1
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Kashyap J, Chhabra A, Kumari N, Tyagi RK. Nuclear localization signal in nuclear receptor VDR facilitates the mitotic genome bookmarking by involving distinct amino acid residues. Mol Cell Endocrinol 2024; 589:112233. [PMID: 38616036 DOI: 10.1016/j.mce.2024.112233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
Mitotic genome-bookmarking preserves epigenetic information, re-establishing progenitor's gene expression profile through transcription factors, chromatin remodelers, and histone modifiers, thereby regulating cell fate and lineage commitment post-mitotically in progeny cells. Our recent study revealed that the constitutive association of VDR with mitotic chromatin involves its DNA-binding domain. However, amino acid residues in this domain, crucial for genome bookmarking, remain elusive. This study demonstrates that nuclear localization signal (NLS) residues between 49 and 55 amino acids in VDR are essential for receptor-chromatin interaction during mitosis. Furthermore, it is revealed that both bipartite nature of VDR-NLS region and N-terminally located positively charged arginine residues are critical for its 'genome-bookmarking' property. Since mitotic chromatin association of heterodimeric partner RXR depends on VDR-chromatin association, interventions in VDR binding also abort RXR-chromatin interaction. Overall, this study documents the mechanistic details underlying VDR-chromatin interactions in genome-bookmarking behavior, potentially aiding in comprehending VDR-mediated diseases attributed to certain SNPs.
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Affiliation(s)
- Jyoti Kashyap
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ayushi Chhabra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India; Special Centre for Systems Medicine (Concurrent Faculty), Jawaharlal Nehru University, New Delhi, 110067, India.
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2
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Chervova A, Molliex A, Baymaz HI, Coux RX, Papadopoulou T, Mueller F, Hercul E, Fournier D, Dubois A, Gaiani N, Beli P, Festuccia N, Navarro P. Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells. Nat Struct Mol Biol 2024; 31:513-522. [PMID: 38196033 PMCID: PMC10948359 DOI: 10.1038/s41594-023-01195-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/30/2023] [Indexed: 01/11/2024]
Abstract
Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential in maintaining pluripotency in mouse embryonic stem cells, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly those most efficiently reactivated in G1. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.
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Affiliation(s)
- Almira Chervova
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Amandine Molliex
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | | | - Rémi-Xavier Coux
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Thaleia Papadopoulou
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Florian Mueller
- Department of Computational Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3691, Imaging and Modeling Unit, Paris, France
| | - Eslande Hercul
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - David Fournier
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Agnès Dubois
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Nicolas Gaiani
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Petra Beli
- Institute of Molecular Biology, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-Universität, Mainz, Germany
| | - Nicola Festuccia
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France.
- Equipe Labéllisée Ligue Contre le cancer, Paris, France.
| | - Pablo Navarro
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France.
- Equipe Labéllisée Ligue Contre le cancer, Paris, France.
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3
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Hayashi S, Seki-Omura R, Yamada S, Kamata T, Sato Y, Oe S, Koike T, Nakano Y, Iwashita H, Hirahara Y, Tanaka S, Sekijima T, Ito T, Yasukochi Y, Higasa K, Kitada M. OLIG2 translocates to chromosomes during mitosis via a temperature downshift: A novel neural cold response of mitotic bookmarking. Gene 2024; 891:147829. [PMID: 37748631 DOI: 10.1016/j.gene.2023.147829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/09/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Affiliation(s)
- Shinichi Hayashi
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan.
| | - Ryohei Seki-Omura
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Shintaro Yamada
- Department of Functional Neuroscience, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Taito Kamata
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-nocho, Niigata, Japan; Faculty of Agriculture, Niigata University, 8050 Ikarashi 2-nocho, Niigata, Japan
| | - Yuki Sato
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Souichi Oe
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Taro Koike
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Yousuke Nakano
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Hikaru Iwashita
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Yukie Hirahara
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan; Faculty of Nursing, Kansai Medical University, Shinmachi 2-2-2, Hirakata, Osaka, Japan
| | - Susumu Tanaka
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan; Department of Anatomy and Physiology, Faculty of Nursing and Nutrition, University of Nagasaki, Manabino 1-1-1, Nagasaki, Japan
| | - Tsuneo Sekijima
- Faculty of Agriculture, Niigata University, 8050 Ikarashi 2-nocho, Niigata, Japan
| | - Takeshi Ito
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Yoshiki Yasukochi
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Masaaki Kitada
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan.
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Sokpor G, Nguyen HP, Tuoc T. Safeguarding transcriptional memory: a mitotic bookmarking role for chromatin remodelers. Signal Transduct Target Ther 2023; 8:380. [PMID: 37788985 PMCID: PMC10547697 DOI: 10.1038/s41392-023-01610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/18/2023] [Accepted: 08/13/2023] [Indexed: 10/05/2023] Open
Affiliation(s)
- Godwin Sokpor
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany.
- Lincoln Medical School, University of Lincoln, Lincoln, UK.
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Tran Tuoc
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany.
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5
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Vimalraj S, Sekaran S. RUNX Family as a Promising Biomarker and a Therapeutic Target in Bone Cancers: A Review on Its Molecular Mechanism(s) behind Tumorigenesis. Cancers (Basel) 2023; 15:3247. [PMID: 37370857 DOI: 10.3390/cancers15123247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The transcription factor runt-related protein (RUNX) family is the major transcription factor responsible for the formation of osteoblasts from bone marrow mesenchymal stem cells, which are involved in bone formation. Accumulating evidence implicates the RUNX family for its role in tumor biology and cancer progression. The RUNX family has been linked to osteosarcoma via its regulation of many tumorigenicity-related factors. In the regulatory network of cancers, with numerous upstream signaling pathways and its potential target molecules downstream, RUNX is a vital molecule. Hence, a pressing need exists to understand the precise process underpinning the occurrence and prognosis of several malignant tumors. Until recently, RUNX has been regarded as one of the therapeutic targets for bone cancer. Therefore, in this review, we have provided insights into various molecular mechanisms behind the tumorigenic role of RUNX in various important cancers. RUNX is anticipated to grow into a novel therapeutic target with the in-depth study of RUNX family-related regulatory processes, aid in the creation of new medications, and enhance clinical efficacy.
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Affiliation(s)
- Selvaraj Vimalraj
- Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Saravanan Sekaran
- Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, Tamil Nadu, India
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6
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Liu S, Xie SM, Liu W, Gagea M, Hanker AB, Nguyen N, Singareeka Raghavendra A, Yang-Kolodji G, Chu F, Neelapu SS, Marchese A, Hanash S, Zimmermann J, Arteaga CL, Tripathy D. Targeting CXCR4 abrogates resistance to trastuzumab by blocking cell cycle progression and synergizes with docetaxel in breast cancer treatment. Breast Cancer Res 2023; 25:62. [PMID: 37280713 DOI: 10.1186/s13058-023-01665-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Although trastuzumab and other HER2-targeted therapies have significantly improved survival in patients with HER2 overexpressed or amplified (HER2+) breast cancer, a significant proportion of patients do not respond or eventually develop clinical resistance. Strategies to reverse trastuzumab resistance remain a high clinical priority. We were the first to report the role of CXCR4 in trastuzumab resistance. The present study aims to explore the therapeutic potential of targeting CXCR4 and better understand the associated mechanisms. METHODS Immunofluorescent staining, confocal microscopy analysis, and immunoblotting were used to analyze CXCR4 expression. BrdU incorporation assays and flow cytometry were used to analyze dynamic CXCR4 expression. Three-dimensional co-culture (tumor cells/breast cancer-associated fibroblasts/human peripheral blood mononuclear cells) or antibody-dependent cellular cytotoxicity assay was used to mimic human tumor microenvironment, which is necessary for testing therapeutic effects of CXCR4 inhibitor or trastuzumab. The FDA-approved CXCR4 antagonist AMD3100, trastuzumab, and docetaxel chemotherapy were used to evaluate therapeutic efficacy in vitro and in vivo. Reverse phase protein array and immunoblotting were used to discern the associated molecular mechanisms. RESULTS Using a panel of cell lines and patient breast cancer samples, we confirmed CXCR4 drives trastuzumab resistance in HER2+ breast cancer and further demonstrated the increased CXCR4 expression in trastuzumab-resistant cells is associated with cell cycle progression with a peak in the G2/M phases. Blocking CXCR4 with AMD3100 inhibits cell proliferation by downregulating mediators of G2-M transition, leading to G2/M arrest and abnormal mitosis. Using a panel of trastuzumab-resistant cell lines and an in vivo established trastuzumab-resistant xenograft mouse model, we demonstrated that targeting CXCR4 with AMD3100 suppresses tumor growth in vitro and in vivo, and synergizes with docetaxel. CONCLUSIONS Our findings support CXCR4 as a novel therapeutic target and a predictive biomarker for trastuzumab resistance in HER2+ breast cancer.
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Affiliation(s)
- Shuying Liu
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shelly M Xie
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenbin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ariella B Hanker
- Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nguyen Nguyen
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Gloria Yang-Kolodji
- Department of Medicine, University of South California, Los Angeles, CA, USA
| | - Fuliang Chu
- Department of Lymphoma-Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sattva S Neelapu
- Department of Lymphoma-Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adriano Marchese
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Carlos L Arteaga
- Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Debasish Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Soujanya M, Bihani A, Hajirnis N, Pathak RU, Mishra RK. Nuclear architecture and the structural basis of mitotic memory. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:8. [PMID: 36725757 DOI: 10.1007/s10577-023-09714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/13/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
The nucleus is a complex organelle that hosts the genome and is essential for vital processes like DNA replication, DNA repair, transcription, and splicing. The genome is non-randomly organized in the three-dimensional space of the nucleus. This functional sub-compartmentalization was thought to be organized on the framework of nuclear matrix (NuMat), a non-chromatin scaffold that functions as a substratum for various molecular processes of the nucleus. More recently, nuclear bodies or membrane-less subcompartments of the nucleus are thought to arise due to phase separation of chromatin, RNA, and proteins. The nuclear architecture is an amalgamation of the relative organization of chromatin, epigenetic landscape, the nuclear bodies, and the nucleoskeleton in the three-dimensional space of the nucleus. During mitosis, the nucleus undergoes drastic changes in morphology to the degree that it ceases to exist as such; various nuclear components, including the envelope that defines the nucleus, disintegrate, and the chromatin acquires mitosis-specific epigenetic marks and condenses to form chromosome. Upon mitotic exit, chromosomes are decondensed, re-establish hierarchical genome organization, and regain epigenetic and transcriptional status similar to that of the mother cell. How this mitotic memory is inherited during cell division remains a puzzle. NuMat components that are a part of the mitotic chromosome in the form of mitotic chromosome scaffold (MiCS) could potentially be the seeds that guide the relative re-establishment of the epigenome, chromosome territories, and the nuclear bodies. Here, we synthesize the advances towards understanding cellular memory of nuclear architecture across mitosis and propose a hypothesis that a subset of NuMat proteome essential for nucleation of various nuclear bodies are retained in MiCS to serve as seeds of mitotic memory, thus ensuring the daughter cells re-establish the complex status of nuclear architecture similar to that of the mother cells, thereby maintaining the pre-mitotic transcriptional status.
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Affiliation(s)
- Mamilla Soujanya
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ashish Bihani
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Nikhil Hajirnis
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, USA
| | - Rashmi U Pathak
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Rakesh K Mishra
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India.
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India.
- TIGS - Tata Institute for Genetics and Society, Bangalore, India.
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8
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Yu Q, Liu X, Fang J, Wu H, Guo C, Zhang W, Liu N, Jiang C, Sha Q, Yuan X, Wang Z, Qu K. Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution. SCIENCE ADVANCES 2023; 9:eadd2175. [PMID: 36696508 PMCID: PMC9876548 DOI: 10.1126/sciadv.add2175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Although mitotic chromosomes are highly compacted and transcriptionally inert, some active chromatin features are retained during mitosis to ensure the proper postmitotic reestablishment of maternal transcriptional programs, a phenomenon termed "mitotic bookmarking." However, the dynamics and regulation of mitotic bookmarking have not been systemically surveyed. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we examined 6538 mitotic L02 human liver cells of variable stages and found that chromatin accessibility remained changing throughout cell division, with a constant decrease until metaphase and a gradual increase as chromosomes segregated. In particular, a subset of chromatin regions were identified to remain open throughout mitosis, and genes associated with these bookmarked regions are primarily linked to rapid reactivation upon mitotic exit. We also demonstrated that nuclear transcription factor Y subunit α (NF-YA) preferentially occupied bookmarked regions and contributed to transcriptional reactivation after mitosis. Our study uncovers the dynamic and regulatory blueprint of mitotic bookmarking.
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Affiliation(s)
- Qiaoni Yu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Xu Liu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Jingwen Fang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Huihui Wu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Chuang Guo
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wen Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Nianping Liu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chen Jiang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qing Sha
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiao Yuan
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Zhikai Wang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Kun Qu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
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9
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Huang Y, Gao BQ, Meng Q, Yang LZ, Ma XK, Wu H, Pan YH, Yang L, Li D, Chen LL. CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos. Genome Biol 2023; 24:15. [PMID: 36658633 PMCID: PMC9854193 DOI: 10.1186/s13059-023-02848-6] [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: 08/17/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Understanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualize RNAs in live cells without genetic manipulation. We optimize this system to track developmentally expressed mRNAs in zebrafish embryos and to understand features of endogenous transcription kinetics and mRNP export. RESULTS We report that zygotic microinjection of purified CRISPR-dCas13-fluorescent proteins and modified guide RNAs allows single- and dual-color tracking of developmentally expressed mRNAs in zebrafish embryos from zygotic genome activation (ZGA) until early segmentation period without genetic manipulation. Using this approach, we uncover non-synchronized de novo transcription between inter-alleles, synchronized post-mitotic re-activation in pairs of alleles, and transcriptional memory as an extrinsic noise that potentially contributes to synchronized post-mitotic re-activation. We also reveal rapid dCas13-engaged mRNP movement in the nucleus with a corralled and diffusive motion, but a wide varying range of rate-limiting mRNP export, which can be shortened by Alyref and Nxf1 overexpression. CONCLUSIONS This optimized dCas13-based toolkit enables robust spatial-temporal tracking of endogenous mRNAs and uncovers features of transcription and mRNP motion, providing a powerful toolkit for endogenous RNA visualization in a multicellular developmental organism.
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Affiliation(s)
- Youkui Huang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Bao-Qing Gao
- grid.410726.60000 0004 1797 8419CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Quan Meng
- grid.418856.60000 0004 1792 5640National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang-Zhong Yang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Xu-Kai Ma
- grid.8547.e0000 0001 0125 2443Center for Molecular Medicine, Children’s Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Wu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yu-Hang Pan
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Li Yang
- grid.8547.e0000 0001 0125 2443Center for Molecular Medicine, Children’s Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dong Li
- grid.418856.60000 0004 1792 5640National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ling-Ling Chen
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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10
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Fritz AJ, Ghule PN, Toor R, Dillac L, Perelman J, Boyd J, Lian JB, Gordon JA, Frietze S, Van Wijnen A, Stein JL, Stein GS. Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle. Crit Rev Eukaryot Gene Expr 2023; 33:85-97. [PMID: 37017672 PMCID: PMC10826887 DOI: 10.1615/critreveukaryotgeneexpr.2022046190] [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] [Indexed: 12/23/2022]
Abstract
Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Rabail Toor
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Louis Dillac
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Jonah Perelman
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Joseph Boyd
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Johnathan A.R. Gordon
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Seth Frietze
- University of Vermont Cancer Center, Burlington, Vermont, USA
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Andre Van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
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11
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van der Zanden SY, Jongsma MLM, Neefjes ACM, Berlin I, Neefjes J. Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis. Trends Cell Biol 2023; 33:18-29. [PMID: 35778326 DOI: 10.1016/j.tcb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.
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Affiliation(s)
- Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Anna C M Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
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12
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Abstract
The control of gene expression in eukaryotes relies on how transcription factors and RNA polymerases manipulate the structure of chromatin. These interactions are especially important in development as gene expression programs change. Chromatin generally limits the accessibility of DNA, and thus exposing sequences at regulatory elements is critical for gene expression. However, it is challenging to understand how transcription factors manipulate chromatin structure and the sequence of regulatory events. The Drosophila embryo has provided a powerful setting to directly observe the establishment and elaboration of chromatin features and experimentally test the causality of transcriptional events that are shared among many metazoans. The large embryo is tractable by live imaging, and a variety of well-developed tools allow the manipulation of factors during early development. The early embryo develops as a syncytium with rapid nuclear divisions and no zygotic transcription, with largely featureless chromatin. Thus, studies in this system have revealed the progression of genome activation triggered by pioneer factors that initiate DNA exposure at regulatory elements and the establishment of chromatin domains, including heterochromatin, the nucleolus, and nuclear bodies. The de novo emergence of nuclear structures in the early embryo reveals features of chromatin dynamics that are likely to be central to transcriptional regulation in all cells.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
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13
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Hayashi S, Oe S, Koike T, Seki-Omura R, Nakano Y, Hirahara Y, Tanaka S, Ito T, Yasukochi Y, Higasa K, Kitada M. OLIG2 is an in vivo bookmarking transcription factor in the developing neural tube in mouse. J Neurochem 2022; 165:303-317. [PMID: 36547371 DOI: 10.1111/jnc.15746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/24/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Cells possess intrinsic features that are inheritable via epigenetic regulation, such as DNA methylation and histone modification. These inheritable features maintain a unique gene expression pattern, underlying cellular memory. Because of the degradation or displacement of mitotic chromosomes, most transcription factors do not contribute to cellular memory. However, accumulating in vitro evidence indicates that some transcription factors can be retained in mitotic chromosomes called as bookmarking. Such transcription factors may contribute to a novel third mechanism of cellular memory. Since most findings of transcription factor bookmarking have been reported in vitro, little is currently known in vivo. In the neural tube of mouse embryos, we discovered that OLIG2, a basic helix loop helix (bHLH) transcription factor that regulates proliferation of neural progenitors and the cell fate of motoneurons and oligodendrocytes, binds to chromatin through every cell cycle including M-phase. OLIG2 chromosomal localization coincides with mitotic cell features such as the phosphorylation of histone H3, KI67, and nuclear membrane breakdown. Chromosomal localization of OLIG2 is regulated by an N-terminus triple serine motif. Photobleaching analysis revealed slow OLIG2 mobility, suggesting a high affinity of OLIG2 to DNA. In Olig2 N-terminal deletion mutant mice, motoneurons and oligodendrocyte progenitor numbers are reduced in the neural tube, suggesting that the bookmarking regulatory domain is important for OLIG2 function. We conclude that OLIG2 is a de novo in vivo bookmarking transcription factor. Our results demonstrate the presence of in vivo bookmarking in a living organism and illustrate a novel function of transcription factors.
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Affiliation(s)
- Shinichi Hayashi
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Souichi Oe
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Taro Koike
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Ryohei Seki-Omura
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Yosuke Nakano
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Yukie Hirahara
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan.,Faculty of Nursing, Kansai Medical University, Osaka, Japan
| | - Susumu Tanaka
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan.,Faculty of Nursing and Nutrition, Department of Anatomy and Physiology, University of Nagasaki, Nagasaki, Japan
| | - Takeshi Ito
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Yoshiki Yasukochi
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Masaaki Kitada
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
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14
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Kashyap J, Tyagi RK. Mitotic genome bookmarking by nuclear receptor VDR advocates transmission of cellular transcriptional memory to progeny cells. Exp Cell Res 2022; 417:113193. [PMID: 35523304 DOI: 10.1016/j.yexcr.2022.113193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/04/2022]
Abstract
Mitosis is an essential process for the self-renewal of cells that is accompanied by dynamic changes in nuclear architecture and chromatin organization. Despite all the changes, the cell manages to re-establish all the parental epigenetic marks, post-mitotically. Recent reports suggest that some sequence-specific transcription factors remain attached to mitotic chromatin during cell division to ensure timely reactivation of a subset of transcription factors necessary to maintain cell identity. These mitotically associated factors are suggested to act as 'genome bookmarking factors' and the phenomenon is termed 'genome bookmarking'. Here, we studied this phenomenon with Vitamin D Receptor (VDR), a key regulator of calcium and phosphate homeostasis and a member of the nuclear receptor superfamily. This study, for the first time, has confirmed VDR as a mitotic bookmarking factor that may be playing a crucial role in the maintenance of cell identity and genome bookmarking. Full 'DNA binding domain (DBD)' present in VDR was identified as essential for enrichment of VDR on mitotic chromatin. Furthermore, the study also demonstrates that VDR evokes mitotic chromatin binding behaviour in its heterodimeric partner Retinoid X receptor (RXR). Interestingly, for promoting bookmarking behaviour in RXR, both DBD and/or ligand-binding domain (LBD) in conjunction with hinge region of VDR were required. Additionally, ChIP analysis showed that VDR remains associated with DR3 (direct repeat 3) region of its specific target gene promoter CYP24A1(Cytochrome P450 family 24 subfamily A member1), during mitosis. Altogether, our study illustrates a novel function of VDR in the epigenetic transmission and control of expression of target proteome for maintenance of cell identity and traits in progeny cells.
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Affiliation(s)
- Jyoti Kashyap
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
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15
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Singh P, Harris PC, Sas DJ, Lieske JC. The genetics of kidney stone disease and nephrocalcinosis. Nat Rev Nephrol 2022; 18:224-240. [PMID: 34907378 DOI: 10.1038/s41581-021-00513-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
Kidney stones (also known as urinary stones or nephrolithiasis) are highly prevalent, affecting approximately 10% of adults worldwide, and the incidence of stone disease is increasing. Kidney stone formation results from an imbalance of inhibitors and promoters of crystallization, and calcium-containing calculi account for over 80% of stones. In most patients, the underlying aetiology is thought to be multifactorial, with environmental, dietary, hormonal and genetic components. The advent of high-throughput sequencing techniques has enabled a monogenic cause of kidney stones to be identified in up to 30% of children and 10% of adults who form stones, with ~35 different genes implicated. In addition, genome-wide association studies have implicated a series of genes involved in renal tubular handling of lithogenic substrates and of inhibitors of crystallization in stone disease in the general population. Such findings will likely lead to the identification of additional treatment targets involving underlying enzymatic or protein defects, including but not limited to those that alter urinary biochemistry.
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Affiliation(s)
- Prince Singh
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Division of Molecular Biology and Biochemistry, Mayo Clinic, Rochester, MN, USA
| | - David J Sas
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Division of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA. .,Division of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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16
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Fritz AJ, El Dika M, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype. Results Probl Cell Differ 2022; 70:339-373. [PMID: 36348114 PMCID: PMC9753575 DOI: 10.1007/978-3-031-06573-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epigenetic gene regulatory mechanisms play a central role in the biological control of cell and tissue structure, function, and phenotype. Identification of epigenetic dysregulation in cancer provides mechanistic into tumor initiation and progression and may prove valuable for a variety of clinical applications. We present an overview of epigenetically driven mechanisms that are obligatory for physiological regulation and parameters of epigenetic control that are modified in tumor cells. The interrelationship between nuclear structure and function is not mutually exclusive but synergistic. We explore concepts influencing the maintenance of chromatin structures, including phase separation, recognition signals, factors that mediate enhancer-promoter looping, and insulation and how these are altered during the cell cycle and in cancer. Understanding how these processes are altered in cancer provides a potential for advancing capabilities for the diagnosis and identification of novel therapeutic targets.
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Affiliation(s)
- Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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17
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El Dika M, Fritz AJ, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Fidelity of Mechanisms Governing the Cell Cycle. Results Probl Cell Differ 2022; 70:375-396. [PMID: 36348115 PMCID: PMC9703624 DOI: 10.1007/978-3-031-06573-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cell cycle is governed by stringent epigenetic mechanisms that, in response to intrinsic and extrinsic regulatory cues, support fidelity of DNA replication and cell division. We will focus on (1) the complex and interdependent processes that are obligatory for control of proliferation and compromised in cancer, (2) epigenetic and topological domains that are associated with distinct phases of the cell cycle that may be altered in cancer initiation and progression, and (3) the requirement for mitotic bookmarking to maintain intranuclear localization of transcriptional regulatory machinery to reinforce cell identity throughout the cell cycle to prevent malignant transformation.
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Affiliation(s)
- Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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18
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Dreval K, Lake RJ, Fan HY. Analyzing the Interaction of RBPJ with Mitotic Chromatin and Its Impact on Transcription Reactivation upon Mitotic Exit. Methods Mol Biol 2022; 2472:95-108. [PMID: 35674895 DOI: 10.1007/978-1-0716-2201-8_9] [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] [Indexed: 06/15/2023]
Abstract
The sequence-specific transcription factor RBPJ, also known as CSL (CBF1, Su(H), Lag1), is an evolutionarily conserved protein that mediates Notch signaling to guide cell fates. When cells enter mitosis, DNA is condensed and most transcription factors dissociate from chromatin; however, a few, select transcription factors, termed bookmarking factors, remain associated. These mitotic chromatin-bound factors are believed to play important roles in maintaining cell fates through cell division. RBPJ is one such factor that remains mitotic chromatin associated and therefore could function as a bookmarking factor. Here, we describe how to obtain highly purified mitotic cells from the mouse embryonal carcinoma cell line F9, perform chromatin immunoprecipitation with mitotic cells, and measure the first run of RNA synthesis upon mitotic exit. These methods serve as basis to understand the roles of mitotic bookmarking by RBPJ in propagating Notch signals through cell division.
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Affiliation(s)
- Kostiantyn Dreval
- The Program in Cellular and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico Health Science Center, Albuquerque, NM, USA
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Robert J Lake
- The Program in Cellular and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Hua-Ying Fan
- The Program in Cellular and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA.
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico Health Science Center, Albuquerque, NM, USA.
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19
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Genomic Insights into Non-steroidal Nuclear Receptors in Prostate and Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:227-239. [DOI: 10.1007/978-3-031-11836-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Komatsu M, Tsukahara H, Bai H, Takahashi M, Wakai T, Kawahara M. Cell-cycle dependent GATA2 subcellular localization in mouse 2-cell embryos. Biochem Biophys Res Commun 2021; 584:1-6. [PMID: 34741809 DOI: 10.1016/j.bbrc.2021.10.077] [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: 10/19/2021] [Accepted: 10/31/2021] [Indexed: 11/24/2022]
Abstract
GATA factors are essential transcription factors for embryonic development that broadly control the transcription of other genes. This study aimed to examine GATA2 protein localization in mouse embryos at the 2-cell stage, when drastic transformation in gene expression occurs for subsequent development in early embryos. We first analyzed GATA2 localization in 2-cell embryos at the interphase and mitotic phases by immunofluorescence analysis. In the interphase, GATA2 protein was localized in the nucleus, as a common transcription factor. In the mitotic phase, GATA2 protein was observed as a focally-aggregated spot around the nucleus of each blastomere. To explore the relationship between GATA2 protein localization and cell cycle progression in mouse 2-cell stage embryos, GFP-labeled GATA2 protein was overexpressed in the blastomere of 2-cell embryos. Overexpression of GFP-labeled GATA2 protein arrested cellular mitosis, focally aggregated GATA2 protein expression was not observed. This mitotic arrest by GATA2 overexpression was not accompanied with the upregulation of a 2-cell stage specific gene, murine endogenous retrovirus-L. These results suggest that GATA2 protein localization changes dynamically depending on cell cycle progression in mouse 2-cell embryos; in particular, focally aggregated localization of GATA2 in the mitotic phase requires appropriate cell cycle progression.
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Affiliation(s)
- Masaya Komatsu
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hayato Tsukahara
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hanako Bai
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masashi Takahashi
- Graduate School of Global Food Resources/Global Center for Food, Land and Water Resources, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Takuya Wakai
- Department of Animal Science, Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Manabu Kawahara
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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21
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Watson AW, Grant AD, Parker SS, Hill S, Whalen MB, Chakrabarti J, Harman MW, Roman MR, Forte BL, Gowan CC, Castro-Portuguez R, Stolze LK, Franck C, Cusanovich DA, Zavros Y, Padi M, Romanoski CE, Mouneimne G. Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning. Cell Rep 2021; 35:109293. [PMID: 34192535 PMCID: PMC8312405 DOI: 10.1016/j.celrep.2021.109293] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/26/2021] [Accepted: 06/03/2021] [Indexed: 11/14/2022] Open
Abstract
While the immediate and transitory response of breast cancer cells to pathological stiffness in their native microenvironment has been well explored, it remains unclear how stiffness-induced phenotypes are maintained over time after cancer cell dissemination in vivo. Here, we show that fibrotic-like matrix stiffness promotes distinct metastatic phenotypes in cancer cells, which are preserved after transition to softer microenvironments, such as bone marrow. Using differential gene expression analysis of stiffness-responsive breast cancer cells, we establish a multigenic score of mechanical conditioning (MeCo) and find that it is associated with bone metastasis in patients with breast cancer. The maintenance of mechanical conditioning is regulated by RUNX2, an osteogenic transcription factor, established driver of bone metastasis, and mitotic bookmarker that preserves chromatin accessibility at target gene loci. Using genetic and functional approaches, we demonstrate that mechanical conditioning maintenance can be simulated, repressed, or extended, with corresponding changes in bone metastatic potential. Watson et al. demonstrate that mechanical conditioning by stiff microenvironments in breast tumors is maintained in cancer cells after dissemination to softer microenvironments, including bone marrow. They show that mechanical conditioning promotes invasion and osteolysis and establish a mechanical conditioning (MeCo) score, associated with bone metastasis in patients.
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Affiliation(s)
- Adam W Watson
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; MeCo Diagnostics, Tucson, AZ 85718, USA
| | - Adam D Grant
- University of Arizona Cancer Center, Tucson, AZ 85724, USA
| | - Sara S Parker
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Samantha Hill
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Michael B Whalen
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Jayati Chakrabarti
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Michael W Harman
- School of Engineering, Brown University, Providence, RI 02912, USA
| | | | | | - Cody C Gowan
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | | | - Lindsey K Stolze
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Christian Franck
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Darren A Cusanovich
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Yana Zavros
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Megha Padi
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA; Bioinformatics Shared Resource, University of Arizona Cancer Center, Tucson, AZ 85724, USA
| | - Casey E Romanoski
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA.
| | - Ghassan Mouneimne
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA.
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22
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Shi W, Zhang G, Ma Z, Li L, Liu M, Qin L, Yu Z, Zhao L, Liu Y, Zhang X, Qin J, Ye H, Jiang X, Zhou H, Sun H, Jiao Z. Hyperactivation of HER2-SHCBP1-PLK1 axis promotes tumor cell mitosis and impairs trastuzumab sensitivity to gastric cancer. Nat Commun 2021; 12:2812. [PMID: 33990570 PMCID: PMC8121856 DOI: 10.1038/s41467-021-23053-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
Trastuzumab is the backbone of HER2-directed gastric cancer therapy, but poor patient response due to insufficient cell sensitivity and drug resistance remains a clinical challenge. Here, we report that HER2 is involved in cell mitotic promotion for tumorigenesis by hyperactivating a crucial HER2-SHCBP1-PLK1 axis that drives trastuzumab sensitivity and is targeted therapeutically. SHCBP1 is an Shc1-binding protein but is detached from scaffold protein Shc1 following HER2 activation. Released SHCBP1 responds to HER2 cascade by translocating into the nucleus following Ser273 phosphorylation, and then contributing to cell mitosis regulation through binding with PLK1 to promote the phosphorylation of the mitotic interactor MISP. Meanwhile, Shc1 is recruited to HER2 for MAPK or PI3K pathways activation. Also, clinical evidence shows that increased SHCBP1 prognosticates a poor response of patients to trastuzumab therapy. Theaflavine-3, 3'-digallate (TFBG) is identified as an inhibitor of the SHCBP1-PLK1 interaction, which is a potential trastuzumab sensitizing agent and, in combination with trastuzumab, is highly efficacious in suppressing HER2-positive gastric cancer growth. These findings suggest an aberrant mitotic HER2-SHCBP1-PLK1 axis underlies trastuzumab sensitivity and offer a new strategy to combat gastric cancer.
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Affiliation(s)
- Wengui Shi
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Gengyuan Zhang
- The Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Zhijian Ma
- The Second Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China
| | - Lianshun Li
- The Second Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China
| | - Miaomiao Liu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China
| | - Long Qin
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Zeyuan Yu
- The Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Lei Zhao
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Yang Liu
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Xue Zhang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China
| | - Junjie Qin
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Huili Ye
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Xiangyan Jiang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China
| | - Huinian Zhou
- The Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Hui Sun
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.
| | - Zuoyi Jiao
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.
- Biobank of Tumors from Plateau of Gansu Province, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.
- The Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.
- The Second Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China.
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23
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Pelham-Webb B, Polyzos A, Wojenski L, Kloetgen A, Li J, Di Giammartino DC, Sakellaropoulos T, Tsirigos A, Core L, Apostolou E. H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization. Mol Cell 2021; 81:1732-1748.e8. [PMID: 33730542 PMCID: PMC8052294 DOI: 10.1016/j.molcel.2021.02.032] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 01/15/2021] [Accepted: 02/22/2021] [Indexed: 01/19/2023]
Abstract
During self-renewal, cell-type-defining features are drastically perturbed in mitosis and must be faithfully reestablished upon G1 entry, a process that remains largely elusive. Here, we characterized at a genome-wide scale the dynamic transcriptional and architectural resetting of mouse pluripotent stem cells (PSCs) upon mitotic exit. We captured distinct waves of transcriptional reactivation with rapid induction of stem cell genes and transient activation of lineage-specific genes. Topological reorganization at different hierarchical levels also occurred in an asynchronous manner and showed partial coordination with transcriptional resetting. Globally, rapid transcriptional and architectural resetting associated with mitotic retention of H3K27 acetylation, supporting a bookmarking function. Indeed, mitotic depletion of H3K27ac impaired the early reactivation of bookmarked, stem-cell-associated genes. However, 3D chromatin reorganization remained largely unaffected, suggesting that these processes are driven by distinct forces upon mitotic exit. This study uncovers principles and mediators of PSC molecular resetting during self-renewal.
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Affiliation(s)
- Bobbie Pelham-Webb
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY 10021, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Luke Wojenski
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Andreas Kloetgen
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Jiexi Li
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Leighton Core
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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24
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Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat Genet 2021; 53:279-287. [PMID: 33558757 DOI: 10.1038/s41588-020-00768-w] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Chromatin accessibility is a hallmark of regulatory regions, entails transcription factor (TF) binding and requires nucleosomal reorganization. However, it remains unclear how dynamic this process is. In the present study, we use small-molecule inhibition of the catalytic subunit of the mouse SWI/SNF remodeler complex to show that accessibility and reduced nucleosome presence at TF-binding sites rely on persistent activity of nucleosome remodelers. Within minutes of remodeler inhibition, accessibility and TF binding decrease. Although this is irrespective of TF function, we show that the activating TF OCT4 (POU5F1) exhibits a faster response than the repressive TF REST. Accessibility, nucleosome depletion and gene expression are rapidly restored on inhibitor removal, suggesting that accessible chromatin is regenerated continuously and in a largely cell-autonomous fashion. We postulate that TF binding to chromatin and remodeler-mediated nucleosomal removal do not represent a stable situation, but instead accessible chromatin reflects an average of a dynamic process under continued renewal.
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25
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Cho YD, Kim WJ, Kim S, Ku Y, Ryoo HM. Surface Topography of Titanium Affects Their Osteogenic Potential through DNA Methylation. Int J Mol Sci 2021; 22:2406. [PMID: 33673700 PMCID: PMC7957554 DOI: 10.3390/ijms22052406] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 01/14/2023] Open
Abstract
It is widely accepted that sandblasted/large-grit/acid-etched (SLA) surfaces of titanium (Ti) have a higher osteogenic potential than machined ones. However, most studies focused on differential gene expression without elucidating the underlying mechanism for this difference. The aim of this study was to evaluate how the surface roughness of dental Ti implants affects their osteogenic potential. Mouse preosteoblast MC3T3-E1 cells were seeded on machined and SLA Ti discs. The cellular activities of the discs were analyzed using confocal laser scanning microscopy, proliferation assays, and real-time polymerase chain reaction (PCR). DNA methylation was evaluated using a methylation-specific PCR. The cell morphology was slightly different between the two types of surfaces. While cellular proliferation was slightly greater on the machined surfaces, the osteogenic response of the SLA surfaces was superior, and they showed increased alkaline phosphatase (Alp) activity and higher bone marker gene expression levels (Type I collagen, Alp, and osteocalcin). The degree of DNA methylation on the Alp gene was lower on the SLA surfaces than on the machined surfaces. DNA methyltransferase inhibitor stimulated the Alp gene expression on the machined surfaces, similar to the SLA surfaces. The superior osteogenic potential of the SLA surfaces can be attributed to a different epigenetic landscape, specifically, the DNA methylation of Alp genes. This finding offers novel insights into epigenetics to supplement genetics and raises the possibility of using epidrugs as potential therapeutic targets to enhance osteogenesis on implant surfaces.
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Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University, and Seoul National University Dental Hospital, Seoul 03080, Korea; (Y.-D.C.); (S.K.); (Y.K.)
| | - Woo-Jin Kim
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul 08826, Korea;
| | - Sungtae Kim
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University, and Seoul National University Dental Hospital, Seoul 03080, Korea; (Y.-D.C.); (S.K.); (Y.K.)
| | - Young Ku
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University, and Seoul National University Dental Hospital, Seoul 03080, Korea; (Y.-D.C.); (S.K.); (Y.K.)
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul 08826, Korea;
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26
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Lui H, Samsonraj RM, Vaquette C, Denbeigh J, Kakar S, Cool SM, Dudakovic A, van Wijnen AJ. Combination of BMP2 and EZH2 Inhibition to Stimulate Osteogenesis in a 3D Bone Reconstruction Model. Tissue Eng Part A 2021; 27:1084-1098. [PMID: 33234056 DOI: 10.1089/ten.tea.2020.0218] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
High concentrations of bone morphogenetic protein 2 (BMP2) in bone regeneration cause adverse events (e.g, heterotopic bone formation and acute inflammation). This study examines novel epigenetic strategies (i.e., EZH2 inhibition) for augmenting osteogenesis, thereby aiming to reduce the required BMP2 dose in vivo for bone regeneration and minimize these adverse effects. Human bone marrow-derived mesenchymal stem cells (BMSCs) were grown on three-dimensional (3D)-printed medical-grade polycaprolactone scaffolds and incubated in osteogenic media containing 50 ng/mL BMP2 and/or 5 μM GSK126 (EZH2 inhibitor) for 6 days (n = 3 per group and timepoint). Constructs were harvested for realtime quantitative polymerase chain reaction analysis at Day 10 and immunofluorescence (IF) microscopy at Day 21. After pretreating for 6 days and maintaining in osteogenic media for 4 days, BMSC-seeded scaffolds were also implanted in an immunocompromised subcutaneous murine model (n = 39; 3/group/donor and 3 control scaffolds) for histological analysis at 8 weeks. Pretreatment of BMSCs with BMP2 and BMP2/GSK126 costimulated expression of osteoblast-related genes (e.g., IBSP, SP7, RUNX2, and DLX5), as well as protein accumulation (e.g., collagen type 1/COL1A1 and osteocalcin/BGLAP) based on IF staining. While in vivo implantation for 8 weeks did not result in bone formation, increased angiogenesis was observed in BMP2 and BMP2/GSK126 groups. This study finds that BMP2 and GSK126 costimulate osteogenic differentiation of MSCs on 3D scaffolds in vitro and may contribute to enhanced vascularization when implanted in vivo to support bone formation. Thus, epigenetic priming with EZH2 inhibitors may have translational potential in bone healing by permitting a reduction of BMP2 dosing in vivo to mitigate its side effects. Impact statement While autografts are still the gold standard for bone reconstruction, tissue availability and donor morbidity are significant limitations. Previous attempts to use high concentrations of bone morphogenetic protein 2 (BMP2) have been shown to cause adverse events such as excessive bone formation and acute inflammation. Overall, the utilization of EZH2 inhibitors to modulate gene expression in favor of bone healing has been demonstrated in vitro in a tissue engineering strategy. Our study will pave the way to developing tissue engineering strategies involving GSK126 as an adjuvant to increase the effects of BMP2 for stimulating cells of interest on a three-dimensional scaffold for bone regeneration.
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Affiliation(s)
- Hayman Lui
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia.,Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rebekah M Samsonraj
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Cedryck Vaquette
- School of Dentistry, The University of Queensland, Brisbane, Queensland, Australia
| | - Janet Denbeigh
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sanjeev Kakar
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Simon M Cool
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
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27
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A framework for understanding the functions of biomolecular condensates across scales. Nat Rev Mol Cell Biol 2020; 22:215-235. [PMID: 33169001 DOI: 10.1038/s41580-020-00303-z] [Citation(s) in RCA: 378] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.
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28
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Ranganayaki S, Govindaraj P, Gayathri N, Srinivas Bharath MM. Exposure to the neurotoxin 3-nitropropionic acid in neuronal cells induces unique histone acetylation pattern: Implications for neurodegeneration. Neurochem Int 2020; 140:104846. [PMID: 32927024 DOI: 10.1016/j.neuint.2020.104846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 10/23/2022]
Abstract
Mitochondrial dysfunction is critical for neurodegeneration in movement disorders. Neurotoxicological models recapitulating movement disorder involve mitochondrial damage including inhibition of mitochondrial complexes. Previously, we demonstrated that neurotoxic models of Parkinson's disease and Manganism showed distinct morphological, electrophysiological and molecular profile indicating disease-specific characteristics. In a recent study, we demonstrated that the transcriptomic changes triggered by the neurotoxic mitochondrial complex II inhibitor 3-nitropropionic acid (3-NPA), was significantly different from the profile induced by the neurotoxic mitochondrial complex I inhibitor 1-methyl-4- phenylpyridinium (MPP+) and mitochondrial toxin Manganese (Mn). Among the plausible pathways, we surmised that epigenetic mechanisms could contribute to 3-NPA specific transcriptomic profile. To address this, we assessed global and individual lys-specific acetylation profile of Histone H3 and H4 in the 3-NPA neuronal cell model. Our data revealed histone acetylation profile unique to the 3-NPA model that was not noted in the MPP+ and Mn models. Among the individual lys, Histone H3K56 showed robust dose and time-dependent hyperacetylation in the 3-NPA model. Chromatin Immunoprecipitation-sequencing (ChIP-seq) revealed that acetylated H3K56 was associated with 13072 chromatin sites, which showed increased occupancy in the transcription start site-promoter site. Acetylated histone H3K56 was associated with 1747 up-regulated and 263 down-regulated genes in the 3-NPA model, which included many up-regulated autophagy and mitophagy genes. Western analysis validated the involvement of PINK1-Parkin dependent mitophagy in the 3-NPA model. We propose that 3-NPA specific chromatin dynamics could contribute to the unique transcriptomic profile with implications for movement disorders.
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Affiliation(s)
- S Ranganayaki
- Department of Neurochemistry, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, Karnataka, India
| | - Periyasamy Govindaraj
- Department of Neuropathology, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, Karnataka, India
| | - N Gayathri
- Department of Neuropathology, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, Karnataka, India
| | - M M Srinivas Bharath
- Department of Clinical Psychopharmacology and Neurotoxicology, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, Karnataka, India.
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29
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Cheng S, Peng T, Zhu X, Zhou F, Wang G, Ju L, Xiao Y, Liu X, Wang X. BORA regulates cell proliferation and migration in bladder cancer. Cancer Cell Int 2020; 20:290. [PMID: 32655322 PMCID: PMC7339433 DOI: 10.1186/s12935-020-01392-8] [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: 04/27/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
Background Bladder cancer is having a gradually increasing incidence in China. Except for the traditional chemotherapy drugs, there are no emerging new drugs for almost 30 years in bladder cancer. New potential therapeutic targets and biomarkers are urgently needed. Methods BORA is the activator of kinase Aurora A and plays an important role in cell cycle progression. To investigate the function of BORA in BCa, we established BORA knockdown and overexpression cell models for in vitro studies, xenograft and pulmonary metastasis mouse models for in vivo studies. Results Our results indicated that BORA was upregulated in human bladder cancer (BCa) compared to the normal bladder and paracancerous tissues at transcriptional and translational levels. We found that BORA was positively related to BCa cell proliferation. Furthermore, BORA knockdown induced cell cycle arrest in G2/M phase while BORA overexpression decreased the proportion of cells in G2/M, associated with PLK1–CDC25C–CDK1 alteration. Interestingly, we observed that knockdown of BORA inhibited BCa cell migration and invasion, accompanied with alterations of epithelial–mesenchymal transition (EMT) pathway related proteins. In vivo studies confirmed the inhibition effect of BORA knockdown on BCa cell growth and migration. Conclusions Our study indicates that BORA regulates BCa cell cycle and growth, meanwhile influences cell motility by EMT, and could be a novel biomarker and potential therapeutic target in BCa.
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Affiliation(s)
- Songtao Cheng
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC USA.,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan, China
| | - Tianchen Peng
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan, China
| | - Xiaolu Zhu
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fenfang Zhou
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan, China
| | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Xuefeng Liu
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC USA
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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30
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Rose JT, Moskovitz E, Boyd JR, Gordon JA, Bouffard NA, Fritz AJ, Illendula A, Bushweller JH, Lian JB, Stein JL, Zaidi SK, Stein GS. Inhibition of the RUNX1-CBFβ transcription factor complex compromises mammary epithelial cell identity: a phenotype potentially stabilized by mitotic gene bookmarking. Oncotarget 2020; 11:2512-2530. [PMID: 32655837 PMCID: PMC7335667 DOI: 10.18632/oncotarget.27637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
RUNX1 has recently been shown to play an important role in determination of mammary epithelial cell identity. However, mechanisms by which loss of the RUNX1 transcription factor in mammary epithelial cells leads to epithelial-to-mesenchymal transition (EMT) are not known. Here, we report that interaction between RUNX1 and its heterodimeric partner CBFβ is essential for sustaining mammary epithelial cell identity. Disruption of RUNX1-CBFβ interaction, DNA binding, and association with mitotic chromosomes alters cell morphology, global protein synthesis, and phenotype-related gene expression. During interphase, RUNX1 is organized as punctate, predominantly nuclear, foci that are dynamically redistributed during mitosis, with a subset localized to mitotic chromosomes. Genome-wide RUNX1 occupancy profiles for asynchronous, mitotically enriched, and early G1 breast epithelial cells reveal RUNX1 associates with RNA Pol II-transcribed protein coding and long non-coding RNA genes and RNA Pol I-transcribed ribosomal genes critical for mammary epithelial proliferation, growth, and phenotype maintenance. A subset of these genes remains occupied by the protein during the mitosis to G1 transition. Together, these findings establish that the RUNX1-CBFβ complex is required for maintenance of the normal mammary epithelial phenotype and its disruption leads to EMT. Importantly, our results suggest, for the first time, that RUNX1 mitotic bookmarking of a subset of epithelial-related genes may be an important epigenetic mechanism that contributes to stabilization of the mammary epithelial cell identity.
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Affiliation(s)
- Joshua T. Rose
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Eliana Moskovitz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Joseph R. Boyd
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jonathan A. Gordon
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Nicole A. Bouffard
- Microscopy Imaging Center at the Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Andrew J. Fritz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - John H. Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jane B. Lian
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Gary S. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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31
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Liu X, Shen J, Xie L, Wei Z, Wong C, Li Y, Zheng X, Li P, Song Y. Mitotic Implantation of the Transcription Factor Prospero via Phase Separation Drives Terminal Neuronal Differentiation. Dev Cell 2020; 52:277-293.e8. [DOI: 10.1016/j.devcel.2019.11.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 10/09/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
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Abstract
The highly reproducible inheritance of chromosomes during mitosis in mammalian cells involves nuclear envelope breakdown, increased chromatin compaction, loss of long-range intrachromosomal interactions, loss of enhancer-promoter proximity, displacement of many transcription regulators from the chromatin and a marked decrease in RNA synthesis. Despite these dramatic changes in the mother cell, daughter cells are able to faithfully re-establish the parental chromatin and gene expression features characteristic of the cell type. Pioneering studies of mitotic chromatin signatures showed that despite global repression of transcription, the Hsp70 gene promoter retains an open chromatin conformation, which was proposed to allow the reactivation of the Hsp70 gene upon completion of mitosis - a phenomenon termed mitotic bookmarking. It was later shown that various cell-type-specific transcription factors, such as GATA-binding factor 1 (GATA1) in erythroblasts and forkhead box protein A1 (FOXA1) in hepatocytes, remain bound at a subset of their interphase binding sites in mitosis. Such bookmarking transcription factors remain on chromosomes in mitosis and have been shown to enable a subset of genes to be reactivated in a timely fashion upon mitotic exit. In addition, sensitive new methods to measure transcription revealed that mitotic cells retain residual transcription at a large number of genes. Furthermore, genes recover their interphase level of transcription in distinct waves. Thus, gene expression is precisely regulated as cells pass through mitosis to ensure faithful propagation of cell identity and function through cellular generations.
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Dreval K, Lake RJ, Fan HY. HDAC1 negatively regulates selective mitotic chromatin binding of the Notch effector RBPJ in a KDM5A-dependent manner. Nucleic Acids Res 2019; 47:4521-4538. [PMID: 30916347 PMCID: PMC6511865 DOI: 10.1093/nar/gkz178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/25/2023] Open
Abstract
Faithful propagation of transcription programs through cell division underlies cell-identity maintenance. Transcriptional regulators selectively bound on mitotic chromatin are emerging critical elements for mitotic transcriptional memory; however, mechanisms governing their site-selective binding remain elusive. By studying how protein-protein interactions impact mitotic chromatin binding of RBPJ, the major downstream effector of the Notch signaling pathway, we found that histone modifying enzymes HDAC1 and KDM5A play critical, regulatory roles in this process. We found that HDAC1 knockdown or inactivation leads to increased RBPJ occupancy on mitotic chromatin in a site-specific manner, with a concomitant increase of KDM5A occupancy at these sites. Strikingly, the presence of KDM5A is essential for increased RBPJ occupancy. Our results uncover a regulatory mechanism in which HDAC1 negatively regulates RBPJ binding on mitotic chromatin in a KDM5A-dependent manner. We propose that relative chromatin affinity of a minimal regulatory complex, reflecting a specific transcription program, renders selective RBPJ binding on mitotic chromatin.
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Affiliation(s)
- Kostiantyn Dreval
- From the Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Robert J Lake
- From the Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Hua-Ying Fan
- From the Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
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34
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Ruiz JL, Tena JJ, Bancells C, Cortés A, Gómez-Skarmeta JL, Gómez-Díaz E. Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2019; 46:9414-9431. [PMID: 30016465 PMCID: PMC6182165 DOI: 10.1093/nar/gky643] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/10/2018] [Indexed: 12/27/2022] Open
Abstract
Human malaria is a devastating disease and a major cause of poverty in resource-limited countries. To develop and adapt within hosts Plasmodium falciparum undergoes drastic switches in gene expression. To identify regulatory regions in the parasite genome, we performed genome-wide profiling of chromatin accessibility in two culture-adapted isogenic subclones at four developmental stages during the intraerythrocytic cycle by using the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). Tn5 transposase hypersensitivity sites (THSSs) localize preferentially at transcriptional start sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3. Our assay allows the identification of novel regulatory regions including TSS and enhancer-like elements. We show that the dynamics in the accessible chromatin profile matches temporal transcription during development. Motif analysis of stage-specific ATAC-seq sites predicts the in vivo binding sites and function of multiple ApiAP2 transcription factors. At last, the alternative expression states of some clonally variant genes (CVGs), including eba, phist, var and clag genes, associate with a differential ATAC-seq signal at their promoters. Altogether, this study identifies genome-wide regulatory regions likely to play an essential function in the developmental transitions and in CVG expression in P. falciparum.
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Affiliation(s)
- José Luis Ruiz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Cristina Bancells
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain
| | - Alfred Cortés
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain.,ICREA, Barcelona, Catalonia 08010, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Elena Gómez-Díaz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain.,Instituto de Parasitología y Biomedicina 'López-Neyra' (IPBLN), Consejo Superior de Investigaciones Científicas, Granada 18016, Spain
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35
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Li KE, Shu X, Gong H, Cheng L, Dong Z, Shu S. Position-dependent correlation between TBX22 exon 5 methylation and palatal shelf fusion in the development of cleft palate. AN ACAD BRAS CIENC 2019; 91:e20180945. [PMID: 31241704 DOI: 10.1590/0001-3765201920180945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/30/2018] [Indexed: 02/05/2023] Open
Abstract
DNA methylation is essential for spatiotemporally-regulated gene expression in embryonic development. TBX22 (Chr X: 107667964-107688978) functioning as a transcriptional repressor affects DNA binding, sumoylation, and transcriptional repression associated with X-linked cleft palate. This study aimed to explore the relationship and potential mechanism between TBX22 exon 5 methylation and palatal shelf fusion induced by all-trans retinoic acid (ATRA). We performed DNA methylation profiling, using MethylRAD-seq, after high throughput sequencing of mouse embryos from control (n=9) and ATRA-treated (to induce cleft palate, n=9) C57BL/6J mice at embryonic gestation days(E) 13.5, 14.5 and 16.5. TBX22 exon 5 was hyper-methylated at the CpG site at E13.5 (P=0.025, log2FC=1.5) and E14.5 (P=0.011, log2FC:1.5) in ATRA-treated, whereas methylation TBX22 exon 5 at the CpG site was not significantly different at E16.5 (P=0.808, log2FC=-0.2) between control and ATRA-treated. MSP results showed a similar trend consistent with the MethylRAD-seq results. qPCR showed the change in TBX22 exon 5 expression level negatively correlated with its TBX22 exon 5 methylation level. These results indicate that changes in TBX22 exon 5 methylation might play an important regulatory role during palatal shelf fusion, and may enlighten the development of novel epigenetic biomarkers in the treatment of CP in the future.
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Affiliation(s)
- K E Li
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Xuan Shu
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Hui Gong
- The Department of Gynaecology, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Liuhanghang Cheng
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Zejun Dong
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Shenyou Shu
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
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36
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Fritz AJ, Gillis NE, Gerrard DL, Rodriguez PD, Hong D, Rose JT, Ghule PN, Bolf EL, Gordon JA, Tye CE, Boyd JR, Tracy KM, Nickerson JA, van Wijnen AJ, Imbalzano AN, Heath JL, Frietze SE, Zaidi SK, Carr FE, Lian JB, Stein JL, Stein GS. Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Genes Chromosomes Cancer 2019; 58:484-499. [PMID: 30873710 DOI: 10.1002/gcc.22731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022] Open
Abstract
Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer-compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.
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Affiliation(s)
- A J Fritz
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - N E Gillis
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - D L Gerrard
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - P D Rodriguez
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - D Hong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - J T Rose
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - P N Ghule
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - E L Bolf
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J A Gordon
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - C E Tye
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J R Boyd
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - K M Tracy
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J A Nickerson
- Division of Genes and Development of the Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - A J van Wijnen
- Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic Minnesota, Rochester, Minnesota
| | - A N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J L Heath
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - S E Frietze
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - S K Zaidi
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - F E Carr
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J B Lian
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J L Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - G S Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
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37
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Palsson R, Indridason OS, Edvardsson VO, Oddsson A. Genetics of common complex kidney stone disease: insights from genome-wide association studies. Urolithiasis 2018; 47:11-21. [PMID: 30523390 DOI: 10.1007/s00240-018-1094-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/08/2018] [Indexed: 12/29/2022]
Abstract
Kidney stone disease is a common disorder in Western countries that is associated with significant suffering, morbidity, and cost for the healthcare system. Numerous studies have demonstrated familial aggregation of nephrolithiasis and a twin study estimated the heritability to be 56%. Over the past decade, genome-wide association studies have uncovered several sequence variants that confer increased risk of common complex kidney stone disease. The first reported variants were observed at the CLDN14 locus in the Icelandic population. This finding has since been replicated in other populations. The CLDN14 gene is expressed in tight junctions of the thick ascending limb of the loop of Henle, where the protein is believed to play a role in regulation of calcium transport. More recent studies have uncovered variants at the ALPL, SLC34A1, CASR, and TRPV5 loci, the first two genes playing a role in renal handling of phosphate, while the latter two are involved in calcium homeostasis. Although genetic data have provided insights into the molecular basis of kidney stone disease, much remains to be learned about the contribution of genetic factors to stone formation. Nevertheless, the progress made in recent years indicates that exciting times lie ahead in genetic research on kidney stone disease.
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Affiliation(s)
- Runolfur Palsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland. .,Division of Nephrology, Internal Medicine Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland.
| | - Olafur S Indridason
- Division of Nephrology, Internal Medicine Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Vidar O Edvardsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Children's Medical Center, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
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38
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Zaidi SK, Fritz AJ, Tracy KM, Gordon JA, Tye CE, Boyd J, Van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Nuclear organization mediates cancer-compromised genetic and epigenetic control. Adv Biol Regul 2018; 69:1-10. [PMID: 29759441 PMCID: PMC6102062 DOI: 10.1016/j.jbior.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/13/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022]
Abstract
Nuclear organization is functionally linked to genetic and epigenetic regulation of gene expression for biological control and is modified in cancer. Nuclear organization supports cell growth and phenotypic properties of normal and cancer cells by facilitating physiologically responsive interactions of chromosomes, genes and regulatory complexes at dynamic three-dimensional microenvironments. We will review nuclear structure/function relationships that include: 1. Epigenetic bookmarking of genes by phenotypic transcription factors to control fidelity and plasticity of gene expression as cells enter and exit mitosis; 2. Contributions of chromatin remodeling to breast cancer nuclear morphology, metabolism and effectiveness of chemotherapy; 3. Relationships between fidelity of nuclear organization and metastasis of breast cancer to bone; 4. Dynamic modifications of higher-order inter- and intra-chromosomal interactions in breast cancer cells; 5. Coordinate control of cell growth and phenotype by tissue-specific transcription factors; 6. Oncofetal epigenetic control by bivalent histone modifications that are functionally related to sustaining the stem cell phenotype; and 7. Noncoding RNA-mediated regulation in the onset and progression of breast cancer. The discovery of components to nuclear organization that are functionally related to cancer and compromise gene expression have the potential for translation to innovative cancer diagnosis and targeted therapy.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Jonathan A Gordon
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Joseph Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andre J Van Wijnen
- Departments of Orthopedic Surgery, Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Jeffrey A Nickerson
- Department of Pediatrics, UMass Medical School, Worcester, MA, United States
| | - Antony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, United States
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
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39
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Zaidi SK, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Mitotic Gene Bookmarking: An Epigenetic Program to Maintain Normal and Cancer Phenotypes. Mol Cancer Res 2018; 16:1617-1624. [PMID: 30002192 DOI: 10.1158/1541-7786.mcr-18-0415] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 06/22/2018] [Indexed: 01/06/2023]
Abstract
Reconfiguration of nuclear structure and function during mitosis presents a significant challenge to resume the next cell cycle in the progeny cells without compromising structural and functional identity of the cells. Equally important is the requirement for cancer cells to retain the transformed phenotype, that is, unrestricted proliferative potential, suppression of cell phenotype, and activation of oncogenic pathways. Mitotic gene bookmarking retention of key regulatory proteins that include sequence-specific transcription factors, chromatin-modifying factors, and components of RNA Pol (RNAP) I and II regulatory machineries at gene loci on mitotic chromosomes plays key roles in coordinate control of cell phenotype, growth, and proliferation postmitotically. There is growing recognition that three distinct protein types, mechanistically, play obligatory roles in mitotic gene bookmarking: (i) Retention of phenotypic transcription factors on mitotic chromosomes is essential to sustain lineage commitment; (ii) Select chromatin modifiers and posttranslational histone modifications/variants retain competency of mitotic chromatin for gene reactivation as cells exit mitosis; and (iii) Functional components of RNAP I and II transcription complexes (e.g., UBF and TBP, respectively) are retained on genes poised for reactivation immediately following mitosis. Importantly, recent findings have identified oncogenes that are associated with target genes on mitotic chromosomes in cancer cells. The current review proposes that mitotic gene bookmarking is an extensively utilized epigenetic mechanism for stringent control of proliferation and identity in normal cells and hypothesizes that bookmarking plays a pivotal role in maintenance of tumor phenotypes, that is, unrestricted proliferation and compromised control of differentiation. Mol Cancer Res; 16(11); 1617-24. ©2018 AACR.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Jeffrey A Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anthony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont.
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40
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Liu Y, Pelham-Webb B, Di Giammartino DC, Li J, Kim D, Kita K, Saiz N, Garg V, Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E. Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells. Cell Rep 2018; 19:1283-1293. [PMID: 28514649 DOI: 10.1016/j.celrep.2017.04.067] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/17/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022] Open
Abstract
During mitosis, transcription is halted and many chromatin features are lost, posing a challenge for the continuity of cell identity, particularly in fast cycling stem cells, which constantly balance self-renewal with differentiation. Here we show that, in pluripotent stem cells, certain histone marks and stem cell regulators remain associated with specific genomic regions of mitotic chromatin, a phenomenon known as mitotic bookmarking. Enhancers of stem cell-related genes are bookmarked by both H3K27ac and the master regulators OCT4, SOX2, and KLF4, while promoters of housekeeping genes retain high levels of mitotic H3K27ac in a cell-type invariant manner. Temporal degradation of OCT4 during mitotic exit compromises its ability both to maintain and induce pluripotency, suggesting that its regulatory function partly depends on its bookmarking activity. Together, our data document a widespread yet specific bookmarking by histone modifications and transcription factors promoting faithful and efficient propagation of stemness after cell division.
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Affiliation(s)
- Yiyuan Liu
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bobbie Pelham-Webb
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Dafne Campigli Di Giammartino
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jiexi Li
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Daleum Kim
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Katsuhiro Kita
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nestor Saiz
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ashley Doane
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Paraskevi Giannakakou
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Effie Apostolou
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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Shao Z, Yao C, Khodadadi-Jamayran A, Xu W, Townes TM, Crowley MR, Hu K. Reprogramming by De-bookmarking the Somatic Transcriptional Program through Targeting of BET Bromodomains. Cell Rep 2018; 16:3138-3145. [PMID: 27653680 DOI: 10.1016/j.celrep.2016.08.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/19/2016] [Accepted: 08/18/2016] [Indexed: 01/11/2023] Open
Abstract
One critical event in reprogramming to pluripotency is erasure of the somatic transcriptional program of starting cells. Here, we present the proof of principle of a strategy for reprogramming to pluripotency facilitated by small molecules that interfere with the somatic transcriptional memory. We show that mild chemical targeting of the acetyllysine-binding pockets of the BET bromodomains, the transcriptional bookmarking domains, robustly enhances reprogramming. Furthermore, we show that chemical targeting of the transcriptional bookmarking BET bromodomains downregulates or turns off the expression of somatic genes in both naive and reprogramming fibroblasts. Chemical blocking of the BET bromodomains also results in loss of fibroblast morphology early in reprogramming. We therefore experimentally demonstrate that cell fate conversion can be achieved by chemically targeting the transcriptional bookmarking BET bromodomains responsible for transcriptional memory.
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Affiliation(s)
- Zhicheng Shao
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Chunping Yao
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA; Department of Radiation Oncology, Shandong Cancer Hospital, Shandong University, Jinan, Shandong 250117, China
| | - Alireza Khodadadi-Jamayran
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Weihua Xu
- Longyan University, Fujian 364012, China
| | - Tim M Townes
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Michael R Crowley
- Howell and Elizabeth Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Kejin Hu
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA.
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Abstract
Multiple mechanisms of epigenetic control that include DNA methylation, histone modification, noncoding RNAs, and mitotic gene bookmarking play pivotal roles in stringent gene regulation during lineage commitment and maintenance. Experimental evidence indicates that bivalent chromatin domains, i.e., genome regions that are marked by both H3K4me3 (activating) and H3K27me3 (repressive) histone modifications, are a key property of pluripotent stem cells. Bivalency of developmental genes during the G1 phase of the pluripotent stem cell cycle contributes to cell fate decisions. Recently, some cancer types have been shown to exhibit partial recapitulation of bivalent chromatin modifications that are lost along with pluripotency, suggesting a mechanism by which cancer cells reacquire properties that are characteristic of undifferentiated, multipotent cells. This bivalent epigenetic control of oncofetal gene expression in cancer cells may offer novel insights into the onset and progression of cancer and may provide specific and selective options for diagnosis as well as for therapeutic intervention.
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44
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Mitotic Gene Bookmarking: An Epigenetic Mechanism for Coordination of Lineage Commitment, Cell Identity and Cell Growth. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:95-102. [PMID: 28299653 DOI: 10.1007/978-981-10-3233-2_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Epigenetic control of gene expression contributes to dynamic responsiveness of cellular processes that include cell cycle, cell growth and differentiation. Mitotic gene bookmarking, retention of sequence-specific transcription factors at target gene loci, including the RUNX regulatory proteins, provide a novel dimension to epigenetic regulation that sustains cellular identity in progeny cells following cell division. Runx transcription factor retention during mitosis coordinates physiological control of cell growth and differentiation in a broad spectrum of biological conditions, and is associated with compromised gene expression in pathologies that include cancer.
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45
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Dudakovic A, van Wijnen AJ. Epigenetic Control of Osteoblast Differentiation by Enhancer of Zeste Homolog 2 (EZH2). ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40610-017-0064-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Andrews FH, Strahl BD, Kutateladze TG. Insights into newly discovered marks and readers of epigenetic information. Nat Chem Biol 2017; 12:662-8. [PMID: 27538025 DOI: 10.1038/nchembio.2149] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023]
Abstract
The field of chromatin biology has been advancing at an accelerated pace. Recent discoveries of previously uncharacterized sites and types of post-translational modifications (PTMs) and the identification of new sets of proteins responsible for the deposition, removal, and reading of these marks continue raising the complexity of an already exceedingly complicated biological phenomenon. In this Perspective article we examine the biological importance of new types and sites of histone PTMs and summarize the molecular mechanisms of chromatin engagement by newly discovered epigenetic readers. We also highlight the imperative role of structural insights in understanding PTM-reader interactions and discuss future directions to enhance the knowledge of PTM readout.
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Affiliation(s)
- Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, the University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
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47
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Semik E, Ząbek T, Gurgul A, Fornal A, Szmatoła T, Pawlina K, Wnuk M, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M. Comparative analysis of DNA methylation patterns of equine sarcoid and healthy skin samples. Vet Comp Oncol 2017; 16:37-46. [DOI: 10.1111/vco.12308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/10/2017] [Accepted: 01/30/2017] [Indexed: 12/21/2022]
Affiliation(s)
- E. Semik
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - T. Ząbek
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - A. Gurgul
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - A. Fornal
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - T. Szmatoła
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - K. Pawlina
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - M. Wnuk
- Department of Genetics, Centre of Applied Biotechnology and Basic Sciences; University of Rzeszow; Rzeszow Poland
| | - J. Klukowska-Rötzler
- Division of Pedriatric Hematology/Oncology, Department of Clinical Research; University of Bern; Bern Switzerland
- Swiss Institute of Equine Medicine ISME, Department of Clinical Veterinary Medicine, Vetsuisse Faculty; University of Bern and Agroscope; Bern Switzerland
| | - C. Koch
- Swiss Institute of Equine Medicine ISME, Department of Clinical Veterinary Medicine, Vetsuisse Faculty; University of Bern and Agroscope; Bern Switzerland
| | - K. Mählmann
- Swiss Institute of Equine Medicine ISME, Department of Clinical Veterinary Medicine, Vetsuisse Faculty; University of Bern and Agroscope; Bern Switzerland
- Equine Clinic, General Surgery and Radiology; Freie Universität Berlin; Berlin Germany
| | - M. Bugno-Poniewierska
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
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48
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Dudakovic A, Gluscevic M, Paradise CR, Dudakovic H, Khani F, Thaler R, Ahmed FS, Li X, Dietz AB, Stein GS, Montecino MA, Deyle DR, Westendorf JJ, van Wijnen AJ. Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing. Gene 2017; 609:28-37. [PMID: 28132772 DOI: 10.1016/j.gene.2017.01.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/20/2017] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms control phenotypic commitment of mesenchymal stromal/stem cells (MSCs) into osteogenic, chondrogenic or adipogenic lineages. To investigate enzymes and chromatin binding proteins controlling the epigenome, we developed a hybrid expression screening strategy that combines semi-automated real-time qPCR (RT-qPCR), next generation RNA sequencing (RNA-seq), and a novel data management application (FileMerge). This strategy was used to interrogate expression of a large cohort (n>300) of human epigenetic regulators (EpiRegs) that generate, interpret and/or edit the histone code. We find that EpiRegs with similar enzymatic functions are variably expressed and specific isoforms dominate over others in human MSCs. This principle is exemplified by analysis of key histone acetyl transferases (HATs) and deacetylases (HDACs), H3 lysine methyltransferases (e.g., EHMTs) and demethylases (KDMs), as well as bromodomain (BRDs) and chromobox (CBX) proteins. Our results show gender-specific expression of H3 lysine 9 [H3K9] demethylases (e.g., KDM5D and UTY) as expected and upregulation of distinct EpiRegs (n>30) during osteogenic differentiation of MSCs (e.g., HDAC5 and HDAC7). The functional significance of HDACs in osteogenic lineage commitment of MSCs was functionally validated using panobinostat (LBH-589). This pan-deacetylase inhibitor suppresses osteoblastic differentiation as evidenced by reductions in bone-specific mRNA markers (e.g., ALPL), alkaline phosphatase activity and calcium deposition (i.e., Alizarin Red staining). Thus, our RT-qPCR platform identifies candidate EpiRegs by expression screening, predicts biological outcomes of their corresponding inhibitors, and enables manipulation of the human epigenome using molecular or pharmacological approaches to control stem cell differentiation.
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Affiliation(s)
- Amel Dudakovic
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Farzaneh Khani
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Roman Thaler
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Farah S Ahmed
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Xiaodong Li
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Allan B Dietz
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont Medical School, Burlington, VT, USA
| | - Martin A Montecino
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | | | - Jennifer J Westendorf
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA; Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Andre J van Wijnen
- Departments of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA; Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA; Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
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49
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The Role of Epigenetic Regulation in Transcriptional Memory in the Immune System. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:43-69. [DOI: 10.1016/bs.apcsb.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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50
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Deluz C, Friman ET, Strebinger D, Benke A, Raccaud M, Callegari A, Leleu M, Manley S, Suter DM. A role for mitotic bookmarking of SOX2 in pluripotency and differentiation. Genes Dev 2016; 30:2538-2550. [PMID: 27920086 PMCID: PMC5159668 DOI: 10.1101/gad.289256.116] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022]
Abstract
Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unexplored in most stem cell types, and its functional relevance for cell fate decisions remains unclear. Here we screened for mitotic chromosome binding within the pluripotency network of embryonic stem (ES) cells and show that SOX2 and OCT4 remain bound to mitotic chromatin through their respective DNA-binding domains. Dynamic characterization using photobleaching-based methods and single-molecule imaging revealed quantitatively similar specific DNA interactions, but different nonspecific DNA interactions, of SOX2 and OCT4 with mitotic chromatin. Using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) to assess the genome-wide distribution of SOX2 on mitotic chromatin, we demonstrate the bookmarking activity of SOX2 on a small set of genes. Finally, we investigated the function of SOX2 mitotic bookmarking in cell fate decisions and show that its absence at the M-G1 transition impairs pluripotency maintenance and abrogates its ability to induce neuroectodermal differentiation but does not affect reprogramming efficiency toward induced pluripotent stem cells. Our study demonstrates the mitotic bookmarking property of SOX2 and reveals its functional importance in pluripotency maintenance and ES cell differentiation.
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Affiliation(s)
- Cédric Deluz
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Elias T Friman
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Daniel Strebinger
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Alexander Benke
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.,Institute of Physics, Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mahé Raccaud
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Andrea Callegari
- Institute of Physics, Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marion Leleu
- Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Suliana Manley
- Institute of Physics, Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - David M Suter
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
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