1
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Zhang T, Liu S, Durojaye O, Xiong F, Fang Z, Ullah T, Fu C, Sun B, Jiang H, Xia P, Wang Z, Yao X, Liu X. Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation. Cell Rep 2024; 43:114739. [PMID: 39276350 DOI: 10.1016/j.celrep.2024.114739] [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: 01/23/2024] [Revised: 06/10/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
FOXA1 serves as a crucial pioneer transcription factor during developmental processes and plays a pivotal role as a mitotic bookmarking factor to perpetuate gene expression profiles and maintain cellular identity. During mitosis, the majority of FOXA1 dissociates from specific DNA binding sites and redistributes to non-specific binding sites; however, the regulatory mechanisms governing molecular dynamics and activity of FOXA1 remain elusive. Here, we show that mitotic kinase Aurora B specifies the different DNA binding modes of FOXA1 and guides FOXA1 biomolecular condensation in mitosis. Mechanistically, Aurora B kinase phosphorylates FOXA1 at Serine 221 (S221) to liberate the specific, but not the non-specific, DNA binding. Interestingly, the phosphorylation of S221 attenuates the FOXA1 condensation that requires specific DNA binding. Importantly, perturbation of the dynamic phosphorylation impairs accurate gene reactivation and cell proliferation, suggesting that reversible mitotic protein phosphorylation emerges as a fundamental mechanism for the spatiotemporal control of mitotic bookmarking.
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Affiliation(s)
- Ting Zhang
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Shuaiyu Liu
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, University of Science and Technology of China, Hefei 230027, China
| | - Olanrewaju Durojaye
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Fangyuan Xiong
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230027, China
| | - Zhiyou Fang
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230027, China
| | - Tahir Ullah
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Chuanhai Fu
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, University of Science and Technology of China, Hefei 230027, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Hao Jiang
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Xia
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Institute of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhikai Wang
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, University of Science and Technology of China, Hefei 230027, China.
| | - Xuebiao Yao
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, University of Science and Technology of China, Hefei 230027, China.
| | - Xing Liu
- MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China; Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, University of Science and Technology of China, Hefei 230027, China.
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2
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Brislinger-Engelhardt MM, Lorenz F, Haas M, Bowden S, Tasca A, Kreutz C, Walentek P. Temporal Notch signaling regulates mucociliary cell fates through Hes-mediated competitive de-repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528675. [PMID: 36824900 PMCID: PMC9949065 DOI: 10.1101/2023.02.15.528675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Tissue functions are determined by the types and ratios of cells present, but little is known about self-organizing principles establishing correct cell type compositions. Mucociliary airway clearance relies on the correct balance between secretory and ciliated cells, which is regulated by Notch signaling across mucociliary systems. Using the airway-like Xenopus epidermis, we investigate how cell fates depend on signaling, how signaling levels are controlled, and how Hes transcription factors regulate cell fates. We show that four mucociliary cell types each require different Notch levels and that their specification is initiated sequentially by a temporal Notch gradient. We describe a novel role for Foxi1 in the generation of Delta-expressing multipotent progenitors through Hes7.1. Hes7.1 is a weak repressor of mucociliary genes and overcomes maternal repression by the strong repressor Hes2 to initiate mucociliary development. Increasing Notch signaling then inhibits Hes7.1 and activates first Hes4, then Hes5.10, which selectively repress cell fates. We have uncovered a self-organizing mechanism of mucociliary cell type composition by competitive de-repression of cell fates by a set of differentially acting repressors. Furthermore, we present an in silico model of this process with predictive abilities.
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Affiliation(s)
- Magdalena Maria Brislinger-Engelhardt
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM Spemann Graduate School for Biology and Medicine, University of Freiburg, Albertstrasse 19A, 79104 Freiburg, Germany
| | - Fabian Lorenz
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- IMBI Institute of Medical Biometry and Statistics, Institute of Medicine and Medical Center Freiburg, Stefan-Meier Strasse 26, 79104 Freiburg, Germany
| | - Maximilian Haas
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
- SGBM Spemann Graduate School for Biology and Medicine, University of Freiburg, Albertstrasse 19A, 79104 Freiburg, Germany
| | - Sarah Bowden
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- IMPRS-IEM International Max Planck Research School of Immunobiology, Epigenetics and Metabolism, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Alexia Tasca
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Clemens Kreutz
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- IMBI Institute of Medical Biometry and Statistics, Institute of Medicine and Medical Center Freiburg, Stefan-Meier Strasse 26, 79104 Freiburg, Germany
| | - Peter Walentek
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM Spemann Graduate School for Biology and Medicine, University of Freiburg, Albertstrasse 19A, 79104 Freiburg, Germany
- IMPRS-IEM International Max Planck Research School of Immunobiology, Epigenetics and Metabolism, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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3
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Castaneda M, den Hollander P, Mani SA. Forkhead Box Transcription Factors: Double-Edged Swords in Cancer. Cancer Res 2022; 82:2057-2065. [PMID: 35315926 PMCID: PMC9258984 DOI: 10.1158/0008-5472.can-21-3371] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/12/2022] [Accepted: 03/14/2022] [Indexed: 01/07/2023]
Abstract
A plethora of treatment options exist for cancer therapeutics, but many are limited by side effects and either intrinsic or acquired resistance. The need for more effective targeted cancer treatment has led to the focus on forkhead box (FOX) transcription factors as possible drug targets. Forkhead factors such as FOXA1 and FOXM1 are involved in hormone regulation, immune system modulation, and disease progression through their regulation of the epithelial-mesenchymal transition. Forkhead factors can influence cancer development, progression, metastasis, and drug resistance. In this review, we discuss the various roles of forkhead factors in biological processes that support cancer as well as their function as pioneering factors and their potential as targetable transcription factors in the fight against cancer.
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Affiliation(s)
- Maria Castaneda
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Petra den Hollander
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sendurai A. Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Corresponding Author: Sendurai A. Mani, Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Suite 910, Houston, TX 77030-3304. Phone: 713-792-9638; E-mail:
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4
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Dai S, Qu L, Li J, Chen Y. Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations. Nucleic Acids Res 2021; 49:10235-10249. [PMID: 34551426 PMCID: PMC8501956 DOI: 10.1093/nar/gkab807] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 01/12/2023] Open
Abstract
Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, >30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Linzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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5
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Sunkel BD, Wang M, LaHaye S, Kelly BJ, Fitch JR, Barr FG, White P, Stanton BZ. Evidence of pioneer factor activity of an oncogenic fusion transcription factor. iScience 2021; 24:102867. [PMID: 34386729 PMCID: PMC8346656 DOI: 10.1016/j.isci.2021.102867] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
Recent characterizations of pioneer transcription factors provide insights into their structures and patterns of chromatin recognition associated with their roles in cell fate commitment and transformation. Intersecting with these basic science concepts, identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. This study defines the cellular and chromatin localization of PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a ChIP-seq workflow with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal insights into inactive chromatin localization of PAX3-FOXO1. Taken together, our studies are consistent with pioneer function for a driver oncoprotein in RMS, with repressed chromatin binding and nucleosome-motif targeting. The fusion oncoprotein PAX3-FOXO1 binds to both active and repressed chromatin PAX3-FOXO1-binding sites are adjacent to H3K9me3 domains PAX3-FOXO1 engages partial DNA motifs at early timepoints PAX3-FOXO1 can bind stably to inaccessible chromatin without inducing accessibility
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Affiliation(s)
- Benjamin D Sunkel
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Meng Wang
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Frederic G Barr
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Benjamin Z Stanton
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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6
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Lee DI, Roy S. GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization. Genome Biol 2021; 22:164. [PMID: 34034791 PMCID: PMC8152090 DOI: 10.1186/s13059-021-02378-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
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Affiliation(s)
- Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, 53715, USA
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, 53715, USA. .,Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, 53715, USA.
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7
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Cook D, Long S, Stanton J, Cusick P, Lawrimore C, Yeh E, Grant S, Bloom K. Behavior of dicentric chromosomes in budding yeast. PLoS Genet 2021; 17:e1009442. [PMID: 33735169 PMCID: PMC8009378 DOI: 10.1371/journal.pgen.1009442] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 03/30/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
DNA double-strand breaks arise in vivo when a dicentric chromosome (two centromeres on one chromosome) goes through mitosis with the two centromeres attached to opposite spindle pole bodies. Repair of the DSBs generates phenotypic diversity due to the range of monocentric derivative chromosomes that arise. To explore whether DSBs may be differentially repaired as a function of their spatial position in the chromosome, we have examined the structure of monocentric derivative chromosomes from cells containing a suite of dicentric chromosomes in which the distance between the two centromeres ranges from 6.5 kb to 57.7 kb. Two major classes of repair products, homology-based (homologous recombination (HR) and single-strand annealing (SSA)) and end-joining (non-homologous (NHEJ) and micro-homology mediated (MMEJ)) were identified. The distribution of repair products varies as a function of distance between the two centromeres. Genetic dependencies on double strand break repair (Rad52), DNA ligase (Lif1), and S phase checkpoint (Mrc1) are indicative of distinct repair pathway choices for DNA breaks in the pericentromeric chromatin versus the arms. A challenge in chromosome biology is to integrate the linear code with spatial organization and chromosome dynamics within the nucleus. The major sub-division of function in the nucleus is the nucleolus, the site of ribosomal RNA synthesis. We report that the pericentromere DNA surrounding the centromere is another region of confined biochemistry. We have found that chromosome breaks between two centromeres that both lie within the pericentromeric region of the chromosomes are repaired via pathways that do not rely on sequence homology (MMEJ or NHEJ). Chromosome breaks in dicentric chromosomes whose centromeres are separated by > 20 kb are repaired via pathways that rely mainly on sequence homology (HR, SSA). The repair of breaks in the pericentromere versus breaks in the arms are differentially dependent on Rad52, Lif1, and Mrc1, further indicative of spatial control over DNA repair pathways.
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Affiliation(s)
- Diana Cook
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sarah Long
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John Stanton
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Patrick Cusick
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Colleen Lawrimore
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elaine Yeh
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sarah Grant
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kerry Bloom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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8
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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9
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Vaquero-Sedas MI, Vega-Palas MA. Assessing the Epigenetic Status of Human Telomeres. Cells 2019; 8:cells8091050. [PMID: 31500249 PMCID: PMC6770363 DOI: 10.3390/cells8091050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/29/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
The epigenetic modifications of human telomeres play a relevant role in telomere functions and cell proliferation. Therefore, their study is becoming an issue of major interest. These epigenetic modifications are usually analyzed by microscopy or by chromatin immunoprecipitation (ChIP). However, these analyses could be challenged by subtelomeres and/or interstitial telomeric sequences (ITSs). Whereas telomeres and subtelomeres cannot be differentiated by microscopy techniques, telomeres and ITSs might not be differentiated in ChIP analyses. In addition, ChIP analyses of telomeres should be properly controlled. Hence, studies focusing on the epigenetic features of human telomeres have to be carefully designed and interpreted. Here, we present a comprehensive discussion on how subtelomeres and ITSs might influence studies of human telomere epigenetics. We specially focus on the influence of ITSs and some experimental aspects of the ChIP technique on ChIP analyses. In addition, we propose a specific pipeline to accurately perform these studies. This pipeline is very simple and can be applied to a wide variety of cells, including cancer cells. Since the epigenetic status of telomeres could influence cancer cells proliferation, this pipeline might help design precise epigenetic treatments for specific cancer types.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
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10
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Cubiles MD, Barroso S, Vaquero-Sedas MI, Enguix A, Aguilera A, Vega-Palas MA. Epigenetic features of human telomeres. Nucleic Acids Res 2019; 46:2347-2355. [PMID: 29361030 PMCID: PMC5861411 DOI: 10.1093/nar/gky006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/09/2018] [Indexed: 01/02/2023] Open
Abstract
Although subtelomeric regions in humans are heterochromatic, the epigenetic nature of human telomeres remains controversial. This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. In addition, different human cell lines might carry diverse epigenetic marks at telomeres. We have developed a reliable procedure to study the chromatin structure of human telomeres independently of subtelomeres and ITSs. This procedure is based on the statistical analysis of multiple ChIP-seq experiments. We have found that human telomeres are not enriched in the heterochromatic H3K9me3 mark in most of the common laboratory cell lines, including embryonic stem cells. Instead, they are labeled with H4K20me1 and H3K27ac, which might be established by p300. These results together with previously published data argue that subtelomeric heterochromatin might control human telomere functions. Interestingly, U2OS cells that exhibit alternative lengthening of telomeres have heterochromatic levels of H3K9me3 in their telomeres.
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Affiliation(s)
- María D Cubiles
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, 41012 Seville, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avd. Américo Vespucio s/n, 41092 Seville, Spain
| | - María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Avd. Américo Vespucio n° 49, 41092 Seville, Spain
| | - Alicia Enguix
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avd. Américo Vespucio s/n, 41092 Seville, Spain
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Avd. Américo Vespucio n° 49, 41092 Seville, Spain
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11
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Festuccia N, Owens N, Papadopoulou T, Gonzalez I, Tachtsidi A, Vandoermel-Pournin S, Gallego E, Gutierrez N, Dubois A, Cohen-Tannoudji M, Navarro P. Transcription factor activity and nucleosome organization in mitosis. Genome Res 2019; 29:250-260. [PMID: 30655337 PMCID: PMC6360816 DOI: 10.1101/gr.243048.118] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/05/2018] [Indexed: 12/23/2022]
Abstract
Mitotic bookmarking transcription factors (BFs) maintain the capacity to bind to their targets during mitosis, despite major rearrangements of the chromatin. While they were thought to propagate gene regulatory information through mitosis by statically occupying their DNA targets, it has recently become clear that BFs are highly dynamic in mitotic cells. This represents both a technical and a conceptual challenge to study and understand the function of BFs: First, formaldehyde has been suggested to be unable to efficiently capture these transient interactions, leading to profound contradictions in the literature; and second, if BFs are not permanently bound to their targets during mitosis, it becomes unclear how they convey regulatory information to daughter cells. Here, comparing formaldehyde to alternative fixatives we clarify the nature of the chromosomal association of previously proposed BFs in embryonic stem cells: While ESRRB can be considered as a canonical BF that binds at selected regulatory regions in mitosis, SOX2 and POU5F1 (also known as OCT4) establish DNA sequence-independent interactions with the mitotic chromosomes, either throughout the chromosomal arms (SOX2) or at pericentromeric regions (POU5F1). Moreover, we show that ordered nucleosomal arrays are retained during mitosis at ESRRB bookmarked sites, whereas regions losing transcription factor binding display a profound loss of order. By maintaining nucleosome positioning during mitosis, ESRRB might ensure the rapid post-mitotic re-establishment of functional regulatory complexes at selected enhancers and promoters. Our results provide a mechanistic framework that reconciles dynamic mitotic binding with the transmission of gene regulatory information across cell division.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Nick Owens
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Thaleia Papadopoulou
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Alexandra Tachtsidi
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer.,Sorbonne Université, Collège Doctoral, F-75005 Paris, France
| | - Sandrine Vandoermel-Pournin
- Mouse Functional Genetics, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 75015 Paris, France
| | - Elena Gallego
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Nancy Gutierrez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Agnès Dubois
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Michel Cohen-Tannoudji
- Mouse Functional Genetics, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
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12
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Palozola KC, Lerner J, Zaret KS. A changing paradigm of transcriptional memory propagation through mitosis. Nat Rev Mol Cell Biol 2019; 20:55-64. [PMID: 30420736 PMCID: PMC6557398 DOI: 10.1038/s41580-018-0077-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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Affiliation(s)
- Katherine C Palozola
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Jonathan Lerner
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA.
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13
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Cui X, Pertile R, Eyles DW. The vitamin D receptor (VDR) binds to the nuclear matrix via its hinge domain: A potential mechanism for the reduction in VDR mediated transcription in mitotic cells. Mol Cell Endocrinol 2018; 472:18-25. [PMID: 29183808 DOI: 10.1016/j.mce.2017.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/17/2022]
Abstract
Vitamin D is best known for its regulation of calcium homeostasis. Vitamin D exerts its genomic actions via the vitamin D receptor (VDR). As a member of the superfamily of nuclear receptors (NR), the VDR is primarily located within the nucleus of non-dividing cells. We show here that the VDR relocates from the nucleus into the cytoplasm across all stages of cell division in CHO cells. Furthermore, we show that the VDR is transcriptionally inert during cell division. In addition, 1α, 25 dihydroxyvitamin D (1,25(OH)2D3) promotes VDR binding to the nuclear matrix. Finally, we assessed the structural nature of VDR binding to the nuclear matrix. Mutation of the hinge domain reduced VDR's ability to bind to the nuclear matrix and to initiate transcription in response to 1,25(OH)2D3. Taken together, our data suggest that the association between the VDR and the nuclear matrix accounts for the apparent cytosolic distribution as the matrix disperses within the cytoplasm when cells divide. This may also explain the dramatic reduction in VDR mediated transcription during cell division. Our data also confirm that similar to other NRs, the hinge domain of the VDR is responsible for this association.
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Affiliation(s)
- Xiaoying Cui
- Queensland Brain Institute, University of Queensland, Qld 4072, Australia
| | - Renata Pertile
- Queensland Brain Institute, University of Queensland, Qld 4072, Australia
| | - Darryl W Eyles
- Queensland Brain Institute, University of Queensland, Qld 4072, Australia; Queensland Centre for Mental Health Research, Wacol, Qld 4076, Australia.
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14
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Novais-Cruz M, Alba Abad M, van IJcken WFJ, Galjart N, Jeyaprakash AA, Maiato H, Ferrás C. Mitotic progression, arrest, exit or death relies on centromere structural integrity, rather than de novo transcription. eLife 2018; 7:36898. [PMID: 30080136 PMCID: PMC6128689 DOI: 10.7554/elife.36898] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/03/2018] [Indexed: 12/30/2022] Open
Abstract
Recent studies have challenged the prevailing dogma that transcription is repressed during mitosis. Transcription was also proposed to sustain a robust spindle assembly checkpoint (SAC) response. Here, we used live-cell imaging of human cells, RNA-seq and qPCR to investigate the requirement for de novo transcription during mitosis. Under conditions of persistently unattached kinetochores, transcription inhibition with actinomycin D, or treatment with other DNA-intercalating drugs, delocalized the chromosomal passenger complex (CPC) protein Aurora B from centromeres, compromising SAC signaling and cell fate. However, we were unable to detect significant changes in mitotic transcript levels. Moreover, inhibition of transcription independently of DNA intercalation had no effect on Aurora B centromeric localization, SAC response, mitotic progression, exit or death. Mechanistically, we show that DNA intercalating agents reduce the interaction of the CPC with nucleosomes. Thus, mitotic progression, arrest, exit or death is determined by centromere structural integrity, rather than de novo transcription.
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Affiliation(s)
- Marco Novais-Cruz
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
| | - Maria Alba Abad
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Niels Galjart
- Department of Cell BiologyErasmus Medical CenterRotterdamNetherlands
| | - A Arockia Jeyaprakash
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | - Helder Maiato
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
- Cell Division Group, Experimental Biology Unit, Department of Biomedicine, Faculdade de MedicinaUniversidade do PortoPortoPortugal
| | - Cristina Ferrás
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
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15
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Rana M, Dash AK, Ponnusamy K, Tyagi RK. Nuclear localization signal region in nuclear receptor PXR governs the receptor association with mitotic chromatin. Chromosome Res 2018; 26:255-276. [DOI: 10.1007/s10577-018-9583-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 12/17/2022]
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16
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Zhang H, Wen W, Yan J. Application of immunohistochemistry technique in hydrobiological studies. AQUACULTURE AND FISHERIES 2017. [DOI: 10.1016/j.aaf.2017.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Grebbin BM, Schulte D. PBX1 as Pioneer Factor: A Case Still Open. Front Cell Dev Biol 2017; 5:9. [PMID: 28261581 PMCID: PMC5306212 DOI: 10.3389/fcell.2017.00009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Pioneer factors are proteins that can recognize their target sites in barely accessible chromatin and initiate a cascade of events that allows for later transcriptional activation of the respective genes. Pioneer factors are therefore particularly well-suited to initiate cell fate changes. To date, only a small number of pioneer factors have been identified and studied in depth, such as FOXD3/FOXA1, OCT4, or SOX2. Interestingly, several recent studies reported that the PBC transcription factor PBX1 can access transcriptionally inactive genomic loci. Here, we summarize the evidence linking PBX1 with transcriptional pioneer functions, suggest potential mechanisms involved and discuss open questions to be resolved.
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Affiliation(s)
- Britta M Grebbin
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, J. W. Goethe University Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, J. W. Goethe University Frankfurt, Germany
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18
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Tissue Extract Fractions from Starfish Undergoing Regeneration Promote Wound Healing and Lower Jaw Blastema Regeneration of Zebrafish. Sci Rep 2016; 6:38693. [PMID: 27974833 PMCID: PMC5156902 DOI: 10.1038/srep38693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/11/2016] [Indexed: 12/23/2022] Open
Abstract
Natural bioactive materials provide an excellent pool of molecules for regenerative therapy. In the present study, we amputate portions of the arms of Archaster typicus starfish, extract and separate the active biomaterials, and compare the effects of each fraction on in vitro wound healing and in vivo lower jaw regeneration of zebrafish. Compared with crude extract, normal hexane fractions (NHFs) have a remarkable effect on cellular proliferation and collective migration, and exhibit fibroblast-like morphology, while methanol-water fractions (MWFs) increase cell size, cell-cell adhesion, and cell death. Relative to moderate mitochondrialand lysosomal aggregation in NHFs-cultured cells, MWFs-cultured cells contain more and bigger lysosomal accumulations and clump detachment. The in vivo zebrafish lower jaw regeneration model reveals that NHFs enhance blastema formation and vasculogenesis, while MWFs inhibit fibrogenesis and induce cellular transformation. Gene expression analyses indicate that NHFs and MWFs separately activate blastema-characteristic genes as well as those genes-related to autophagy, proteasome, and apoptosis either during cell scratch healing or ganciclovir-induced apoptosis. Our results suggest that bioactive compounds from NHFs and MWFs could induce blastema formation and remodeling, respectively, and prevent tissue overgrowth.
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19
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Singh S, Groves AK. The molecular basis of craniofacial placode development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:363-76. [PMID: 26952139 DOI: 10.1002/wdev.226] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/22/2015] [Accepted: 12/27/2015] [Indexed: 12/20/2022]
Abstract
The sensory organs of the vertebrate head originate from simple ectodermal structures known as cranial placodes. All cranial placodes derive from a common domain adjacent to the neural plate, the preplacodal region, which is induced at the border of neural and non-neural ectoderm during gastrulation. Induction and specification of the preplacodal region is regulated by the fibroblast growth factor, bone morphogenetic protein, WNT, and retinoic acid signaling pathways, and characterized by expression of the EYA and SIX family of transcriptional regulators. Once the preplacodal region is specified, different combinations of local signaling molecules and placode-specific transcription factors, including competence factors, promote the induction of individual cranial placodes along the neural axis of the head region. In this review, we summarize the steps of cranial placode development and discuss the roles of the main signaling molecules and transcription factors that regulate these steps during placode induction, specification, and development. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Andrew K Groves
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
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20
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Birol O, Ohyama T, Edlund RK, Drakou K, Georgiades P, Groves AK. The mouse Foxi3 transcription factor is necessary for the development of posterior placodes. Dev Biol 2015; 409:139-151. [PMID: 26550799 DOI: 10.1016/j.ydbio.2015.09.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 02/01/2023]
Abstract
The inner ear develops from the otic placode, one of the cranial placodes that arise from a region of ectoderm adjacent to the anterior neural plate called the pre-placodal domain. We have identified a Forkhead family transcription factor, Foxi3, that is expressed in the pre-placodal domain and down-regulated when the otic placode is induced. We now show that Foxi3 mutant mice do not form otic placodes as evidenced by expression changes in early molecular markers and the lack of thickened placodal ectoderm, an otic cup or otocyst. Some preplacodal genes downstream of Foxi3-Gata3, Six1 and Eya1-are not expressed in the ectoderm of Foxi3 mutant mice, and the ectoderm exhibits signs of increased apoptosis. We also show that Fgf signals from the hindbrain and cranial mesoderm, which are necessary for otic placode induction, are received by pre-placodal ectoderm in Foxi3 mutants, but do not initiate otic induction. Finally, we show that the epibranchial placodes that develop in close proximity to the otic placode and the mandibular division of the trigeminal ganglion are missing in Foxi3 mutants. Our data suggest that Foxi3 is necessary to prime pre-placodal ectoderm for the correct interpretation of inductive signals for the otic and epibranchial placodes.
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Affiliation(s)
- Onur Birol
- Program in Developmental Biology, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Takahiro Ohyama
- USC Caruso Department of Otolaryngology - Head & Neck Surgery, Keck Medicine of USC, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033-4503, USA; Zilkha Neurogenetic Institute, Keck Medicine of USC, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033-4503, USA
| | - Renée K Edlund
- Program in Developmental Biology, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Katerina Drakou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Pantelis Georgiades
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Neurosc ience, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston, TX 77030, USA.
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21
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Gou Y, Zhang T, Xu J. Transcription Factors in Craniofacial Development: From Receptor Signaling to Transcriptional and Epigenetic Regulation. Curr Top Dev Biol 2015; 115:377-410. [PMID: 26589933 DOI: 10.1016/bs.ctdb.2015.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Craniofacial morphogenesis is driven by spatial-temporal terrains of gene expression, which give rise to stereotypical pattern formation. Transcription factors are key cellular components that control these gene expressions. They are information hubs that integrate inputs from extracellular factors and environmental cues, direct epigenetic modifications, and define transcriptional status. These activities allow transcription factors to confer specificity and potency to transcription regulation during development.
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Affiliation(s)
- Yongchao Gou
- State Key Laboratory of Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Center for Craniofacial Molecular Biology, School of Dentistry, University of Southern California, Los Angeles, USA
| | - Tingwei Zhang
- Center for Craniofacial Molecular Biology, School of Dentistry, University of Southern California, Los Angeles, USA; State Key Laboratory of Oral Diseases, Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jian Xu
- Center for Craniofacial Molecular Biology, School of Dentistry, University of Southern California, Los Angeles, USA.
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22
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Abstract
The androgen receptor (AR) is a critical oncogene in prostate cancer (PCa) development and progression. In this study, we demonstrate cell-cycle-dependent regulation of AR activity, localization, and phosphorylation. We show that for three AR-target genes, androgen-stimulated AR transactivation is highest during the G1 phase, decreased during S-phase, and abrogated during G2/M. This change in AR transactivation parallels changes in AR localization and phosphorylation. A combination of imaging techniques and quantitative analysis reveals nuclear AR localization during interphase and the exclusion of the majority, but not all, AR from chromatin during mitosis. Flow cytometry analyses using a phospho-S308 AR-specific antibody in asynchronous and chemically enriched G2/M PCa cells revealed ligand-independent induction of S308 phosphorylation in mitosis when CDK1 is activated. Consistent with our flow cytometry data, IP-western blotting revealed an increase in S308 phosphorylation in G2/M, and the results of an in vitro kinase assay indicated that CDK1 was able to phosphorylate the AR on S308. Pharmacological inhibition of CDK1 activity resulted in decreased S308 phosphorylation in PCa cells. Importantly, using a combination of anti-total AR and phospho-S308-specific antibodies in immunofluorescence experiments, we showed that the AR is excluded from condensed chromatin in mitotic cells when it was phosphorylated on S308. In summary, we show that the phosphorylation of the AR on S308 by CDK1 during mitosis regulates AR localization and correlates with changes in AR transcriptional activity. These findings have important implications for understanding the function of AR as an oncogene.
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Affiliation(s)
- Yulia Koryakina
- Department of MicrobiologyImmunology, and Cancer Biology, University of Virginia, Jordan Hall Room 2-16, 1300 Jefferson Park Avenue, PO Box 800734, Charlottesville, Virginia 22908, USASidney Kimmel Cancer CenterThomas Jefferson University, Philadelphia, Pennsylvania, USACancer Center MemberUniversity of Virginia, Charlottesville, Virginia, USA
| | - Karen E Knudsen
- Department of MicrobiologyImmunology, and Cancer Biology, University of Virginia, Jordan Hall Room 2-16, 1300 Jefferson Park Avenue, PO Box 800734, Charlottesville, Virginia 22908, USASidney Kimmel Cancer CenterThomas Jefferson University, Philadelphia, Pennsylvania, USACancer Center MemberUniversity of Virginia, Charlottesville, Virginia, USA
| | - Daniel Gioeli
- Department of MicrobiologyImmunology, and Cancer Biology, University of Virginia, Jordan Hall Room 2-16, 1300 Jefferson Park Avenue, PO Box 800734, Charlottesville, Virginia 22908, USASidney Kimmel Cancer CenterThomas Jefferson University, Philadelphia, Pennsylvania, USACancer Center MemberUniversity of Virginia, Charlottesville, Virginia, USA Department of MicrobiologyImmunology, and Cancer Biology, University of Virginia, Jordan Hall Room 2-16, 1300 Jefferson Park Avenue, PO Box 800734, Charlottesville, Virginia 22908, USASidney Kimmel Cancer CenterThomas Jefferson University, Philadelphia, Pennsylvania, USACancer Center MemberUniversity of Virginia, Charlottesville, Virginia, USA
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23
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Zhang H, Wang X, Lyu K, Gao S, Wang G, Fan C, Zhang XA, Yan J. Time Point-Based Integrative Analyses of Deep-Transcriptome Identify Four Signal Pathways in Blastemal Regeneration of Zebrafish Lower Jaw. Stem Cells 2015; 33:806-18. [DOI: 10.1002/stem.1899] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 10/09/2014] [Accepted: 10/30/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Hui Zhang
- Department of Biology; Institute for Marine Biosystem and Neurosciences, College of Fisheries and Life Sciences; Shanghai Ocean University Shanghai People's Republic of China
| | - Xuelong Wang
- Department of Biology; Institute for Marine Biosystem and Neurosciences, College of Fisheries and Life Sciences; Shanghai Ocean University Shanghai People's Republic of China
| | - Kailun Lyu
- Department of Biology; Institute for Marine Biosystem and Neurosciences, College of Fisheries and Life Sciences; Shanghai Ocean University Shanghai People's Republic of China
| | - Siqi Gao
- Department of Biology; Institute for Marine Biosystem and Neurosciences, College of Fisheries and Life Sciences; Shanghai Ocean University Shanghai People's Republic of China
| | - Guan Wang
- Genergy Biotechnology (Shanghai) Co., Ltd.; Shanghai People's Republic of China
| | - Chunxin Fan
- Department of Biology; Institute for Marine Biosystem and Neurosciences, College of Fisheries and Life Sciences; Shanghai Ocean University Shanghai People's Republic of China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources; Ministry of Education, Shanghai Ocean University; Shanghai People's Republic of China
| | - Xin A. Zhang
- Stephenson Cancer Center and Department of Physiology; The University of Oklahoma Health Sciences Center; Oklahoma City Oklahoma USA
| | - Jizhou Yan
- Department of Biology; Institute for Marine Biosystem and Neurosciences, College of Fisheries and Life Sciences; Shanghai Ocean University Shanghai People's Republic of China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources; Ministry of Education, Shanghai Ocean University; Shanghai People's Republic of China
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24
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Nie X, Zhang K, Wang L, Ou G, Zhu H, Gao WQ. Transcription factor STOX1 regulates proliferation of inner ear epithelial cells via the AKT pathway. Cell Prolif 2015; 48:209-20. [PMID: 25677106 DOI: 10.1111/cpr.12174] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 11/02/2014] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Storkhead box 1 (STOX1) belongs to the forkhead family of transcription factors, and is reported to be involved in apoptosis of Caenorhabditis elegans. However, up to now the precise role of STOX1 in mammalian epithelial development has not been established. Here, we report that it plays an important role in regulation of proliferation of inner ear epithelial cells. MATERIALS AND METHODS Immunohistochemistry and reverse transcription-PCR assays were used to determine expression pattern of STOX1 in the mouse inner ear. Furthermore, its overexpression and knockdown effects on mouse inner ear epithelial cells were studied using RT-PCR, immunofluorescence, MTT assay, BrdU labelling and western blotting. RESULTS Storkhead box 1 was selectively expressed in epithelial cells, but not in stromal cells of the inner ear. Its over-expression enhanced cell proliferation and sphere formation, however, STOX1 knockdown inhibited cell proliferation and sphere formation in purified utricular epithelial cells in culture. Consistently, several cell cycle regulatory genes such as for PCNA, cyclin A and cyclin E, were up-regulated by STOX1 over-expression. Furthermore, biochemical analyses indicated that proliferation-promoting effects induced by STOX1 were mediated via phosphorylation of AKT in these cells. CONCLUSIONS Taken together, we demonstrate that STOX1 is a novel stimulatory factor for inner ear epithelial cell proliferation and might be an important target to be considered in regeneration or repair of inner ear epithelium.
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Affiliation(s)
- Xiaowei Nie
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 210027, China
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25
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Edlund RK, Birol O, Groves AK. The role of foxi family transcription factors in the development of the ear and jaw. Curr Top Dev Biol 2015; 111:461-95. [PMID: 25662269 DOI: 10.1016/bs.ctdb.2014.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mammalian outer, middle, and inner ears have different embryonic origins and evolved at different times in the vertebrate lineage. The outer ear is derived from first and second branchial arch ectoderm and mesoderm, the middle ear ossicles are derived from neural crest mesenchymal cells that invade the first and second branchial arches, whereas the inner ear and its associated vestibule-acoustic (VIIIth) ganglion are derived from the otic placode. In this chapter, we discuss recent findings in the development of these structures and describe the contributions of members of a Forkhead transcription factor family, the Foxi family to their formation. Foxi transcription factors are critical for formation of the otic placode, survival of the branchial arch neural crest, and developmental remodeling of the branchial arch ectoderm.
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Affiliation(s)
- Renée K Edlund
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Onur Birol
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.
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26
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DeGraff DJ, Grabowska MM, Case T, Yu X, Herrick MK, Hayward W, Strand DW, Cates JM, Hayward SW, Gao N, Walter MA, Buttyan R, Yi Y, Kaestner KH, Matusik RJ. FOXA1 deletion in luminal epithelium causes prostatic hyperplasia and alteration of differentiated phenotype. J Transl Med 2014; 94:726-39. [PMID: 24840332 PMCID: PMC4451837 DOI: 10.1038/labinvest.2014.64] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/20/2014] [Accepted: 03/26/2014] [Indexed: 01/25/2023] Open
Abstract
The forkhead box (Fox) superfamily of transcription factors has essential roles in organogenesis and tissue differentiation. Foxa1 and Foxa2 are expressed during prostate budding and ductal morphogenesis, whereas Foxa1 expression is retained in adult prostate epithelium. Previous characterization of prostatic tissue rescued from embryonic Foxa1 knockout mice revealed Foxa1 to be essential for ductal morphogenesis and epithelial maturation. However, it is unknown whether Foxa1 is required to maintain the differentiated status in adult prostate epithelium. Here, we employed the PBCre4 transgenic system and determined the impact of prostate-specific Foxa1 deletion in adult murine epithelium. PBCre4/Foxa1(loxp/loxp) mouse prostates showed progressive florid hyperplasia with extensive cribriform patterning, with the anterior prostate being most affected. Immunohistochemistry studies show mosaic Foxa1 KO consistent with PBCre4 activity, with Foxa1 KO epithelial cells specifically exhibiting altered cell morphology, increased proliferation, and elevated expression of basal cell markers. Castration studies showed that, while PBCre4/Foxa1(loxp/loxp) prostates did not exhibit altered sensitivity in response to hormone ablation compared with control prostates, the number of Foxa1-positive cells in mosaic Foxa1 KO prostates was significantly reduced compared with Foxa1-negative cells following castration. Unexpectedly, gene expression profile analyses revealed that Foxa1 deletion caused abnormal expression of seminal vesicle-associated genes in KO prostates. In summary, these results indicate Foxa1 expression is required for the maintenance of prostatic cellular differentiation.
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Affiliation(s)
- David J. DeGraff
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | | | - Tom Case
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | - Xiuping Yu
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | - Mary K. Herrick
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | - William Hayward
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | - Douglas W. Strand
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | - Justin M. Cates
- Department of Pathology, Vanderbilt University Medical Center, Nashville TN
| | - Simon W. Hayward
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark NJ
| | | | | | - Yajun Yi
- Institute for Integrative Genomics and Department of Medicine, Vanderbilt University, Nashville TN
| | | | - Robert J. Matusik
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville TN,Department of Cell and Developmental Biology, Vanderbilt University, Nashville TN,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville TN,Correspondence and reprint requests should be made to: Robert J. Matusik, Ph.D., William L. Bray Chair of Urologic Surgery, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, TN 37232,
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Foxi3 is necessary for the induction of the chick otic placode in response to FGF signaling. Dev Biol 2014; 391:158-69. [PMID: 24780628 DOI: 10.1016/j.ydbio.2014.04.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 03/19/2014] [Accepted: 04/20/2014] [Indexed: 01/06/2023]
Abstract
Vertebrate cranial sensory organs are derived from region at the border of the anterior neural plate called the pre-placodal region (PPR). The otic placode, the anlagen of the inner ear, is induced from PPR ectoderm by FGF signaling. We have previously shown that competence of embryonic ectoderm to respond to FGF signaling during otic placode induction correlates with the expression of PPR genes, but the molecular basis of this competence is poorly understood. Here, we characterize the function of a transcription factor, Foxi3 that is expressed at very early stages in the non-neural ectoderm and later in the PPR of chick embryos. Ablation experiments showed that the underlying hypoblast is necessary for the initiation of Foxi3 expression. Mis-expression of Foxi3 was sufficient to induce markers of non-neural ectoderm such as Dlx5, and the PPR such as Six1 and Eya2. Electroporation of Dlx5, or Six1 together with Eya1 also induced Foxi3, suggesting direct or indirect positive regulation between non-neural ectoderm genes and PPR genes. Knockdown of Foxi3 in chick embryos prevented the induction of otic placode markers, and was able to prevent competent cranial ectoderm from expressing otic markers in response to FGF2. In contrast, Foxi3 expression alone was not sufficient to confer competence to respond to FGF on embryonic ectoderm. Our analysis of PPR and FGF-responsive genes after Foxi3 knockdown at gastrula stages suggests it is not necessary for the expression of PPR genes at these stages, nor for the transduction of FGF signals. The early expression but late requirement for Foxi3 in ear induction suggests it may have some of the properties associated with pioneer transcription factors.
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Setting appropriate boundaries: fate, patterning and competence at the neural plate border. Dev Biol 2013; 389:2-12. [PMID: 24321819 DOI: 10.1016/j.ydbio.2013.11.027] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 11/20/2022]
Abstract
The neural crest and craniofacial placodes are two distinct progenitor populations that arise at the border of the vertebrate neural plate. This border region develops through a series of inductive interactions that begins before gastrulation and progressively divide embryonic ectoderm into neural and non-neural regions, followed by the emergence of neural crest and placodal progenitors. In this review, we describe how a limited repertoire of inductive signals-principally FGFs, Wnts and BMPs-set up domains of transcription factors in the border region which establish these progenitor territories by both cross-inhibitory and cross-autoregulatory interactions. The gradual assembly of different cohorts of transcription factors that results from these interactions is one mechanism to provide the competence to respond to inductive signals in different ways, ultimately generating the neural crest and cranial placodes.
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Abstract
Forkhead box (FOX) proteins are multifaceted transcription factors that are responsible for fine-tuning the spatial and temporal expression of a broad range of genes both during development and in adult tissues. This function is engrained in their ability to integrate a multitude of cellular and environmental signals and to act with remarkable fidelity. Several key members of the FOXA, FOXC, FOXM, FOXO and FOXP subfamilies are strongly implicated in cancer, driving initiation, maintenance, progression and drug resistance. The functional complexities of FOX proteins are coming to light and have established these transcription factors as possible therapeutic targets and putative biomarkers for specific cancers.
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Affiliation(s)
- Eric W-F Lam
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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Kadauke S, Blobel GA. Mitotic bookmarking by transcription factors. Epigenetics Chromatin 2013; 6:6. [PMID: 23547918 PMCID: PMC3621617 DOI: 10.1186/1756-8935-6-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/11/2013] [Indexed: 11/30/2022] Open
Abstract
Mitosis is accompanied by dramatic changes in chromatin organization and nuclear architecture. Transcription halts globally and most sequence-specific transcription factors and co-factors are ejected from mitotic chromatin. How then does the cell maintain its transcriptional identity throughout the cell division cycle? It has become clear that not all traces of active transcription and gene repression are erased within mitotic chromatin. Many histone modifications are stable or only partially diminished throughout mitosis. In addition, some sequence-specific DNA binding factors have emerged that remain bound to select sites within mitotic chromatin, raising the possibility that they function to transmit regulatory information through the transcriptionally silent mitotic phase, a concept that has been termed “mitotic bookmarking.” Here we review recent approaches to studying potential bookmarking factors with regards to their mitotic partitioning, and summarize emerging ideas concerning the in vivo functions of mitotically bound nuclear factors.
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Affiliation(s)
- Stephan Kadauke
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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Caravaca JM, Donahue G, Becker JS, He X, Vinson C, Zaret KS. Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev 2013; 27:251-60. [PMID: 23355396 DOI: 10.1101/gad.206458.112] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
While most transcription factors exit the chromatin during mitosis and the genome becomes silent, a subset of factors remains and "bookmarks" genes for rapid reactivation as cells progress through the cell cycle. However, it is unknown whether such bookmarking factors bind to chromatin similarly in mitosis and how different binding capacities among them relate to function. We compared a diverse set of transcription factors involved in liver differentiation and found markedly different extents of mitotic chromosome binding. Among them, the pioneer factor FoxA1 exhibits the greatest extent of mitotic chromosome binding. Genomically, ~15% of the FoxA1 interphase target sites are bound in mitosis, including at genes that are important for liver differentiation. Biophysical, genome mapping, and mutagenesis studies of FoxA1 reveals two different modes of binding to mitotic chromatin. Specific binding in mitosis occurs at sites that continue to be bound from interphase. Nonspecific binding in mitosis occurs across the chromosome due to the intrinsic chromatin affinity of FoxA1. Both specific and nonspecific binding contribute to timely reactivation of target genes post-mitosis. These studies reveal an unexpected diversity in the mechanisms by which transcription factors help retain cell identity during mitosis.
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Affiliation(s)
- Juan Manuel Caravaca
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Smilow Center for Translation Research, Philadelphia, PA 19104, USA
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Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell 2012; 150:725-37. [PMID: 22901805 DOI: 10.1016/j.cell.2012.06.038] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 03/11/2012] [Accepted: 06/04/2012] [Indexed: 12/21/2022]
Abstract
Tissue-specific transcription patterns are preserved throughout cell divisions to maintain lineage fidelity. We investigated whether transcription factor GATA1 plays a role in transmitting hematopoietic gene expression programs through mitosis when transcription is transiently silenced. Live-cell imaging revealed that a fraction of GATA1 is retained focally within mitotic chromatin. ChIP-seq of highly purified mitotic cells uncovered that key hematopoietic regulatory genes are occupied by GATA1 in mitosis. The GATA1 coregulators FOG1 and TAL1 dissociate from mitotic chromatin, suggesting that GATA1 functions as platform for their postmitotic recruitment. Mitotic GATA1 target genes tend to reactivate more rapidly upon entry into G1 than genes from which GATA1 dissociates. Mitosis-specific destruction of GATA1 delays reactivation selectively of genes that retain GATA1 during mitosis. These studies suggest a requirement of mitotic "bookmarking" by GATA1 for the faithful propagation of cell-type-specific transcription programs through cell division.
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Affiliation(s)
- Stephan Kadauke
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Pereira CF, Lemischka IR, Moore K. Reprogramming cell fates: insights from combinatorial approaches. Ann N Y Acad Sci 2012; 1266:7-17. [PMID: 22901251 DOI: 10.1111/j.1749-6632.2012.06508.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epigenetic reprogramming can be achieved in different ways, including nuclear transfer, cell fusion, or the expression of transcription factors (TFs). Combinatorial overexpression provides an opportunity to define the minimal core network of TFs that instructs specific cell fates. This approach has been employed to induce mouse and human pluripotency and differentiated cell types from cells that can be also as distant as cells from different germ layers. This suggests the possibility that any specific cell type may be directly converted into another if the appropriate reprogramming TF core is determined. Herein, we review the factors used for reprogramming multiple cell identities and raise the question of whether there is a common underlying blueprint for reprogramming factors. In addition to the generation of human cell types of interest for cell-replacement therapies, we propose that the TF-mediated conversion of differentiated cell types, especially somatic stem cells, will have an impact on our understanding of their biological development.
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Affiliation(s)
- Carlos-Filipe Pereira
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York, USA.
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Similarities between the Epstein-Barr Virus (EBV) Nuclear Protein EBNA1 and the Pioneer Transcription Factor FoxA: Is EBNA1 a "Bookmarking" Oncoprotein that Alters the Host Cell Epigenotype? Pathogens 2012; 1:37-51. [PMID: 25436603 PMCID: PMC4235684 DOI: 10.3390/pathogens1010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 08/21/2012] [Accepted: 09/04/2012] [Indexed: 11/19/2022] Open
Abstract
EBNA1, a nuclear protein expressed in all EBV-associated neoplasms is indispensable for the maintenance of the viral episomes in latently infected cells. EBNA1 may induce genetic alterations by upregulating cellular recombinases, production of reactive oxygen species (ROS) and affecting p53 levels and function. All these changes may contribute to tumorigenesis. In this overview we focus, however, on the epigenetic alterations elicited by EBNA1 by drawing a parallel between EBNA1 and the FoxA family of pioneer transcription factors. Both EBNA1 and FoxA induce local DNA demethylation, nucleosome destabilization and bind to mitotic chromosomes. Local DNA demethylation and nucleosome rearrangement mark active promoters and enhancers. In addition, EBNA1 and FoxA, when associated with mitotic chromatin may “bookmark” active genes and ensure their reactivation in postmitotic cells (epigenetic memory). We speculate that DNA looping induced by EBNA1-EBNA1 interactions may reorganize the cellular genome. Such chromatin loops, sustained in mitotic chromatin similarly to the long-distance interactions mediated by the insulator protein CTCF, may also mediate the epigenetic inheritance of gene expression patterns. We suggest that EBNA1 has the potential to induce patho-epigenetic alterations contributing to tumorigenesis.
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Epigenetic obstacles encountered by transcription factors: reprogramming against all odds. Curr Opin Genet Dev 2012; 22:409-15. [PMID: 22922161 DOI: 10.1016/j.gde.2012.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/24/2012] [Accepted: 08/02/2012] [Indexed: 12/24/2022]
Abstract
Reprogramming of a somatic nucleus to an induced pluripotent state can be achieved in vitro through ectopic expression of Oct4 (Pou5f1), Sox2, Klf4 and c-Myc. While the ability of these factors to regulate transcription in a pluripotent context has been studied extensively, their ability to interact with and remodel a somatic genome remains underexplored. Several recent studies have begun to provide mechanistic insights that will eventually lead to a more rational design and improved understanding of nuclear reprogramming.
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Lalmansingh AS, Karmakar S, Jin Y, Nagaich AK. Multiple modes of chromatin remodeling by Forkhead box proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:707-15. [PMID: 22406422 DOI: 10.1016/j.bbagrm.2012.02.018] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/08/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
Abstract
Forkhead box (FOX) proteins represent a large family of transcriptional regulators unified by their DNA binding domain (DBD) known as a 'forkhead' or 'winged helix' domain. Over 40 FOX genes have been identified in the mammalian genome. FOX proteins share significant sequence similarities in the DBD which allow them to bind to a consensus DNA response element. However, their modes of action are quite diverse as they regulate gene expression by acting as pioneer factors, transcription factors, or both. This review focuses on the mechanisms of chromatin remodeling with an emphasis on three sub-classes-FOXA, FOXO, and FOXP members. FOXA proteins serve as pioneer factors to open up local chromatin structure and thereby increase accessibility of chromatin to factors regulating transcription. FOXP proteins, in contrast, function as classic transcription factors to recruit a variety of chromatin modifying enzymes to regulate gene expression. FOXO proteins represent a hybrid subclass having dual roles as pioneering factors and transcription factors. A subset of FOX proteins interacts with condensed mitotic chromatin and may function as 'bookmarking' agents to maintain transcriptional competence at specific genomic sites. The overall diversity in chromatin remodeling function by FOX proteins is related to unique structural motifs present within the DBD flanking regions that govern selective interactions with core histones and/or chromatin coregulatory proteins. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Avin S Lalmansingh
- Division of Therapeutic Proteins, Office of Biotechnology Products, Office of Pharmaceutical Sciences, Center for Drug Evaluation and Research, Food and Drug administration, Bethesda, MD 20892, USA
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van Abel D, Abdul-Hamid O, van Dijk M, Oudejans CBM. Transcription factor STOX1A promotes mitotic entry by binding to the CCNB1 promotor. PLoS One 2012; 7:e29769. [PMID: 22253775 PMCID: PMC3258242 DOI: 10.1371/journal.pone.0029769] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 12/05/2011] [Indexed: 11/19/2022] Open
Abstract
Background In this study we investigated the involvement of the transcription factor STOX1A in the regulation of the cell cycle. Methodology/Principal Findings We found that several major cell cycle regulatory genes were differentially expressed upon STOX1A stimulation and knockdown in the neuroblastoma cell line SH-SY5Y. This includes STOX1A dependent differential regulation of cyclin B1 expression, a cyclin which is known to regulate mitotic entry during the cell cycle. The differential regulation of cyclin B1 expression by STOX1A is direct as shown with chromatin immunoprecipitation. Results furthermore suggest that mitotic entry is enhanced through the direct upregulation of cyclin B1 expression effectuated by STOX1A. Conclusions In conclusion we hereby show that STOX1A is directly involved in the regulation of the cell cycle.
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Affiliation(s)
- Daan van Abel
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
| | - Omar Abdul-Hamid
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
| | - Marie van Dijk
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
| | - Cees B. M. Oudejans
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail:
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Retention and transmission of active transcription memory from progenitor to progeny cells via ligand-modulated transcription factors: elucidation of a concept by BIOPIT model. Cell Biol Int 2012; 36:177-82. [DOI: 10.1042/cbi20090329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Yan J, Burgess SM. Using a yeast inverse one-hybrid system to identify functional binding sites of transcription factors. Methods Mol Biol 2012; 786:275-290. [PMID: 21938633 DOI: 10.1007/978-1-61779-292-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Binding of transcription factors to promoters is a necessary step to initiate transcription. From an evolutionary standpoint, the regulatory proteins and their binding sites are considered to have molecularly coevolved. We developed an efficient yeast strategy, an "inverse one-hybrid system", to identify binding targets of transcription factors globally in a genome of interest. The technique consists of a yeast strain expressing a -transcription factor of interest mated to yeast containing a library of random genomic fragments cloned upstream of a reporter gene (URA3). Positive growth on media without uracil denotes a fragment being bound by the transcription factor, e.g., zebrafish FoxI1. The bound fragments in hundreds of positive clones are sequenced and retested for their binding activities using a colony PCR and sequencing strategy. The resulting tools allow for rapid and genomic-wide identification of transcriptional binding targets.
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Affiliation(s)
- Jizhou Yan
- Institute for Marine Biosystem and Neurosciences, Department of Hydrobiology, Shanghai Ocean University, College of Fisheries and Life Sciences, Lingang New City, Shanghai, China
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40
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Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011; 25:2227-41. [PMID: 22056668 DOI: 10.1101/gad.176826.111] [Citation(s) in RCA: 1145] [Impact Index Per Article: 88.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special "pioneer transcription factors" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.
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Affiliation(s)
- Kenneth S Zaret
- Epigenetics Program, Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, USA.
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41
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Pioneer factors: directing transcriptional regulators within the chromatin environment. Trends Genet 2011; 27:465-74. [PMID: 21885149 DOI: 10.1016/j.tig.2011.07.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 07/09/2011] [Accepted: 07/11/2011] [Indexed: 11/20/2022]
Abstract
Chromatin is a well-known obstacle to transcription as it controls DNA accessibility, which directly impacts the recruitment of the transcriptional machinery. The recent burst of functional genomic studies provides new clues as to how transcriptional competency is regulated in this context. In this review, we discuss how these studies have shed light on a specialized subset of transcription factors, defined as pioneer factors, which direct recruitment of downstream transcription factors to establish lineage-specific transcriptional programs. In particular, we present evidence of an interplay between pioneer factors and the epigenome that could be central to this process. Finally, we discuss how pioneer factors, whose expression and function are altered in tumors, are also being considered for their prognostic value and should therefore be regarded as potential therapeutic targets. Thus, pioneer factors emerge as key players that connect the epigenome and transcription in health and disease.
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Benayoun BA, Caburet S, Veitia RA. Forkhead transcription factors: key players in health and disease. Trends Genet 2011; 27:224-32. [PMID: 21507500 DOI: 10.1016/j.tig.2011.03.003] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 12/16/2022]
Abstract
Forkhead box (FOX) proteins constitute an evolutionarily conserved family of transcription factors with a central role not only during development, but also in the adult organism. Thus, the misregulation and/or mutation of FOX genes often induce human genetic diseases, promote cancer or deregulate ageing. Indeed, germinal FOX gene mutations cause diseases ranging from infertility to language and/or speech disorders and immunological defects. Moreover, because of their central role in signalling pathways and in the regulation of homeostasis, somatic misregulation and/or mutation of FOX genes are associated with cancer. FOX proteins have undergone diversification in terms of their sequence, regulation and function. In addition to dedicated roles, evidence suggests that Forkhead factors have retained some functional redundancy. Thus, combinations of slightly defective alleles might induce disease phenotypes in humans, acting as quantitative trait loci. Uncovering such variants would be a big step towards understanding the functional interdependencies of different FOX members and their implications in complex pathologies.
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Affiliation(s)
- Bérénice A Benayoun
- CNRS UMR 7592, Institut Jacques Monod, Equipe Génétique et Génomique du Développement Gonadique, 75205 Paris Cedex 13, France
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Stein GS, van Wijnen AJ, Imbalzano AN, Montecino M, Zaidi SK, Lian JB, Nickerson JA, Stein JL. Architectural genetic and epigenetic control of regulatory networks: compartmentalizing machinery for transcription and chromatin remodeling in nuclear microenvironments. Crit Rev Eukaryot Gene Expr 2011; 20:149-55. [PMID: 21133844 DOI: 10.1615/critreveukargeneexpr.v20.i2.50] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The regulatory machinery that governs genetic and epigenetic control of gene expression for biological processes and cancer is organized in nuclear microenvironments. Strategic placement of transcription factors at target gene promoters in punctate microenvironments of interphase nuclei supports scaffolding of co- regulatory proteins and the convergence as well as integration of regulatory networks. The organization and localization of regulatory complexes within the nucleus can provide signatures that are linked to regulatory activity. Retention of transcription factors at gene loci in mitotic chromosomes contributes to epigenetic control of cell fate and lineage commitment, as well as to persistence of transformed and tumor phenotypes. Mechanistic understanding of the architectural assembly of regulatory machinery can serve as a basis for treating cancer with high specificity and minimal off-target effects.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School and Cancer Center, Worcester, MA 01655, USA.
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The nude mutant gene Foxn1 is a HOXC13 regulatory target during hair follicle and nail differentiation. J Invest Dermatol 2010; 131:828-37. [PMID: 21191399 DOI: 10.1038/jid.2010.391] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Among the Hox genes, homeobox C13 (Hoxc13) has been shown to be essential for proper hair shaft differentiation, as Hoxc13 gene-targeted (Hoxc13(tm1Mrc)) mice completely lack external hair. Because of the remarkable overt phenotypic parallels to the Foxn1(nu) (nude) mutant mice, we sought to determine whether Hoxc13 and forkhead box N1 (Foxn1) might act in a common pathway of hair follicle (HF) differentiation. We show that the alopecia exhibited by both the Hoxc13(tm1Mrc) and Foxn1(nu) mice is because of strikingly similar defects in hair shaft differentiation and that both mutants suffer from a severe nail dystrophy. These phenotypic similarities are consistent with the extensive overlap between Hoxc13 and Foxn1 expression patterns in the HF and the nail matrix. Furthermore, DNA microarray analysis of skin from Hoxc13(tm1Mrc) mice identified Foxn1 as significantly downregulated along with numerous hair keratin genes. This Foxn1 downregulation apparently reflects the loss of direct transcriptional control by HOXC13 as indicated by our results obtained through co-transfection and chromatin immunoprecipitation (ChIP) assays. As presented in the discussion, these data support a regulatory model of keratinocyte differentiation in which HOXC13-dependent activation of Foxn1 is part of a regulatory cascade controlling the expression of terminal differentiation markers.
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Santisteban P, Recacha P, Metzger DE, Zaret KS. Dynamic expression of Groucho-related genes Grg1 and Grg3 in foregut endoderm and antagonism of differentiation. Dev Dyn 2010; 239:980-6. [PMID: 20108349 DOI: 10.1002/dvdy.22217] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
While much is known about Groucho corepressors in Drosophila development, less is known about Grg homologs in mammalian embryogenesis. The transcription factors FoxA1 and FoxA2 are redundantly necessary for liver-inductive competence of the endoderm, and recently we found that FoxA factors bind Grg3, recruit the corepressor to FoxA target genes, and cause transcriptional repression, when Grg3 is ectopically expressed in adult liver cell lines that express little or no endogenous Grg. Unexpectedly, we now find that Grg1 and Grg3 mRNAs are co-expressed with FoxA factors in the foregut endoderm, prior to liver differentiation, though only Grg3 protein is expressed there. Grg3 mRNA and protein are extinguished at the onset of liver differentiation. Lentiviral delivery of Grg3 to explants of foregut endoderm suppresses liver gene induction. We suggest that Grg expression in the endoderm helps suppress the liver program and find that endodermal competence involves a balance between activators and corepressors.
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Affiliation(s)
- Pilar Santisteban
- Instituto de Investigaciones Biomédicas, Alberto Sols Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
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Kwon HJ, Bhat N, Sweet EM, Cornell RA, Riley BB. Identification of early requirements for preplacodal ectoderm and sensory organ development. PLoS Genet 2010; 6:e1001133. [PMID: 20885782 PMCID: PMC2944784 DOI: 10.1371/journal.pgen.1001133] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 08/22/2010] [Indexed: 11/25/2022] Open
Abstract
Preplacodal ectoderm arises near the end of gastrulation as a narrow band of cells surrounding the anterior neural plate. This domain later resolves into discrete cranial placodes that, together with neural crest, produce paired sensory structures of the head. Unlike the better-characterized neural crest, little is known about early regulation of preplacodal development. Classical models of ectodermal patterning posit that preplacodal identity is specified by readout of a discrete level of Bmp signaling along a DV gradient. More recent studies indicate that Bmp-antagonists are critical for promoting preplacodal development. However, it is unclear whether Bmp-antagonists establish the proper level of Bmp signaling within a morphogen gradient or, alternatively, block Bmp altogether. To begin addressing these issues, we treated zebrafish embryos with a pharmacological inhibitor of Bmp, sometimes combined with heat shock-induction of Chordin and dominant-negative Bmp receptor, to fully block Bmp signaling at various developmental stages. We find that preplacodal development occurs in two phases with opposing Bmp requirements. Initially, Bmp is required before gastrulation to co-induce four transcription factors, Tfap2a, Tfap2c, Foxi1, and Gata3, which establish preplacodal competence throughout the nonneural ectoderm. Subsequently, Bmp must be fully blocked in late gastrulation by dorsally expressed Bmp-antagonists, together with dorsally expressed Fgf and Pdgf, to specify preplacodal identity within competent cells abutting the neural plate. Localized ventral misexpression of Fgf8 and Chordin can activate ectopic preplacodal development anywhere within the zone of competence, whereas dorsal misexpression of one or more competence factors can activate ectopic preplacodal development in the neural plate. Conversely, morpholino-knockdown of competence factors specifically ablates preplacodal development. Our work supports a relatively simple two-step model that traces regulation of preplacodal development to late blastula stage, resolves two distinct phases of Bmp dependence, and identifies the main factors required for preplacodal competence and specification. Cranial placodes, which produce sensory structures in the head, arise from a contiguous band of preplacodal ectoderm surrounding the anterior neural plate during gastrulation. Little is known about early regulation of preplacodal ectoderm, but modulation of signaling through Bone Morphogenetic Protein (Bmp) is clearly involved. Recent studies show that dorsally expressed Bmp-antagonists help establish preplacodal ectoderm, but it is not clear whether antagonists titrate Bmp to a discrete low level that actively induces preplacodal fate or, alternatively, whether Bmp must be fully blocked to permit preplacodal development. We show that in zebrafish preplacodal development occurs in distinct phases with differing Bmp requirements. Initially, Bmp is required before gastrulation to render all ventral ectoderm competent to form preplacodal tissue. We further show that four transcription factors, Foxi1, Gata3, Tfap2a, and Tfap2c, specifically mediate preplacodal competence. Once induced, these factors no longer require Bmp. Thereafter, Bmp must be fully blocked by dorsally expressed Bmp-antagonists to permit preplacodal development. In addition, dorsally expressed Fgf and/or Pdgf are also required, activating preplacodal development in competent cells abutting the neural plate. Thus, we have resolved the role of Bmp and traced the regulation of preplacodal development to pre-gastrula stage.
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Affiliation(s)
- Hye-Joo Kwon
- Biology Department, Texas A&M University, College Station, Texas, United States of America
| | - Neha Bhat
- Biology Department, Texas A&M University, College Station, Texas, United States of America
| | - Elly M. Sweet
- Biology Department, Texas A&M University, College Station, Texas, United States of America
| | - Robert A. Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Bruce B. Riley
- Biology Department, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Marais A, Ji Z, Child ES, Krause E, Mann DJ, Sharrocks AD. Cell cycle-dependent regulation of the forkhead transcription factor FOXK2 by CDK·cyclin complexes. J Biol Chem 2010; 285:35728-39. [PMID: 20810654 PMCID: PMC2975197 DOI: 10.1074/jbc.m110.154005] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Several mammalian forkhead transcription factors have been shown to impact on cell cycle regulation and are themselves linked to cell cycle control systems. Here we have investigated the little studied mammalian forkhead transcription factor FOXK2 and demonstrate that it is subject to control by cell cycle-regulated protein kinases. FOXK2 exhibits a periodic rise in its phosphorylation levels during the cell cycle, with hyperphosphorylation occurring in mitotic cells. Hyperphosphorylation occurs in a cyclin-dependent kinase (CDK)·cyclin-dependent manner with CDK1·cyclin B as the major kinase complex, although CDK2 and cyclin A also appear to be important. We have mapped two CDK phosphorylation sites, serines 368 and 423, which play a role in defining FOXK2 function through regulating its stability and its activity as a transcriptional repressor protein. These two CDK sites appear vital for FOXK2 function because expression of a mutant lacking these sites cannot be tolerated and causes apoptosis.
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Affiliation(s)
- Anett Marais
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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Taube JH, Allton K, Duncan SA, Shen L, Barton MC. Foxa1 functions as a pioneer transcription factor at transposable elements to activate Afp during differentiation of embryonic stem cells. J Biol Chem 2010; 285:16135-44. [PMID: 20348100 DOI: 10.1074/jbc.m109.088096] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Epigenetic control of genes that are silent in embryonic stem cells, but destined for expression during differentiation, includes distinctive hallmarks, such as simultaneous activating/repressing (bivalent) modifications of chromatin and DNA hypomethylation at enhancers of gene expression. Although alpha-fetoprotein (Afp) falls into this class of genes, as it is silent in pluripotent stem cells and activated during differentiation of endoderm, we find that Afp chromatin lacks bivalent histone modifications. However, critical regulatory sites for Afp activation, overlapping Foxa1/p53/Smad-binding elements, are located within a 300-bp region lacking DNA methylation, due to transposed elements underrepresented in CpG sequences: a short interspersed transposable element and a medium reiterated sequence 1 element. Forkhead family member Foxa1 is activated by retinoic acid treatment of embryonic stem cells, binds its DNA consensus site within the short interspersed transposable/medium reiterated sequence 1 elements, and displaces linker histone H1 from silent Afp chromatin. Small interfering RNA depletion of Foxa1 showed that Foxa1 is essential in providing chromatin access to transforming growth factor beta-activated Smad2 and Smad4 and their subsequent DNA binding. Together these transcription factors establish highly acetylated chromatin and promote expression of Afp. Foxa1 acts as a pioneer transcription factor in de novo activation of Afp, by exploiting a lack of methylation at juxtaposed transposed elements, to bind and poise chromatin for intersection with transforming growth factor beta signaling during differentiation of embryonic stem cells.
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Affiliation(s)
- Joseph H Taube
- Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, Center for Stem Cell and Developmental Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Dey A, Nishiyama A, Karpova T, McNally J, Ozato K. Brd4 marks select genes on mitotic chromatin and directs postmitotic transcription. Mol Biol Cell 2009; 20:4899-909. [PMID: 19812244 DOI: 10.1091/mbc.e09-05-0380] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
On entry into mitosis, many transcription factors dissociate from chromatin, resulting in global transcriptional shutdown. During mitosis, some genes are marked to ensure the inheritance of their expression in the next generation of cells. The nature of mitotic gene marking, however, has been obscure. Brd4 is a double bromodomain protein that localizes to chromosomes during mitosis and is implicated in holding mitotic memory. In interphase, Brd4 interacts with P-TEFb and functions as a global transcriptional coactivator. We found that throughout mitosis, Brd4 remained bound to the transcription start sites of many M/G1 genes that are programmed to be expressed at the end of, or immediately after mitosis. In contrast, Brd4 did not bind to genes that are expressed at later phases of cell cycle. Brd4 binding to M/G1 genes increased at telophase, the end phase of mitosis, coinciding with increased acetylation of histone H3 and H4 in these genes. Increased Brd4 binding was accompanied by the recruitment of P-TEFb and de novo M/G1 gene transcription, the events impaired in Brd4 knockdown cells. In sum, Brd4 marks M/G1 genes for transcriptional memory during mitosis, and upon exiting mitosis, this mark acts as a signal for initiating their prompt transcription in daughter cells.
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Affiliation(s)
- Anup Dey
- Laboratory of Molecular Growth Regulation, Program in Genomics of Differentiation, National Institute of Child Health and Human Development and Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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