (PcG) proteins are epigenetic transcriptional repressors that orchestrate numerous developmental processes and have been implicated in the maintenance of embryonic stem (ES) cell state. More recent evidence suggests that a subset of PcG proteins engages in transcriptional activation in some cellular contexts, but how this property is exerted remains largely unknown. Here, we generated ES cells with single or combined disruption of polycomb group RING finger protein 3 (Pcgf3) and Pcgf5 with the CRISPR-Cas9 technique. We report that although these mutant cells maintained their self-renewal and colony-forming capacity, they displayed severe defects in mesoderm differentiation in vitro and in vivo Using RNA-seq to analyze transcriptional profiles of ES cells with single or combined Pcgf3/5 deficiencies, we found that in contrast to the canonical role of the related polycomb repressive complex 1 (PRC1) in gene repression, Pcgf3/5 mainly function as transcriptional activators driving expression of many genes involved in mesoderm differentiation. Proteomic approaches and promoter occupancy analyses helped to establish an extended Pcgf3/5 interactome and identified several novel Pcgf3/5 interactors. These included testis-expressed 10 (Tex10), which may directly contribute to transcriptional activation via the transcriptional co-activator p300. Furthermore, Pcgf3/5 deletion in ES cells substantially reduced the occupancy of Tex10 and p300 at target genes. Finally, we demonstrated that Pcgf3/5 are essential for regulating global levels of the histone modifier H2AK119ub1 in ES cells. Our findings establish Pcgf3/5 as transcriptional activators that interact with Tex10 and p300 in ES cells and point to redundant activity of Pcgf3/5 in pluripotency maintenance.
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Affiliation(s)
- Wukui Zhao
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Yikai Huang
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Jingzi Zhang
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Mengjie Liu
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Haijing Ji
- the College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210014
| | - Congcong Wang
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Ning Cao
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Chaojun Li
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061
| | - Yin Xia
- the School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, and
| | - Qing Jiang
- the Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing 21008, China
| | - Jinzhong Qin
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, 12 Xuefu Road, Nanjing, Jiangsu 210061,
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Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? SCIENCE ADVANCES 2017; 3:eaao2110. [PMID: 28959731 PMCID: PMC5617379 DOI: 10.1126/sciadv.aao2110] [Citation(s) in RCA: 466] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/12/2017] [Indexed: 05/11/2023]
Abstract
It has recently become apparent that RNA, itself the product of transcription, is a major regulator of the transcriptional process. In particular, long noncoding RNAs (lncRNAs), which are so numerous in eukaryotes, function in many cases as transcriptional regulators. These RNAs function through binding to histone-modifying complexes, to DNA binding proteins (including transcription factors), and even to RNA polymerase II. In other cases, it is the act of lncRNA transcription rather than the lncRNA product that appears to be regulatory. We review recent progress in elucidating the molecular mechanisms by which lncRNAs modulate gene expression and future opportunities in this research field.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Xueyin Wang
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Daniel T. Youmans
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Thomas R. Cech
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Corresponding author.
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Downregulation of PARP1 transcription by promoter-associated E2F4-RBL2-HDAC1-BRM complex contributes to repression of pluripotency stem cell factors in human monocytes. Sci Rep 2017; 7:9483. [PMID: 28842672 PMCID: PMC5572705 DOI: 10.1038/s41598-017-10307-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/27/2017] [Indexed: 01/10/2023] Open
Abstract
Differentiation of certain cell types is followed by a downregulation of PARP1 expression. We show that the reduction in the abundance of PARP1 in hematopoietic progenitor cells and monocytes is tightly controlled by the cell cycle. The differentiation-associated cell cycle exit induces E2F1 replacement with E2F4 at the PARP1 promoter and the assembly of an E2F4-RBL2-HDAC1-BRM(SWI/SNF) repressor complex which deacetylates nucleosomes and compacts chromatin. In G1 arrested cells, PARP1 transcription is reduced by the recruitment of E2F1-RB1-HDAC1-EZH2(PRC2)-BRM/BRG1(SWI/SNF), which additionally trimethylates H3K27 and causes an even higher increase in nucleosome density. The re-establishment of an active chromatin structure by treating post-mitotic monocytes with the HDAC inhibitor and G1 arrested cells with a combination of HDAC and EZH2 inhibitors restores PARP1 expression completely but does not affect the interaction between the components of the repressor complex with chromatin. This suggests that RB1 and RBL2, as well as PRC2, SWI/SNF and HDAC1, do not interfere with the transcription machinery. Interestingly, reinstatement of PARP1 expression by the silencing of RBL2 or by the inhibition of HDACs in monocytes and by transfection with the PARP1 expression vector in differentiated THP-1 cells substantially increased transcription of pluripotency stem cell factors such as POU5F1, SOX2 and NANOG.
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Shen Z, Kang J, Shakya A, Tabaka M, Jarboe EA, Regev A, Tantin D. Enforcement of developmental lineage specificity by transcription factor Oct1. eLife 2017; 6:20937. [PMID: 28537559 PMCID: PMC5466424 DOI: 10.7554/elife.20937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/23/2017] [Indexed: 12/26/2022] Open
Abstract
Embryonic stem cells co-express Oct4 and Oct1, a related protein with similar DNA-binding specificity. To study the role of Oct1 in ESC pluripotency and transcriptional control, we constructed germline and inducible-conditional Oct1-deficient ESC lines. ESCs lacking Oct1 show normal appearance, self-renewal and growth but manifest defects upon differentiation. They fail to form beating cardiomyocytes, generate neurons poorly, form small, poorly differentiated teratomas, and cannot generate chimeric mice. Upon RA-mediated differentiation, Oct1-deficient cells induce lineage-appropriate developmentally poised genes poorly while lineage-inappropriate genes, including extra-embryonic genes, are aberrantly expressed. In ESCs, Oct1 co-occupies a specific set of targets with Oct4, but does not occupy differentially expressed developmental targets. Instead, Oct1 occupies these targets as cells differentiate and Oct4 declines. These results identify a dynamic interplay between Oct1 and Oct4, in particular during the critical window immediately after loss of pluripotency when cells make the earliest developmental fate decisions. DOI:http://dx.doi.org/10.7554/eLife.20937.001 Humans and most other animals are composed of hundreds of different types of cell, including nerve cells, muscle cells and blood cells. Despite performing many different roles, these cells all develop from a single fertilized egg, which divides to make a particular group of cells that when studied in the laboratory are called embryonic stem cells (or ESCs for short). The ability of a cell to become a different cell type is defined as “potency”. ESCs are unique because they can specialize into any type of cell present in the adult organism, and they are therefore called “pluripotent”. However, as the embryo develops, its ESCs gradually lose their potency, and become more and more specialized. The activity of a great number of genes must be regulated during the transition from pluripotent to specialized cells, and some of the mechanisms involved in this transition are still unclear. ESCs are known to need a gene-regulating protein called Oct4 to remain pluripotent and Shen, Kang, Shakya et al. now show that a similar protein named Oct1 is essential for their transition to becoming more specialized. When the gene for Oct1 was deleted from mouse ECSs, they behaved largely like “normal” ESCs, but could not properly mature into certain cell types such as heart and nerve cells. Molecular analyses revealed that Oct4 and Oct1 compete to regulate the activity of many common genes with opposing outcomes: Oct4 keeps ESCs pluripotent while Oct1 leads them to specialize. The Oct4 protein is abundant in ESCs and prevails over Oct1, but as the cells mature, the levels of Oct4 drop, and Oct1 takes over in the regulation of their common target genes. Going forward, a better understanding of how ESCs become specialized will help basic research in the laboratory and allow scientists to tackle new questions about how the human body develops and how our organs work. In the longer-term, these findings might also have applications in the field of regenerative medicine, which aims to repair or replace a person’s cells, tissues or organs to improve their health. DOI:http://dx.doi.org/10.7554/eLife.20937.002
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Jinsuk Kang
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Arvind Shakya
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Marcin Tabaka
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Elke A Jarboe
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
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50
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Zhao H, Han Z, Liu X, Gu J, Tang F, Wei G, Jin Y. The chromatin remodeler Chd4 maintains embryonic stem cell identity by controlling pluripotency- and differentiation-associated genes. J Biol Chem 2017; 292:8507-8519. [PMID: 28298436 DOI: 10.1074/jbc.m116.770248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/13/2017] [Indexed: 12/23/2022] Open
Abstract
The unique properties of embryonic stem cells (ESCs), including unlimited self-renewal and pluripotent differentiation potential, are sustained by integrated genetic and epigenetic networks composed of transcriptional factors and epigenetic modulators. However, the molecular mechanisms underlying the function of these regulators are not fully elucidated. Chromodomain helicase DNA-binding protein 4 (Chd4), an ATPase subunit of the nucleosome remodeling and deacetylase (NuRD) complex, is highly expressed in ESCs. However, its function in ESC regulation remains elusive. Here we report that Chd4 is required for the maintenance of ESC self-renewal. RNAi-mediated silencing of Chd4 disrupted self-renewal and up-regulated lineage commitment-associated genes under self-renewal culture conditions. During ESC differentiation in embryoid body formation, we observed significantly stronger induction of differentiation-associated genes in Chd4-deficient cells. The phenotype was different from that caused by the deletion of Mbd3, another subunit of the NuRD complex. Transcriptomic analyses revealed that Chd4 secured ESC identity by controlling the expression of subsets of pluripotency- and differentiation-associated genes. Importantly, Chd4 repressed the transcription of T box protein 3 (Tbx3), a transcription factor with important functions in ESC fate determination. Tbx3 knockdown partially rescued aberrant activation of differentiation-associated genes, especially of endoderm-associated genes, induced by Chd4 depletion. Moreover, we identified an interaction of Chd4 with the histone variant H2A.Z. This variant stabilized Chd4 by inhibiting Chd4 protein degradation through the ubiquitin-proteasome pathway. Collectively, this study identifies the Chd4-Tbx3 axis in controlling ESC fate and a role of H2A.Z in maintaining the stability of Chd4 proteins.
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Affiliation(s)
- Haixin Zhao
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China; University of the Chinese Academy of Sciences
| | - Zhijun Han
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyuan Liu
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China
| | - Junjie Gu
- Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Fan Tang
- Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying Jin
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China; Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China.
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