1
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Glancy E, Choy N, Eckersley-Maslin MA. Bivalent chromatin: a developmental balancing act tipped in cancer. Biochem Soc Trans 2024; 52:217-229. [PMID: 38385532 PMCID: PMC10903468 DOI: 10.1042/bst20230426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Bivalent chromatin is defined by the co-occurrence of otherwise opposing H3K4me3 and H3K27me3 modifications and is typically located at unmethylated promoters of lowly transcribed genes. In embryonic stem cells, bivalent chromatin has been proposed to poise developmental genes for future activation, silencing or stable repression upon lineage commitment. Normally, bivalent chromatin is kept in tight balance in cells, in part through the activity of the MLL/COMPASS-like and Polycomb repressive complexes that deposit the H3K4me3 and H3K27me3 modifications, respectively, but also emerging novel regulators including DPPA2/4, QSER1, BEND3, TET1 and METTL14. In cancers, both the deregulation of existing domains and the creation of de novo bivalent states is associated with either the activation or silencing of transcriptional programmes. This may facilitate diverse aspects of cancer pathology including epithelial-to-mesenchymal plasticity, chemoresistance and immune evasion. Here, we review current methods for detecting bivalent chromatin and discuss the factors involved in the formation and fine-tuning of bivalent domains. Finally, we examine how the deregulation of chromatin bivalency in the context of cancer could facilitate and/or reflect cancer cell adaptation. We propose a model in which bivalent chromatin represents a dynamic balance between otherwise opposing states, where the underlying DNA sequence is primed for the future activation or repression. Shifting this balance in any direction disrupts the tight equilibrium and tips cells into an altered epigenetic and phenotypic space, facilitating both developmental and cancer processes.
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Affiliation(s)
- Eleanor Glancy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Natalie Choy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melanie A. Eckersley-Maslin
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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2
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Wang Z, Wen S, Zhong M, Yang Z, Xiong W, Zhang K, Yang S, Li H, Guo S. Epigenetics: Novel crucial approach for osteogenesis of mesenchymal stem cells. J Tissue Eng 2023; 14:20417314231175364. [PMID: 37342486 PMCID: PMC10278427 DOI: 10.1177/20417314231175364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/26/2023] [Indexed: 06/23/2023] Open
Abstract
Bone has a robust regenerative potential, but its capacity to repair critical-sized bone defects is limited. In recent years, stem cells have attracted significant interest for their potential in tissue engineering. Applying mesenchymal stem cells (MSCs) for enhancing bone regeneration is a promising therapeutic strategy. However, maintaining optimal cell efficacy or viability of MSCs is limited by several factors. Epigenetic modification can cause changes in gene expression levels without changing its sequence, mainly including nucleic acids methylation, histone modification, and non-coding RNAs. This modification is believed to be one of the determinants of MSCs fate and differentiation. Understanding the epigenetic modification of MSCs can improve the activity and function of stem cells. This review summarizes recent advances in the epigenetic mechanisms of MSCs differentiation into osteoblast lineages. We expound that epigenetic modification of MSCs can be harnessed to treat bone defects and promote bone regeneration, providing potential therapeutic targets for bone-related diseases.
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Affiliation(s)
- Zhaohua Wang
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Si Wen
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Meiqi Zhong
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Ziming Yang
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Wei Xiong
- Department of Plastic Surgery, The First Hospital of Shihezi University School of Medicine, Shihezi, China
| | - Kuo Zhang
- College of Humanities and Social Sciences, Dalian Medical University, Dalian, Liaoning Province, China
| | - Shude Yang
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Huizheng Li
- Department of Otorhinolaryngology & Head and Neck Surgery, Dalian Friendship Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Shu Guo
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
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3
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Hirata M, Ichiyanagi T, Katoh H, Hashimoto T, Suzuki H, Nitta H, Kawase M, Nakai R, Imamura M, Ichiyanagi K. Sequence divergence and retrotransposon insertion underlie interspecific epigenetic differences in primates. Mol Biol Evol 2022; 39:msac208. [PMID: 36219870 PMCID: PMC9577543 DOI: 10.1093/molbev/msac208] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/27/2022] [Accepted: 09/21/2022] [Indexed: 11/14/2022] Open
Abstract
Changes in the epigenome can affect the phenotype without the presence of changes in the genomic sequence. Given the high identity of the human and chimpanzee genome sequences, a substantial portion of their phenotypic divergence likely arises from epigenomic differences between the two species. In this study, the transcriptome and epigenome were determined for induced pluripotent stem cells (iPSCs) generated from human and chimpanzee individuals. The transcriptome and epigenomes for trimethylated histone H3 at lysine-4 (H3K4me3) and lysine-27 (H3K27me3) showed high levels of similarity between the two species. However, there were some differences in histone modifications. Although such regions, in general, did not show significant enrichment of interspecies nucleotide variations, gains in binding motifs for pluripotency-related transcription factors, especially POU5F1 and SOX2, were frequently found in species-specific H3K4me3 regions. We also revealed that species-specific insertions of retrotransposons, including the LTR5_Hs subfamily in human and a newly identified LTR5_Pt subfamily in chimpanzee, created species-specific H3K4me3 regions associated with increased expression of nearby genes. Human iPSCs have more species-specific H3K27me3 regions, resulting in more abundant bivalent domains. Only a limited number of these species-specific H3K4me3 and H3K27me3 regions overlap with species-biased enhancers in cranial neural crest cells, suggesting that differences in the epigenetic state of developmental enhancers appear late in development. Therefore, iPSCs serve as a suitable starting material for studying evolutionary changes in epigenome dynamics during development.
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Affiliation(s)
- Mayu Hirata
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoko Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirokazu Katoh
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takuma Hashimoto
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hikaru Suzuki
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirohisa Nitta
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Risako Nakai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Masanori Imamura
- Molecular Biology Section, Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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4
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Xue J, Fu Y, Fan S, Cao X, Huang W, Zhang J, Zhao Y, Chen F. Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations. Chem Commun (Camb) 2022; 58:10020-10023. [PMID: 35983894 DOI: 10.1039/d2cc03833a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigating the spatial information of post-translational modifications (PTMs) in distinct cell subpopulations represents a new direction toward single-cell analysis. The specific capture of cell populations combined with PTM spatial proximity visualization making it practically challenging. Here, we develop branched immunochip-integrated pairwise barcoding amplification, termed biChip-PBA, which can perform the respective capture of cell subpopulations expressing different membrane proteins and successive PBA-based fluorescence imaging of PTM proximities. Our work may provide multilevel information for new insights into epigenetic regulation and cell function.
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Affiliation(s)
- Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Youlan Fu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Siyue Fan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Wei Huang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
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5
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Ford BR, Vignali PDA, Rittenhouse NL, Scharping NE, Peralta R, Lontos K, Frisch AT, Delgoffe GM, Poholek AC. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells. Sci Immunol 2022; 7:eabj9123. [PMID: 35930654 PMCID: PMC9851604 DOI: 10.1126/sciimmunol.abj9123] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Response rates to immunotherapy in solid tumors remain low due in part to the elevated prevalence of terminally exhausted T cells, a hypofunctional differentiation state induced through persistent antigen and stress signaling. However, the mechanisms promoting progression to terminal exhaustion in the tumor remain undefined. Using the low-input chromatin immunoprecipitation sequencing method CUT&RUN, we profiled the histone modification landscape of tumor-infiltrating CD8+ T cells throughout differentiation. We found that terminally exhausted T cells had unexpected chromatin features that limit their transcriptional potential. Terminally exhausted T cells had a substantial fraction of active chromatin, including active enhancers enriched for bZIP/AP-1 transcription factor motifs that lacked correlated gene expression, which was restored by immunotherapeutic costimulatory signaling. Reduced transcriptional potential was also driven by an increase in histone bivalency, which we linked directly to hypoxia exposure. Enforced expression of the hypoxia-insensitive histone demethylase Kdm6b was sufficient to overcome hypoxia, increase function, and promote antitumor immunity. Our study reveals the specific epigenetic changes mediated by histone modifications during T cell differentiation that support exhaustion in cancer, highlighting that their altered function is driven by improper costimulatory signals and environmental factors. These data suggest that even terminally exhausted T cells may remain competent for transcription in settings of increased costimulatory signaling and reduced hypoxia.
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Affiliation(s)
- B. Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paolo D. A. Vignali
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Natalie L. Rittenhouse
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicole E. Scharping
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ronal Peralta
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Konstantinos Lontos
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Andrew T. Frisch
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Greg M. Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
| | - Amanda C. Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
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6
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Hattori N, Asada K, Miyajima N, Mori A, Nakanishi Y, Kimura K, Wakabayashi M, Takeshima H, Nitani C, Hara J, Ushijima T. Combination of a synthetic retinoid and a DNA demethylating agent induced differentiation of neuroblastoma through retinoic acid signal reprogramming. Br J Cancer 2021; 125:1647-1656. [PMID: 34635821 DOI: 10.1038/s41416-021-01571-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/16/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The CpG island methylator phenotype of neuroblastoma (NBL) is strongly associated with poor prognosis and can be targeted by 5-aza-2'-deoxycytidine (5-aza-dC). Differentiation therapy is a standard maintenance therapy for high-risk NBLs. However, the in vivo effect of tamibarotene, a synthetic retinoic acid, and the efficacy of its combination with 5-aza-dC have not been studied. Here, we conducted a preclinical study to assess the in vivo tamibarotene effect and the combination. METHODS Treatment effects were analysed by in vitro cell growth and differentiation state and by in vivo xenograft suppression. Demethylated genes were analysed by DNA methylation microarrays and geneset enrichment. RESULTS Tamibarotene monotherapy induced neural extension and upregulation of differentiation markers of NBL cells in vitro, and tumour regression without severe side effects in vivo. 5-Aza-dC monotherapy suppressed tumour growth both in vitro and in vivo, and induced demethylation of genes related to nervous system development and function. Pre-treatment with 5-aza-dC in vitro enhanced upregulation of differentiation markers and genes involved in retinoic acid signaling. Pre-treatment with 5-aza-dC in vivo significantly suppressed tumour growth and reduced the variation in tumour sizes. CONCLUSIONS Epigenetic drug-based differentiation therapy using 5-aza-dC and TBT is a promising strategy for refractory NBLs.
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Affiliation(s)
- Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
| | - Kiyoshi Asada
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nozomu Miyajima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Mori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Nakanishi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kana Kimura
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Chika Nitani
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka, Japan
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
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7
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Chen F, Bai M, Cao X, Xue J, Zhao Y, Wu N, Wang L, Zhang D, Zhao Y. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications. Nat Commun 2021; 12:1965. [PMID: 33785750 PMCID: PMC8009891 DOI: 10.1038/s41467-021-22284-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3'-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.
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Affiliation(s)
- Feng Chen
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Min Bai
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Xiaowen Cao
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Jing Xue
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Yue Zhao
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Na Wu
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Lei Wang
- grid.233520.50000 0004 1761 4404Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi’an, Shaanxi PR China
| | - Dexin Zhang
- grid.43169.390000 0001 0599 1243Department of Respiratory Medicine, The Second Affiliated Hospital of Medical College, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
| | - Yongxi Zhao
- grid.43169.390000 0001 0599 1243Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi PR China
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8
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Wada KI, Hosokawa K, Ito Y, Maeda M. A Microfluidic Device for Modulation of Organellar Heterogeneity in Live Single Cells. ANAL SCI 2021; 37:499-505. [PMID: 33281140 DOI: 10.2116/analsci.20scp11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The quantitatively controlled organellar transfer between living single cells provides a unique experimental platform to analyze the contribution of organellar heterogeneity on cellular phenotypes. We previously developed a microfluidic device which can perform quantitatively controlled mitochondrial transfer between live single cells by promoting strictured cytoplasmic connections between live single cells, but its application to other organelles is unclear. In this study, we investigated the quantitative properties of peroxisome transfer in our microfluidic device. When cells were fused through a 10 or 4 μm long microtunnel by a Sendai virus envelope-based method, a strictured cytoplasmic connection was achieved with a length corresponding to that of the microtunnel, and a subsequent recovery culture disconnected the fused cells. The peroxisome number being transferred through a 10 μm length of the microtunnel was smaller than that of 4 μm. These data suggest that our microfuidic device can perform a quantitative control of peroxisome transfer.
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Affiliation(s)
- Ken-Ichi Wada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Kazuo Hosokawa
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
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9
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Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2020; 47:11481-11496. [PMID: 31724731 PMCID: PMC7145697 DOI: 10.1093/nar/gkz1038] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/19/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression is precisely controlled in a stage and cell-type-specific manner, largely through the interaction between cis-regulatory elements and their associated trans-acting factors. Where these components aggregate in promoters and enhancers, they are able to cooperate to modulate chromatin structure and support the engagement in long-range 3D superstructures that shape the dynamics of a cell's genomic architecture. Recently, the term 'super-enhancer' has been introduced to describe a hyper-active regulatory domain comprising a complex array of sequence elements that work together to control the key gene networks involved in cell identity. Here, we survey the unique characteristics of super-enhancers compared to other enhancer types and summarize the recent advances in our understanding of their biological role in gene regulation. In particular, we discuss their capacity to attract the formation of phase-separated condensates, and capacity to generate three-dimensional genome structures that precisely activate their target genes. We also propose a multi-stage transition model to explain the evolutionary pressure driving the development of super-enhancers in complex organisms, and highlight the potential for involvement in tumorigenesis. Finally, we discuss more broadly the role of super-enhancers in human health disorders and related potential in therapeutic interventions.
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Affiliation(s)
- Xi Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Division of Theoretical Systems Biology, Germany Cancer Research Center, Heidelberg 69115, Germany.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia; and Hunter Medical Research Institute
| | - Jian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong S.A.R., China
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10
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Maeda M, Takeshima H, Iida N, Hattori N, Yamashita S, Moro H, Yasukawa Y, Nishiyama K, Hashimoto T, Sekine S, Ishii G, Ochiai A, Fukagawa T, Katai H, Sakai Y, Ushijima T. Cancer cell niche factors secreted from cancer-associated fibroblast by loss of H3K27me3. Gut 2020; 69:243-251. [PMID: 31085554 DOI: 10.1136/gutjnl-2018-317645] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/25/2019] [Accepted: 04/21/2019] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Cancer-associated fibroblasts (CAFs), a major component of cancer stroma, can confer aggressive properties to cancer cells by secreting multiple factors. Their phenotypes are stably maintained, but the mechanisms are not fully understood. We aimed to show the critical role of epigenetic changes in CAFs in maintaining their tumour-promoting capacity and to show the validity of the epigenomic approach in identifying therapeutic targets from CAFs to starve cancer cells. DESIGN Twelve pairs of primary gastric CAFs and their corresponding non-CAFs (NCAFs) were established from surgical specimens. Genome-wide DNA methylation and H3K27me3 analyses were conducted by BeadArray 450K and ChIP-on-Chip, respectively. Functions of potential a therapeutic target were analysed by inhibiting it, and prognostic impact was assessed in a database. RESULTS CAFs had diverse and distinct DNA methylation and H3K27me3 patterns compared with NCAFs. Loss of H3K27me3, but not DNA methylation, in CAFs was enriched for genes involved in stem cell niche, cell growth, tissue development and stromal-epithelial interactions, such as WNT5A, GREM1, NOG and IGF2. Among these, we revealed that WNT5A, which had been considered to be derived from cancer cells, was highly expressed in cancer stromal fibroblasts, and was associated with poor prognosis. Inhibition of secreted WNT5A from CAFs suppressed cancer cell growth and migration. CONCLUSIONS H3K27me3 plays a crucial role in defining tumour-promoting capacities of CAFs, and multiple stem cell niche factors were secreted from CAFs due to loss of H3K27me3. The validity of the epigenetic approach to uncover therapeutic targets for cancer-starving therapy was demonstrated.
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Affiliation(s)
- Masahiro Maeda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastrointestinal Surgery, Faculty of Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroshi Moro
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshimi Yasukawa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhiro Nishiyama
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Taiki Hashimoto
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Shigeki Sekine
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Genichiro Ishii
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, Chiba, Japan
| | - Atsushi Ochiai
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Takeo Fukagawa
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiharu Sakai
- Department of Gastrointestinal Surgery, Faculty of Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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11
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Pradhan R, Ranade D, Sengupta K. Emerin modulates spatial organization of chromosome territories in cells on softer matrices. Nucleic Acids Res 2018; 46:5561-5586. [PMID: 29684168 PMCID: PMC6009696 DOI: 10.1093/nar/gky288] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1. Furthermore, 3-Dimensional fluorescence in situ hybridization (3D-FISH) analyses showed a significant mislocalization of Chromosome 1 and 19 Territories (CT) into the nuclear interior, consistent with their transcriptional deregulation. However, CT18 with relatively lower transcriptional dysregulation, also mislocalized into the nuclear interior. Furthermore, nuclear Lamins that regulate chromosome positioning, were mislocalized into the nuclear interior in response to lowered matrix stiffness. Notably, Lamin B2 overexpression retained CT18 near the nuclear periphery in cells on softer matrices. While, cells on softer matrices also activated emerin phosphorylation at a novel Tyr99 residue, the inhibition of which in a phospho-deficient mutant (emerinY99F), selectively retained chromosome 18 and 19 but not chromosome 1 territories at their conserved nuclear locations. Taken together, emerin functions as a key mechanosensor, that modulates the spatial organization of chromosome territories in the interphase nucleus.
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Affiliation(s)
- Roopali Pradhan
- Biology, Main Building, First Floor, Room#B-216, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Devika Ranade
- Biology, Main Building, First Floor, Room#B-216, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Kundan Sengupta
- Biology, Main Building, First Floor, Room#B-216, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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12
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Tekel SJ, Barrett C, Vargas D, Haynes KA. Design, Construction, and Validation of Histone-Binding Effectors in Vitro and in Cells. Biochemistry 2018; 57:4707-4716. [PMID: 29791133 DOI: 10.1021/acs.biochem.8b00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromatin is a system of nuclear proteins and nucleic acids that plays a pivotal role in gene expression and cell behavior and is therefore the subject of intense study for cell development and cancer research. Biochemistry, crystallography, and reverse genetics have elucidated the macromolecular interactions that drive chromatin regulation. One of the central mechanisms is the recognition of post-translational modifications (PTMs) on histone proteins by a family of nuclear proteins known as "readers". This knowledge has launched a wave of activity around the rational design of proteins that interact with histone PTMs. Useful molecular tools have emerged from this work, enabling researchers to probe and manipulate chromatin states in live cells. Chromatin-based proteins represent a vast design space that remains underexplored. Therefore, we have developed a rapid prototyping platform to identify engineered fusion proteins that bind histone PTMs in vitro and regulate genes near the same histone PTMs in living cells. We have used our system to build gene activators with strong avidity for the gene silencing-associated histone PTM H3K27me3. Here, we describe procedures and data for cell-free production of fluorescently tagged fusion proteins, enzyme-linked immunosorbent assay-based measurement of histone PTM binding, and a live cell assay to demonstrate that the fusion proteins modulate transcriptional activation at a site that carries the target histone PTM. This pipeline will be useful for synthetic biologists who are interested in designing novel histone PTM-binding actuators and probes.
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Affiliation(s)
- Stefan J Tekel
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Cassandra Barrett
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Daniel Vargas
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
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13
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Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells. Cell Chem Biol 2018; 25:51-56.e6. [DOI: 10.1016/j.chembiol.2017.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/18/2017] [Accepted: 10/18/2017] [Indexed: 02/08/2023]
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14
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Xu Q, Xie W. Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment. Trends Cell Biol 2017; 28:237-253. [PMID: 29217127 DOI: 10.1016/j.tcb.2017.10.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023]
Abstract
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development. The latest studies, including many from genome-wide perspectives, have revealed unusual principles of reprogramming for histone modifications, chromatin accessibility, and 3D chromatin architecture. These advances have shed light on the regulatory network controlling the earliest development and maternal-zygotic transition.
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Affiliation(s)
- Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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15
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Semba Y, Harada A, Maehara K, Oki S, Meno C, Ueda J, Yamagata K, Suzuki A, Onimaru M, Nogami J, Okada S, Akashi K, Ohkawa Y. Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells. Nucleic Acids Res 2017; 45:8758-8772. [PMID: 28549158 PMCID: PMC5587750 DOI: 10.1093/nar/gkx475] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/15/2017] [Indexed: 12/21/2022] Open
Abstract
Chromatin reorganization is necessary for pluripotent stem cells, including embryonic stem cells (ESCs), to acquire lineage potential. However, it remains unclear how ESCs maintain their characteristic chromatin state for appropriate gene expression upon differentiation. Here, we demonstrate that chromodomain helicase DNA-binding domain 2 (Chd2) is required to maintain the differentiation potential of mouse ESCs. Chd2-depleted ESCs showed suppressed expression of developmentally regulated genes upon differentiation and subsequent differentiation defects without affecting gene expression in the undifferentiated state. Furthermore, chromatin immunoprecipitation followed by sequencing revealed alterations in the nucleosome occupancy of the histone variant H3.3 for developmentally regulated genes in Chd2-depleted ESCs, which in turn led to elevated trimethylation of the histone H3 lysine 27. These results suggest that Chd2 is essential in preventing suppressive chromatin formation for developmentally regulated genes and determines subsequent effects on developmental processes in the undifferentiated state.
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Affiliation(s)
- Yuichiro Semba
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Jun Ueda
- Center of Education in Laboratory Animal Research, Chubu University, Aichi 487-8501, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, KINDAI University, Wakayama 649-6493, Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mitsuho Onimaru
- Pathophysiological and Experimental Pathology, Department of Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Seiji Okada
- Department of Advanced Medical Initiatives, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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16
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Targeting of super-enhancers and mutant BRAF can suppress growth of BRAF -mutant colon cancer cells via repression of MAPK signaling pathway. Cancer Lett 2017; 402:100-109. [DOI: 10.1016/j.canlet.2017.05.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 11/24/2022]
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17
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de Castro IJ, Budzak J, Di Giacinto ML, Ligammari L, Gokhan E, Spanos C, Moralli D, Richardson C, de las Heras JI, Salatino S, Schirmer EC, Ullman KS, Bickmore WA, Green C, Rappsilber J, Lamble S, Goldberg MW, Vinciotti V, Vagnarelli P. Repo-Man/PP1 regulates heterochromatin formation in interphase. Nat Commun 2017; 8:14048. [PMID: 28091603 PMCID: PMC5241828 DOI: 10.1038/ncomms14048] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022] Open
Abstract
Repo-Man is a protein phosphatase 1 (PP1) targeting subunit that regulates mitotic progression and chromatin remodelling. After mitosis, Repo-Man/PP1 remains associated with chromatin but its function in interphase is not known. Here we show that Repo-Man, via Nup153, is enriched on condensed chromatin at the nuclear periphery and at the edge of the nucleopore basket. Repo-Man/PP1 regulates the formation of heterochromatin, dephosphorylates H3S28 and it is necessary and sufficient for heterochromatin protein 1 binding and H3K27me3 recruitment. Using a novel proteogenomic approach, we show that Repo-Man is enriched at subtelomeric regions together with H2AZ and H3.3 and that depletion of Repo-Man alters the peripheral localization of a subset of these regions and alleviates repression of some polycomb telomeric genes. This study shows a role for a mitotic phosphatase in the regulation of the epigenetic landscape and gene expression in interphase.
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Affiliation(s)
- Inês J. de Castro
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - James Budzak
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Maria L. Di Giacinto
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Lorena Ligammari
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Ezgi Gokhan
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
| | - Daniela Moralli
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Silvia Salatino
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Katharine S. Ullman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Catherine Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
- Technische Universitat Berlin, 13355 Berlin, Germany
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Martin W. Goldberg
- School of Biological and Medical Science, Durham University, Durham DH1 3LE, UK
| | - Veronica Vinciotti
- College of Engineering, Design and Technology, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
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18
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Robert VJ, Garvis S, Palladino F. Repression of somatic cell fate in the germline. Cell Mol Life Sci 2015; 72:3599-620. [PMID: 26043973 PMCID: PMC11113910 DOI: 10.1007/s00018-015-1942-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/13/2023]
Abstract
Germ cells must transmit genetic information across generations, and produce gametes while also maintaining the potential to form all cell types after fertilization. Preventing the activation of somatic programs is, therefore, crucial to the maintenance of germ cell identity. Studies in Caenorhabditis elegans, Drosophila melanogaster, and mouse have revealed both similarities and differences in how somatic gene expression is repressed in germ cells, thereby preventing their conversion into somatic tissues. This review will focus on recent developments in our understanding of how global or gene-specific transcriptional repression, chromatin regulation, and translational repression operate in the germline to maintain germ cell identity and repress somatic differentiation programs.
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Affiliation(s)
- Valérie J Robert
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France
| | - Steve Garvis
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France
| | - Francesca Palladino
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France.
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19
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Pin CL, Ryan JF, Mehmood R. Acinar cell reprogramming: a clinically important target in pancreatic disease. Epigenomics 2015; 7:267-81. [PMID: 25942535 DOI: 10.2217/epi.14.83] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Acinar cells of the pancreas produce the majority of enzymes required for digestion and make up >90% of the cells within the pancreas. Due to a common developmental origin and the plastic nature of the acinar cell phenotype, these cells have been identified as a possible source of β cells as a therapeutic option for Type I diabetes. However, recent evidence indicates that acinar cells are the main source of pancreatic intraepithelial neoplasias (PanINs), the predecessor of pancreatic ductal adenocarcinoma (PDAC). The conversion of acinar cells to either β cells or precursors to PDAC is dependent on reprogramming of the cells to a more primitive, progenitor-like phenotype, which involves changes in transcription factor expression and activity, and changes in their epigenetic program. This review will focus on the mechanisms that promote acinar cell reprogramming, as well as the factors that may affect these mechanisms.
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Affiliation(s)
- Christopher L Pin
- Department of Paediatrics, Physiology & Pharmacology, & Oncology, University of Western Ontario, London, ON N6C 2V5, Canada
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20
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Recent advances and current issues in single-cell sequencing of tumors. Cancer Lett 2015; 365:1-10. [PMID: 26003306 DOI: 10.1016/j.canlet.2015.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/19/2015] [Accepted: 04/20/2015] [Indexed: 12/28/2022]
Abstract
Intratumoral heterogeneity is a recently recognized but important feature of cancer that underlies the various biocharacteristics of cancer tissues. The advent of next-generation sequencing technologies has facilitated large scale capture of genomic data, while the recent development of single-cell sequencing has allowed for more in-depth studies into the complex molecular mechanisms of intratumoral heterogeneity. In this review, the recent advances and current challenges in single-cell sequencing methodologies are discussed, highlighting the potential power of these data to provide insights into oncological processes, from tumorigenesis through progression to metastasis and therapy resistance.
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21
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Abstract
Single-cell analysis heralds a new era that allows “omics” analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are regarded as homogeneous. It provides an ultra-sensitive tool to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. It also facilitates the clinical investigation of patients when a very low quantity or a single cell is available for analysis, such as noninvasive prenatal diagnosis and cancer screening, and genetic evaluation for in vitro fertilization. Within a few short years, single-cell analysis, especially whole genomic sequencing and transcriptomic sequencing, is becoming robust and broadly accessible, although not yet a routine practice. Here, with single cell RNA-seq emphasized, an overview of the discipline, progresses, and prospects of single-cell analysis and its applications in biology and medicine are given with a series of logic and theoretical considerations.
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Affiliation(s)
- Xinghua Pan
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
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22
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Puri D, Gala H, Mishra R, Dhawan J. High-wire act: the poised genome and cellular memory. FEBS J 2014; 282:1675-91. [PMID: 25440020 DOI: 10.1111/febs.13165] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/22/2014] [Accepted: 11/27/2014] [Indexed: 12/12/2022]
Abstract
Emerging evidence aided by genome-wide analysis of chromatin and transcriptional states has shed light on the mechanisms by which stem cells achieve cellular memory. The epigenetic and transcriptional plasticity governing stem cell behavior is highlighted by the identification of 'poised' genes, which permit cells to maintain readiness to undertake alternate developmental fates. This review focuses on two crucial mechanisms of gene poising: bivalent chromatin marks and RNA polymerase II stalling. We provide the context for these mechanisms by exploring the current consensus on the regulation of chromatin states, especially in quiescent adult stem cells, where poised genes are critical for recapitulating developmental choices, leading to regenerative function.
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Affiliation(s)
- Deepika Puri
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad, India
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23
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Abstract
Poised (bivalent) chromatin is defined by the simultaneous presence of histone modifications associated with both gene activation and repression. This epigenetic feature was first observed at promoters of lineage-specific regulatory genes in embryonic stem cells in culture. More recent work has shown that, in vivo, mammalian germ cells maintain poised chromatin at promoters of many genes that regulate somatic development, and that they retain this state from fetal stages through meiosis and gametogenesis. We hypothesize that the poised chromatin state is essential for germ cell identity and function. We propose three roles for poised chromatin in the mammalian germ line: prevention of DNA methylation, maintenance of germ cell identity and preparation for totipotency. We discuss these roles in the context of recently proposed models for germline potency and epigenetic inheritance.
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Affiliation(s)
- Bluma J Lesch
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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Hyun BR, McElwee JL, Soloway PD. Single molecule and single cell epigenomics. Methods 2014; 72:41-50. [PMID: 25204781 DOI: 10.1016/j.ymeth.2014.08.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/24/2023] Open
Abstract
Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells.
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Affiliation(s)
- Byung-Ryool Hyun
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - John L McElwee
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Paul D Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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25
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Alvarez-Saavedra M, De Repentigny Y, Lagali PS, Raghu Ram EVS, Yan K, Hashem E, Ivanochko D, Huh MS, Yang D, Mears AJ, Todd MAM, Corcoran CP, Bassett EA, Tokarew NJA, Kokavec J, Majumder R, Ioshikhes I, Wallace VA, Kothary R, Meshorer E, Stopka T, Skoultchi AI, Picketts DJ. Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation. Nat Commun 2014; 5:4181. [PMID: 24946904 PMCID: PMC4083431 DOI: 10.1038/ncomms5181] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/15/2014] [Indexed: 12/28/2022] Open
Abstract
Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain. Here we show that mice conditionally inactivated for Snf2h in neural progenitors have reduced levels of histone H1 and H2A variants that compromise chromatin fluidity and transcriptional programs within the developing cerebellum. Disorganized chromatin limits Purkinje and granule neuron progenitor expansion, resulting in abnormal post-natal foliation, while deregulated transcriptional programs contribute to altered neural maturation, motor dysfunction and death. However, mice survive to young adulthood, in part from Snf2l compensation that restores Engrailed-1 expression. Similarly, Purkinje-specific Snf2h ablation affects chromatin ultrastructure and dendritic arborization, but alters cognitive skills rather than motor control. Our studies reveal that Snf2h controls chromatin organization and histone H1 dynamics for the establishment of gene expression programs underlying cerebellar morphogenesis and neural maturation.
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Affiliation(s)
- Matías Alvarez-Saavedra
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Yves De Repentigny
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Pamela S Lagali
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Edupuganti V S Raghu Ram
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Emile Hashem
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Danton Ivanochko
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Michael S Huh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Doo Yang
- 1] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [2] Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Alan J Mears
- Vision Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Matthew A M Todd
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Chelsea P Corcoran
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Erin A Bassett
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Nicholas J A Tokarew
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Juraj Kokavec
- Institute of Pathologic Physiology, First Faculty of Medicine, Charles University in Prague, Prague 12853, Czech Republic
| | - Romit Majumder
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Ilya Ioshikhes
- 1] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [2] Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Valerie A Wallace
- 1] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [2] Vision Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Rashmi Kothary
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tomas Stopka
- Institute of Pathologic Physiology, First Faculty of Medicine, Charles University in Prague, Prague 12853, Czech Republic
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - David J Picketts
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [3] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
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26
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Satija R, Shalek AK. Heterogeneity in immune responses: from populations to single cells. Trends Immunol 2014; 35:219-29. [PMID: 24746883 DOI: 10.1016/j.it.2014.03.004] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 12/18/2022]
Abstract
The mammalian immune system is tasked with protecting the host against a broad range of threats. Understanding how immune populations leverage cellular diversity to achieve this breadth and flexibility, particularly during dynamic processes such as differentiation and antigenic response, is a core challenge that is well suited for single cell analysis. Recent years have witnessed transformative and intersecting advances in nanofabrication and genomics that enable deep profiling of individual cells, affording exciting opportunities to study heterogeneity in the immune response at an unprecedented scope. In light of these advances, here we review recent work exploring how immune populations generate and leverage cellular heterogeneity at multiple molecular and phenotypic levels. Additionally, we highlight opportunities for single cell technologies to shed light on the causes and consequences of heterogeneity in the immune system.
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Affiliation(s)
- Rahul Satija
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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27
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Jung HR, Sidoli S, Haldbo S, Sprenger RR, Schwämmle V, Pasini D, Helin K, Jensen ON. Precision Mapping of Coexisting Modifications in Histone H3 Tails from Embryonic Stem Cells by ETD-MS/MS. Anal Chem 2013; 85:8232-9. [DOI: 10.1021/ac401299w] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hye Ryung Jung
- Centre for Epigenetics, Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Simone Sidoli
- Centre for Epigenetics, Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Simon Haldbo
- Centre for Epigenetics, Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Richard R. Sprenger
- Centre for Epigenetics, Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Veit Schwämmle
- Centre for Epigenetics, Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Diego Pasini
- Centre for Epigenetics, Biotech
Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kristian Helin
- Centre for Epigenetics, Biotech
Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
- The Danish Stem Cell Center, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen
N, Denmark
| | - Ole N. Jensen
- Centre for Epigenetics, Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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