151
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Osborne CC, Perry KJ, Shankland M, Henry JQ. Ectomesoderm and epithelial-mesenchymal transition-related genes in spiralian development. Dev Dyn 2018; 247:1097-1120. [PMID: 30133032 DOI: 10.1002/dvdy.24667] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Spiralians (e.g., annelids, molluscs, and flatworms) possess two sources of mesoderm. One is from endodermal precursors (endomesoderm), which is considered to be the ancestral source in metazoans. The second is from ectoderm (ectomesoderm) and may represent a novel cell type in the Spiralia. In the mollusc Crepidula fornicata, ectomesoderm is derived from micromere daughters within the A and B cell quadrants. Their progeny lie along the anterolateral edges of the blastopore. There they undergo epithelial-mesenchymal transition (EMT), become rounded and undergo delamination/ingression. Subsequently, they assume the mesenchymal phenotype, and migrate beneath the surface ectoderm to differentiate various cell types, including muscles and pigment cells. RESULTS We examined expression of several genes whose homologs are known to regulate Type 1 EMT in other metazoans. Most of these genes were expressed within spiralian ectomesoderm during EMT. CONCLUSIONS We propose that spiralian ectomesoderm, which exhibits analogous cellular behaviors to other populations of mesenchymal cells, may be controlled by the same genes that drive EMT in other metazoans. Perhaps these genes comprise a conserved metazoan EMT gene regulatory network (GRN). This study represents the first step in elucidating the GRN controlling the development of a novel spiralian cell type (ectomesoderm). Developmental Dynamics 247:1097-1120, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- C Cornelia Osborne
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | - Kimberly J Perry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | - Marty Shankland
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | - Jonathan Q Henry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
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152
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Chen C, Aihemaiti M, Zhang X, Qu H, Jiao J, Sun Q, Yu W. FOXD4 induces tumor progression in colorectal cancer by regulation of the SNAI3/CDH1 axis. Cancer Biol Ther 2018; 19:1065-1071. [PMID: 30252597 DOI: 10.1080/15384047.2018.1480291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is ranked third as the most common malignancy, and it develops into metastasis at a high rate. Importantly, distant metastasis is considered to be a key factor for colorectal therapy. In the present study, we identified FOXD4, a transcription factor belonging to the forkhead/winged helix-box (FOX) family, as a novel biomarker for diagnosis and treatment of patients with CRC. We revealed that FOXD4 was up-regulated in CRC tissues and increased the metastatic ability of CRC cells. Additionally, FOXD4 affected the metastasis of CRC by inducing the epithelial-mesenchymal transition (EMT) process. Furthermore, FOXD4 could directly bind the SNAI3 promoter during EMT in CRC and then facilitate CRC metastasis. In summary, the present research strongly suggests that FOXD4 is a valuable marker for CRC, and that targeting FOXD4 may be a novel strategy for enhancing the treatment outcomes of CRC therapy.
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Affiliation(s)
- Cheng Chen
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
| | - Maimaiti Aihemaiti
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
| | - Xin Zhang
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
| | - Hui Qu
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
| | - Jie Jiao
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
| | - Qilong Sun
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
| | - Wenbin Yu
- a Department of General Surgery , Qilu Hospital of Shandong University , JiNan , China
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153
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Liao GB, Li XZ, Zeng S, Liu C, Yang SM, Yang L, Hu CJ, Bai JY. Regulation of the master regulator FOXM1 in cancer. Cell Commun Signal 2018; 16:57. [PMID: 30208972 PMCID: PMC6134757 DOI: 10.1186/s12964-018-0266-6] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023] Open
Abstract
FOXM1 (forkhead box protein M1) is a critical proliferation-associated transcription factor that is widely spatiotemporally expressed during the cell cycle. It is closely involved with the processes of cell proliferation, self-renewal, and tumorigenesis. In most human cancers, FOXM1 is overexpressed, and this indicates a poor prognosis for cancer patients. FOXM1 maintains cancer hallmarks by regulating the expression of target genes at the transcriptional level. Due to its potential role as molecular target in cancer therapy, FOXM1 was named the Molecule of the Year in 2010. However, the mechanism of FOXM1 dysregulation remains indistinct. A comprehensive understanding of FOXM1 regulation will provide novel insight for cancer and other diseases in which FOXM1 plays a major role. Here, we summarize the transcriptional regulation, post-transcriptional regulation and post-translational modifications of FOXM1, which will provide extremely important implications for novel strategies targeting FOXM1.
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Affiliation(s)
- Guo-Bin Liao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Xin-Zhe Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Shuo Zeng
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Cheng Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Li Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
| | - Jian-Ying Bai
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037 China
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154
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Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Proc Natl Acad Sci U S A 2018; 115:E9075-E9084. [PMID: 30201718 DOI: 10.1073/pnas.1809842115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA replication restart, the essential process that reinitiates prematurely terminated genome replication reactions, relies on exquisitely specific recognition of abandoned DNA replication-fork structures. The PriA DNA helicase mediates this process in bacteria through mechanisms that remain poorly defined. We report the crystal structure of a PriA/replication-fork complex, which resolves leading-strand duplex DNA bound to the protein. Interaction with PriA unpairs one end of the DNA and sequesters the 3'-most nucleotide from the nascent leading strand into a conserved protein pocket. Cross-linking studies reveal a surface on the winged-helix domain of PriA that binds to parental duplex DNA. Deleting the winged-helix domain alters PriA's structure-specific DNA unwinding properties and impairs its activity in vivo. Our observations lead to a model in which coordinated parental-, leading-, and lagging-strand DNA binding provide PriA with the structural specificity needed to act on abandoned DNA replication forks.
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155
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Abstract
The forkhead box O3 (FOXO3, or FKHRL1) protein is a member of the FOXO subclass of transcription factors. FOXO proteins were originally identified as regulators of insulin-related genes; however, they are now established regulators of genes involved in vital biological processes, including substrate metabolism, protein turnover, cell survival, and cell death.
FOXO3 is one of the rare genes that have been consistently linked to longevity in
in vivo models. This review provides an update of the most recent research pertaining to the role of FOXO3 in (i) the regulation of protein turnover in skeletal muscle, the largest protein pool of the body, and (ii) the genetic basis of longevity. Finally, it examines (iii) the role of microRNAs in the regulation of FOXO3 and its impact on the regulation of the cell cycle.
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Affiliation(s)
- Renae J Stefanetti
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah Voisin
- Institute for Health and Sport, Victoria University, Footscray, Australia
| | - Aaron Russell
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
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156
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Schill D, Nord J, Cirillo LA. FoxO1 and FoxA1/2 form a complex on DNA and cooperate to open chromatin at insulin-regulated genes. Biochem Cell Biol 2018; 97:118-129. [PMID: 30142277 DOI: 10.1139/bcb-2018-0104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We have previously shown that cooperative, interdependent binding by the pioneer factors FoxO1 and FoxA1/2 is required for recruitment of RNA polymerase II and H3K27 acetylation to the promoters of insulin-regulated genes. However, the underlying mechanisms are unknown. In this study, we demonstrate that, in HepG2 cells, FoxO1 and FoxA2 form a complex on DNA that is disrupted by insulin treatment. Insulin-mediated phosphorylation of FoxO1 and FoxA2 does not impair their cooperative binding to mononucleosome particles assembled from the IGFBP1 promoter, indicating that direct disruption of complex formation by phosphorylation is not responsible for the loss of interdependent FoxO1:FoxA1/2 binding following insulin treatment. Since FoxO1 and FoxA1/2 binding is required for the establishment and maintenance of transcriptionally active chromatin at insulin-regulated genes, we hypothesized that cooperative FoxO1 and FoxA1/2 binding dictates the chromatin remodeling events required for the initial activation of these genes. In support of this idea, we demonstrate that FoxO1 and FoxA2 cooperatively open linker histone compacted chromatin templates containing the IGFBP1 promoter. Taken together, these results provide a mechanism for how interdependent FoxO1:FoxA1/2 binding is negatively impacted by insulin and provide a developmental context for cooperative gene activation by these factors.
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Affiliation(s)
- Daniel Schill
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Joshua Nord
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Lisa Ann Cirillo
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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157
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The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell. J Struct Biol 2018; 204:191-198. [PMID: 30110657 DOI: 10.1016/j.jsb.2018.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/05/2018] [Accepted: 08/09/2018] [Indexed: 11/21/2022]
Abstract
Protein-DNA interactions are highly dependent on salt concentration. To gain insight into how such interactions are maintained in the highly saline cytoplasm of halophilic archaea, we determined the 3-D structure of VNG0258H/RosR, the first haloarchaeal DNA-binding protein from the extreme halophilic archaeon Halobactrium salinarum. It is a dimeric winged-helix-turn-helix (wHTH) protein with unique features due to adaptation to the halophilic environment. As ions are major players in DNA binding processes, particularly in halophilic environments, we investigated the solution structure of the ionic envelope and located anions in the first shell around the protein in the crystal using anomalous scattering. Anions that were found to be tightly bound to residues in the positively charged DNA-binding site would probably be released upon DNA binding and will thus make significant contribution to the driving force of the binding process. Unexpectedly, ions were also found in a buried internal cavity connected to the external medium by a tunnel. Our structure lays a solid groundwork for future structural, computational and biochemical studies on complexes of the protein with cognate DNA sequences, with implications to protein-DNA interactions in hyper-saline environments.
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158
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Lai X, Verhage L, Hugouvieux V, Zubieta C. Pioneer Factors in Animals and Plants-Colonizing Chromatin for Gene Regulation. Molecules 2018; 23:E1914. [PMID: 30065231 PMCID: PMC6222629 DOI: 10.3390/molecules23081914] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 01/08/2023] Open
Abstract
Unlike most transcription factors (TF), pioneer TFs have a specialized role in binding closed regions of chromatin and initiating the subsequent opening of these regions. Thus, pioneer TFs are key factors in gene regulation with critical roles in developmental transitions, including organ biogenesis, tissue development, and cellular differentiation. These developmental events involve some major reprogramming of gene expression patterns, specifically the opening and closing of distinct chromatin regions. Here, we discuss how pioneer TFs are identified using biochemical and genome-wide techniques. What is known about pioneer TFs from animals and plants is reviewed, with a focus on the strategies used by pioneer factors in different organisms. Finally, the different molecular mechanisms pioneer factors used are discussed, highlighting the roles that tertiary and quaternary structures play in nucleosome-compatible DNA-binding.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
| | - Leonie Verhage
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
| | - Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
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159
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Liu L, Zhai C, Pan Y, Zhu Y, Shi W, Wang J, Yan X, Su X, Song Y, Gao L, Li M. Sphingosine-1-phosphate induces airway smooth muscle cell proliferation, migration, and contraction by modulating Hippo signaling effector YAP. Am J Physiol Lung Cell Mol Physiol 2018; 315:L609-L621. [PMID: 29999407 DOI: 10.1152/ajplung.00554.2017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Sphingosine-1-phosphate (S1P), a bioactive lipid, has been shown to be elevated in the airways of individuals with asthma and modulates the airway smooth muscle cell (ASMC) functions, yet its underlying molecular mechanisms are not completely understood. The aim of the present study is to address this issue. S1P induced yes-associated protein (YAP) dephosphorylation and nuclear localization via the S1PR2/3/Rho-associated protein kinase (ROCK) pathway, and this in turn increased forkhead box M1 (FOXM1) and cyclin D1 expression leading to ASMC proliferation, migration, and contraction. Pretreatment of cells with S1PR2 antagonist JTE013, S1PR3 antagonist CAY10444, or ROCK inhibitor Y27632 blocked S1P-induced alterations of YAP, FOXM1, cyclin D1, and ASMC proliferation, migration, and contraction. In addition, prior silencing of YAP or FOXM1 with siRNA reversed the effect of S1P on ASMC functions. Taken together, our study indicates that S1P stimulates ASMC proliferation, migration, and contraction by binding to S1PR2/3 and modulating ROCK/YAP/FOXM1 axis and suggests that targeting this pathway might have potential value in the management of asthma.
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Affiliation(s)
- Lu Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Cui Zhai
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Yilin Pan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Yanting Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Wenhua Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Jian Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Xin Yan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Xiaofan Su
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Yang Song
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
| | - Li Gao
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Manxiang Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an, Shaanxi , People's Republic of China
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160
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Abstract
Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within nucleosome-depleted regions of DNA fall into six distinct classes. These patterns are highly consistent across cell types and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest that TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence. Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ∼500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers.
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161
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Foxn1 in Skin Development, Homeostasis and Wound Healing. Int J Mol Sci 2018; 19:ijms19071956. [PMID: 29973508 PMCID: PMC6073674 DOI: 10.3390/ijms19071956] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023] Open
Abstract
Intensive research effort has focused on cellular and molecular mechanisms that regulate skin biology, including the phenomenon of scar-free skin healing during foetal life. Transcription factors are the key molecules that tune gene expression and either promote or suppress gene transcription. The epidermis is the source of transcription factors that regulate many functions of epidermal cells such as proliferation, differentiation, apoptosis, and migration. Furthermore, the activation of epidermal transcription factors also causes changes in the dermal compartment of the skin. This review focuses on the transcription factor Foxn1 and its role in skin biology. The regulatory function of Foxn1 in the skin relates to physiological (development and homeostasis) and pathological (skin wound healing) conditions. In particular, the pivotal role of Foxn1 in skin development and the acquisition of the adult skin phenotype, which coincides with losing the ability of scar-free healing, is discussed. Thus, genetic manipulations with Foxn1 expression, specifically those introducing conditional Foxn1 silencing in a Foxn1+/+ organism or its knock-in in a Foxn1−/− model, may provide future perspectives for regenerative medicine.
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162
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Quintero-Ronderos P, Laissue P. The multisystemic functions of FOXD1 in development and disease. J Mol Med (Berl) 2018; 96:725-739. [PMID: 29959475 DOI: 10.1007/s00109-018-1665-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/18/2018] [Accepted: 06/21/2018] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) participate in a wide range of cellular processes due to their inherent function as essential regulatory proteins. Their dysfunction has been linked to numerous human diseases. The forkhead box (FOX) family of TFs belongs to the "winged helix" superfamily, consisting of proteins sharing a related winged helix-turn-helix DNA-binding motif. FOX genes have been extensively present during vertebrates and invertebrates' evolution, participating in numerous molecular cascades and biological functions, such as embryonic development and organogenesis, cell cycle regulation, metabolism control, stem cell niche maintenance, signal transduction, and many others. FOXD1, a forkhead TF, has been related to different key biological processes such as kidney and retina development and embryo implantation. FOXD1 dysfunction has been linked to different pathologies, thereby constituting a diagnostic biomarker and a promising target for future therapies. This paper aims to present, for the first time, a comprehensive review of FOXD1's role in mouse development and human disease. Molecular, structural, and functional aspects of FOXD1 are presented in light of physiological and pathogenic conditions, including its role in human disease aetiology, such as cancer and recurrent pregnancy loss. Taken together, the information given here should enable a better understanding of FOXD1 function for basic science researchers and clinicians.
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Affiliation(s)
- Paula Quintero-Ronderos
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, Colombia
| | - Paul Laissue
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, Colombia.
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163
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Fuglerud BM, Ledsaak M, Rogne M, Eskeland R, Gabrielsen OS. The pioneer factor activity of c-Myb involves recruitment of p300 and induction of histone acetylation followed by acetylation-induced chromatin dissociation. Epigenetics Chromatin 2018; 11:35. [PMID: 29954426 PMCID: PMC6022509 DOI: 10.1186/s13072-018-0208-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background The concept of pioneer transcription factors is emerging as an essential part of the epigenetic regulation, taking place during cell development and differentiation. However, the precise molecular mechanism underlying pioneer factor activity remains poorly understood. We recently reported that the transcription factor c-Myb acts as a pioneer factor in haematopoiesis, and a point mutation in its DNA binding domain, D152V, is able to abrogate this function. Results Here, we show that specific histone modifications, including H3K27ac, prevent binding of c-Myb to histone tails, representing a novel effect of histone modifications, namely restricting binding of a pioneer factor to chromatin. Furthermore, we have taken advantage of the pioneer-defect D152V mutant to investigate mechanisms of c-Myb’s pioneer factor activity. We show that c-Myb-dependent transcriptional activation of a gene in inaccessible chromatin relies on c-Myb binding to histones, as well as on c-Myb interacting with the histone acetyltransferase p300. ChIP assays show that both wild type and the D152V mutant of c-Myb bind to a selected target gene at its promoter and enhancer, but only wild-type c-Myb causes opening and activation of the locus. Enhancement of histone acetylation restores activation of the same gene in the absence of c-Myb, suggesting that facilitating histone acetylation is a crucial part of the pioneer factor function of c-Myb. Conclusions We suggest a pioneer factor model in which c-Myb binds to regions of closed chromatin and then recruits histone acetyltransferases. By binding to histones, c-Myb facilitates histone acetylation, acting as a cofactor for p300 at c-Myb bound sites. The resulting H3K27ac leads to chromatin opening and detachment of c-Myb from the acetylated chromatin. We propose that the latter phenomenon, acetylation-induced chromatin dissociation, represents a mechanism for controlling the dynamics of pioneer factor binding to chromatin. Electronic supplementary material The online version of this article (10.1186/s13072-018-0208-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bettina M Fuglerud
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Marit Ledsaak
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Marie Rogne
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, 0379, Norway
| | - Odd S Gabrielsen
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway.
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164
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Iwafuchi-Doi M. The mechanistic basis for chromatin regulation by pioneer transcription factors. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1427. [PMID: 29949240 PMCID: PMC6585746 DOI: 10.1002/wsbm.1427] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/18/2018] [Accepted: 06/05/2018] [Indexed: 01/30/2023]
Abstract
Pioneer transcription factors play a primary role in establishing competence for gene expression and initiating cellular programming and reprogramming, and their dysregulation causes severe effects on human health, such as promoting tumorigenesis. Although more than 200 transcription factors are expressed in each cell type, only a small number of transcription factors are necessary to elicit dramatic cell‐fate changes in embryonic development and cell‐fate conversion. Among these key transcription factors, a subset called “pioneer transcription factors” have a remarkable ability to target nucleosomal DNA, or closed chromatin, early in development, often leading to the local opening of chromatin, thereby establishing competence for gene expression. Although more key transcription factors have been identified as pioneer transcription factors, the molecular mechanisms behind their special properties are only beginning to be revealed. Understanding the pioneering mechanisms will enhance our ability to precisely control cell fate at will for research and therapeutic purposes. This article is categorized under:Biological Mechanisms > Cell Fates Biological Mechanisms > Regulatory Biology Developmental Biology > Lineages
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
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165
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Morris G, Stoychev S, Naicker P, Dirr HW, Fanucchi S. The forkhead domain hinge-loop plays a pivotal role in DNA binding and transcriptional activity of FOXP2. Biol Chem 2018; 399:881-893. [DOI: 10.1515/hsz-2018-0185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/26/2018] [Indexed: 01/01/2023]
Abstract
Abstract
Forkhead box (FOX) proteins are a ubiquitously expressed family of transcription factors that regulate the development and differentiation of a wide range of tissues in animals. The FOXP subfamily members are the only known FOX proteins capable of forming domain-swapped forkhead domain (FHD) dimers. This is proposed to be due to an evolutionary mutation (P539A) that lies in the FHD hinge loop, a key region thought to fine-tune DNA sequence specificity in the FOX transcription factors. Considering the importance of the hinge loop in both the dimerisation mechanism of the FOXP FHD and its role in tuning DNA binding, a detailed investigation into the implications of mutations within this region could provide important insight into the evolution of the FOX family. Isothermal titration calorimetry and hydrogen exchange mass spectroscopy were used to study the thermodynamic binding signature and changes in backbone dynamics of FOXP2 FHD DNA binding. Dual luciferase reporter assays were performed to study the effect that the hinge-loop mutation has on FOXP2 transcriptional activity in vivo. We demonstrate that the change in dynamics of the hinge-loop region of FOXP2 alters the energetics and mechanism of DNA binding highlighting the critical role of hinge loop mutations in regulating DNA binding characteristics of the FOX proteins.
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Affiliation(s)
- Gavin Morris
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology , University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein , 2050 Johannesburg, Gauteng , South Africa
| | - Stoyan Stoychev
- CSIR Biosciences, CSIR, Meiring Naude Road , Brummeria, 0001 Pretoria, Gauteng , South Africa
| | - Previn Naicker
- CSIR Biosciences, CSIR, Meiring Naude Road , Brummeria, 0001 Pretoria, Gauteng , South Africa
| | - Heini W. Dirr
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology , University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein , 2050 Johannesburg, Gauteng , South Africa
| | - Sylvia Fanucchi
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology , University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein , 2050 Johannesburg, Gauteng , South Africa
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166
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Sartorelli V, Puri PL. Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master. Mol Cell 2018; 71:375-388. [PMID: 29887393 DOI: 10.1016/j.molcel.2018.04.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/05/2018] [Accepted: 04/27/2018] [Indexed: 01/14/2023]
Abstract
Since its discovery as a skeletal muscle-specific transcription factor able to reprogram somatic cells into differentiated myofibers, MyoD has provided an instructive model to understand how transcription factors regulate gene expression. Reciprocally, studies of other transcriptional regulators have provided testable hypotheses to further understand how MyoD activates transcription. Using MyoD as a reference, in this review, we discuss the similarities and differences in the regulatory mechanisms employed by tissue-specific transcription factors to access DNA and regulate gene expression by cooperatively shaping the chromatin landscape within the context of cellular differentiation.
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Affiliation(s)
- Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA 92037, USA; Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, Rome, Italy.
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167
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Whitton H, Singh LN, Patrick MA, Price AJ, Osorio FG, López‐Otín C, Bochkis IM. Changes at the nuclear lamina alter binding of pioneer factor Foxa2 in aged liver. Aging Cell 2018; 17:e12742. [PMID: 29484800 PMCID: PMC5946061 DOI: 10.1111/acel.12742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2018] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that regulation of heterochromatin at the nuclear envelope underlies metabolic disease susceptibility and age-dependent metabolic changes, but the mechanism is unknown. Here, we profile lamina-associated domains (LADs) using lamin B1 ChIP-Seq in young and old hepatocytes and find that, although lamin B1 resides at a large fraction of domains at both ages, a third of lamin B1-associated regions are bound exclusively at each age in vivo. Regions occupied by lamin B1 solely in young livers are enriched for the forkhead motif, bound by Foxa pioneer factors. We also show that Foxa2 binds more sites in Zmpste24 mutant mice, a progeroid laminopathy model, similar to increased Foxa2 occupancy in old livers. Aged and Zmpste24-deficient livers share several features, including nuclear lamina abnormalities, increased Foxa2 binding, de-repression of PPAR- and LXR-dependent gene expression, and fatty liver. In old livers, additional Foxa2 binding is correlated to loss of lamin B1 and heterochromatin (H3K9me3 occupancy) at these loci. Our observations suggest that changes at the nuclear lamina are linked to altered Foxa2 binding, enabling opening of chromatin and de-repression of genes encoding lipid synthesis and storage targets that contribute to etiology of hepatic steatosis.
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Affiliation(s)
| | - Larry N. Singh
- Center for Mitochondrial and Epigenomic MedicineChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | | | - Andrew J. Price
- Department of PharmacologyUniversity of VirginiaCharlottesvilleVAUSA
| | - Fernando G. Osorio
- Departamento de Bioquímica y Biología MolecularFacultad de MedicinaInstituto Universitario de Oncología (IUOPA)Universidad de OviedoOviedoSpain
| | - Carlos López‐Otín
- Departamento de Bioquímica y Biología MolecularFacultad de MedicinaInstituto Universitario de Oncología (IUOPA)Universidad de OviedoOviedoSpain
- Centro de Investigación Biomédica en Red de CáncerMadridSpain
| | - Irina M. Bochkis
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Department of PharmacologyUniversity of VirginiaCharlottesvilleVAUSA
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168
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Jiang S, Yang Z, Di S, Hu W, Ma Z, Chen F, Yang Y. Novel role of forkhead box O 4 transcription factor in cancer: Bringing out the good or the bad. Semin Cancer Biol 2018; 50:1-12. [DOI: 10.1016/j.semcancer.2018.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 04/28/2018] [Indexed: 10/17/2022]
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169
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Wei C, Lin H, Cui S. The Forkhead Transcription Factor FOXC2 Is Required for Maintaining Murine Spermatogonial Stem Cells. Stem Cells Dev 2018; 27:624-636. [DOI: 10.1089/scd.2017.0233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Chao Wei
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Hao Lin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Sheng Cui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
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170
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Malik V, Zimmer D, Jauch R. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming. Cell Mol Life Sci 2018; 75:1587-1612. [PMID: 29335749 PMCID: PMC11105716 DOI: 10.1007/s00018-018-2748-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite 'two-in-one' DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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171
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Ramirez-Sarmiento CA, Komives EA. Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions. Methods 2018; 144:43-52. [PMID: 29627358 DOI: 10.1016/j.ymeth.2018.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 11/29/2022] Open
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDXMS) has emerged as a powerful approach for revealing folding and allostery in protein-protein interactions. The advent of higher resolution mass spectrometers combined with ion mobility separation and ultra performance liquid chromatographic separations have allowed the complete coverage of large protein sequences and multi-protein complexes. Liquid-handling robots have improved the reproducibility and accurate temperature control of the sample preparation. Many researchers are also appreciating the power of combining biophysical approaches such as stopped-flow fluorescence, single molecule FRET, and molecular dynamics simulations with HDXMS. In this review, we focus on studies that have used a combination of approaches to reveal (re)folding of proteins as well as on long-distance allosteric changes upon interaction.
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Affiliation(s)
- Cesar A Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, United States.
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172
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Abstract
Pioneer transcription factors have the unique and important role of unmasking chromatin domains during development to allow the implementation of new cellular programs. Compared with those of other transcription factors, this activity implies that pioneer factors can recognize their target DNA sequences in so-called compacted or "closed" heterochromatin and can trigger remodeling of the adjoining chromatin landscape to provide accessibility to nonpioneer transcription factors. Recent studies identified several steps of pioneer action, namely rapid but weak initial binding to heterochromatin and stabilization of binding followed by chromatin opening and loss of cytosine-phosphate-guanine (CpG) methylation that provides epigenetic memory. Whereas CpG demethylation depends on replication, chromatin opening does not. In this Minireview, we highlight the unique properties of this transcription factor class and the challenges of understanding their mechanism of action.
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Affiliation(s)
- Alexandre Mayran
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
| | - Jacques Drouin
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
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173
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Sakaguchi I, Fukasawa T, Fujimoto K, Inouye M. Immobilization of Crosslinked Peptides that Possess High Helical Contents and Their Binding to Target DNAs on Au Surfaces. CHEM LETT 2018. [DOI: 10.1246/cl.171153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ikumi Sakaguchi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Toshiaki Fukasawa
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kazuhisa Fujimoto
- Department of Applied Chemistry and Biochemistry, Kyushu Sangyo University, Fukuoka 813-8503, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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174
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Casey BH, Kollipara RK, Pozo K, Johnson JE. Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors. Genome Res 2018; 28:484-496. [PMID: 29500235 PMCID: PMC5880239 DOI: 10.1101/gr.224360.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 02/28/2018] [Indexed: 12/27/2022]
Abstract
During development, transcription factors select distinct gene programs, providing the necessary regulatory complexity for temporal and tissue-specific gene expression. How related factors retain specificity, especially when they recognize the same DNA motifs, is not understood. We address this paradox using basic helix-loop-helix (bHLH) transcription factors ASCL1, ASCL2, and MYOD1, crucial mediators of lineage specification. In vivo, these factors recognize the same DNA motifs, yet bind largely different genomic sites and regulate distinct transcriptional programs. This suggests that their ability to identify regulatory targets is defined either by the cellular environment of the partially defined lineages in which they are endogenously expressed, or by intrinsic properties of the factors themselves. To distinguish between these mechanisms, we directly compared the chromatin binding properties of this subset of bHLH factors when ectopically expressed in embryonic stem cells, presenting them with a common chromatin landscape and cellular components. We find that these factors retain distinct binding sites; thus, specificity of binding is an intrinsic property not requiring a restricted landscape or lineage-specific cofactors. Although the ASCL factors and MYOD1 have some distinct DNA motif preference, it is not sufficient to explain the extent of the differential binding. All three factors can bind inaccessible chromatin and induce changes in chromatin accessibility and H3K27ac. A reiterated pattern of DNA binding motifs is uniquely enriched in inaccessible chromatin at sites bound by these bHLH factors. These combined properties define a subclass of lineage-specific bHLH factors and provide context for their central roles in development and disease.
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Affiliation(s)
- Bradford H Casey
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Karine Pozo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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175
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Wang Y, Yun Y, Wu B, Wen L, Wen M, Yang H, Zhao L, Liu W, Huang S, Wen N, Li Y. FOXM1 promotes reprogramming of glucose metabolism in epithelial ovarian cancer cells via activation of GLUT1 and HK2 transcription. Oncotarget 2018; 7:47985-47997. [PMID: 27351131 PMCID: PMC5216994 DOI: 10.18632/oncotarget.10103] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/12/2016] [Indexed: 02/07/2023] Open
Abstract
Cancer cells exhibit the reprogrammed metabolism mainly via aerobic glycolysis, a phenomenon known historically as the Warburg effect; however, the underlying mechanisms remain largely unknown. In this study, we characterized the critical role of transcription factor Forkhead box protein M1 (FOXM1) in aerobic glycolysis of human epithelial ovarian cancer (EOC) and its molecular mechanisms. Our data showed that aberrant expression of FOXM1 significantly contributed to the reprogramming of glucose metabolism in EOC cells. Aerobic glycolysis and cell proliferation were down-regulated in EOC cells when FOXM1 gene expression was suppressed by RNA interference. Moreover, knockdown of FOXM1 in EOC cells significantly reduced glucose transporter 1 (GLUT1) and hexokinase 2 (HK2) expression. FOXM1 bound directly to the GLUT1 and HK2 promoter regions and regulated the promoter activities and the expression of the genes at the transcriptional level. This reveals a novel mechanism by which glucose metabolism is regulated by FOXM1. Importantly, we further demonstrated that the expression levels of FOXM1, GLUT1 and HK2 were significantly increased in human EOC tissues relative to normal ovarian tissues, and that FOXM1 expression was positively correlated with GLUT1 and HK2 expression. Taken together, our results show that FOXM1 promotes reprogramming of glucose metabolism in EOC cells via activation of GLUT1 and HK2 transcription, suggesting that FOXM1 may be an important target in aerobic glycolysis pathway for developing novel anticancer agents.
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Affiliation(s)
- Yu Wang
- Department of Oncology, State Key Discipline of Cell Biology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China.,Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Yuyu Yun
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Bo Wu
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Li Wen
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Mingling Wen
- Department of Pharmacy, Affiliated Hospital of Academy of Military Medical Sciences, Beijing, China
| | - Huiling Yang
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Lisheng Zhao
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Wenchao Liu
- Department of Oncology, State Key Discipline of Cell Biology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Suyun Huang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Program in Cancer Biology, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas, USA
| | - Ning Wen
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Yu Li
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, Shaanxi, China
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176
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Vajravelu ME, Chai J, Krock B, Baker S, Langdon D, Alter C, De León DD. Congenital Hyperinsulinism and Hypopituitarism Attributable to a Mutation in FOXA2. J Clin Endocrinol Metab 2018; 103:1042-1047. [PMID: 29329447 PMCID: PMC6276717 DOI: 10.1210/jc.2017-02157] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/05/2018] [Indexed: 12/14/2022]
Abstract
CONTEXT Persistent hypoglycemia in the newborn period most commonly occurs as a result of hyperinsulinism. The phenotype of hypoketotic hypoglycemia can also result from pituitary hormone deficiencies, including growth hormone and adrenocorticotropic hormone deficiency. Forkhead box A2 (Foxa2) is a transcription factor shown in mouse models to influence insulin secretion by pancreatic β cells. In addition, Foxa2 is involved in regulation of pituitary development, and deletions of FOXA2 have been linked to panhypopituitarism. OBJECTIVE To describe an infant with congenital hyperinsulinism and hypopituitarism as a result of a mutation in FOXA2 and to determine the functional impact of the identified mutation. MAIN OUTCOME MEASURE Difference in wild-type (WT) vs mutant Foxa2 transactivation of target genes that are critical for β cell function (ABCC8, KNCJ11, HADH) and pituitary development (GLI2, NKX2-2, SHH). RESULTS Transactivation by mutant Foxa2 of all genes studied was substantially decreased compared with WT. CONCLUSIONS We report a mutation in FOXA2 leading to congenital hyperinsulinism and hypopituitarism and provide functional evidence of the molecular mechanism responsible for this phenotype.
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Affiliation(s)
- Mary Ellen Vajravelu
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Jinghua Chai
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Bryan Krock
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Samuel Baker
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - David Langdon
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Craig Alter
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Diva D De León
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Correspondence and Reprint Requests: Diva D. De León, MD, Division of Endocrinology and Diabetes, Children’s Hospital
of Philadelphia, 3615 Civic Center Boulevard, Ambramson Research Center, Room 802A,
Philadelphia, Pennsylvania 19104. E-mail:
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177
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Zhang F, Ma X, Li H, Zhang Y, Li X, Chen L, Guo G, Gao Y, Gu L, Xie Y, Duan J, Zhang X. FOXK2 suppresses the malignant phenotype and induces apoptosis through inhibition of EGFR in clear-cell renal cell carcinoma. Int J Cancer 2018; 142:2543-2557. [PMID: 29368368 DOI: 10.1002/ijc.31278] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 08/18/2017] [Accepted: 01/18/2018] [Indexed: 12/26/2022]
Abstract
Forkhead box K2 (FOXK2) belongs to the forkhead box transcription factor family. Recent studies have revealed that FOXK2 plays essential roles in cancer cell proliferation and survival. However, the biological function of FOXK2 in renal cell carcinoma remains unexplored. In our study, we demonstrated that FOXK2 mRNA and protein levels were decreased in clear-cell renal cell carcinoma (ccRCC) tissues compared to those in corresponding non-tumor renal tissues, and decreased FOXK2 levels were associated with poor prognosis in ccRCC patients after nephrectomy. FOXK2 suppressed proliferation, migration and invasion capabilities of ccRCC cells and induced cellular apoptosis in vitro. Moreover, we found that FOXK2 overexpression inhibited xenograft tumor growth and promoted apoptosis in vivo. Genome-wide transcriptome profiling using FOXK2 overexpressed 769-P cells revealed that the epidermal growth factor receptor (EGFR) was a potential downstream gene of FOXK2. Overexpression of EGFR is able to rescue the inhibited proliferation capacity and the enhanced apoptosis capacity due to the overexpression of FOXK2 in 769-P cells. Collectively, our results indicate that FOXK2 inhibits the malignant phenotype of ccRCC and acts as a tumor suppressor possibly through the inhibition of EGFR.
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Affiliation(s)
- Fan Zhang
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Xin Ma
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Hongzhao Li
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Xintao Li
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Luyao Chen
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Gang Guo
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yu Gao
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Liangyou Gu
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yongpeng Xie
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China.,Medical School, Nankai University, Tianjin, People's Republic of China
| | - Junyao Duan
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China.,Medical School, Nankai University, Tianjin, People's Republic of China
| | - Xu Zhang
- State Key Laboratory of Kidney Diseases, Department of Urology, Chinese PLA General Hospital, Beijing, People's Republic of China
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178
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Takakado A, Nakasone Y, Terazima M. Sequential DNA Binding and Dimerization Processes of the Photosensory Protein EL222. Biochemistry 2018; 57:1603-1610. [DOI: 10.1021/acs.biochem.7b01206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akira Takakado
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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179
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Lv C, Zhao G, Sun X, Wang P, Xie N, Luo J, Tong T. Acetylation of FOXM1 is essential for its transactivation and tumor growth stimulation. Oncotarget 2018; 7:60366-60382. [PMID: 27542221 PMCID: PMC5312389 DOI: 10.18632/oncotarget.11332] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/10/2016] [Indexed: 11/25/2022] Open
Abstract
Forkhead box transcription factor M1 (FOXM1) plays crucial roles in a wide array of biological processes, including cell proliferation and differentiation, the cell cycle, and tumorigenesis by regulating the expression of its target genes. Elevated expression of FOXM1 is frequently observed in a multitude of malignancies. Here we show that FOXM1 can be acetylated by p300/CBP at lysines K63, K422, K440, K603 and K614 in vivo. This modification is essential for its transactivation on the target genes. Acetylation of FOXM1 increases during the S phase and remains high throughout the G2 and M phases, when FOXM1 transcriptional activity is required. We find that the acetylation-deficient FOXM1 mutant is less active and exhibits significantly weaker tumorigenic activities compared to wild-type FOXM1. Mechanistically, the acetylation of FOXM1 enhances its transcriptional activity by increasing its DNA binding affinity, protein stability, and phosphorylation sensitivity. In addition, we demonstrate that NAD-dependent histone deacetylase SIRT1 physically binds to and deacetylates FOXM1 in vivo. The deacetylation of FOXM1 by SIRT1 attenuates its transcriptional activity and decreases its protein stability. Together, our findings demonstrate that the reversible acetylation of FOXM1 by p300/CBP and SIRT1 modulates its transactivation function.
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Affiliation(s)
- Cuicui Lv
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Ganye Zhao
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Xinpei Sun
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Pan Wang
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Nan Xie
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Jianyuan Luo
- Center for Medical Genetics, Department of Medical Genetics, Peking University Health Science Center, Beijing, China
| | - Tanjun Tong
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
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180
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Elian FA, Yan E, Walter MA. FOXC1, the new player in the cancer sandbox. Oncotarget 2018; 9:8165-8178. [PMID: 29487724 PMCID: PMC5814291 DOI: 10.18632/oncotarget.22742] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/28/2017] [Indexed: 01/01/2023] Open
Abstract
In recent years, rapidly accumulating evidence implicates forkhead box C1 (FOXC1) in cancer, especially in studies of basal-like breast cancer (BLBC). Other studies have followed suit, demonstrating that FOXC1 is not only a major player in this breast cancer subtype, but also in hepatocellular carcinoma (HCC), endometrial cancer, Hodgkin's lymphoma (HL), and non-Hodgkin's lymphoma (NHL). The FOXC1 gene encodes a transcription factor that is crucial to mesodermal, neural crest, and ocular development, and mutations found in FOXC1 have been found to cause dominantly inherited Axenfeld-Rieger Syndrome (ARS). Interestingly, while FOXC1 missense mutations that are associated with ARS usually reduce gene activity, increased FOXC1 function now appears to be often linked to more aggressive cancer phenotypes in BLBC, HCC, HL, and NHL. This review discusses not only the role of FOXC1 in cancer cell progression, proliferation, differentiation, and metastasis, but also the underlying mechanisms of how FOXC1 can contribute to aggressive cancer phenotypes.
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Affiliation(s)
- Fahed A. Elian
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elizabeth Yan
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael A. Walter
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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181
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Wang Y, Zhang W, Wen L, Yang H, Wen M, Yun Y, Zhao L, Zhu X, Tian L, Luo E, Li Y, Liu W, Wen N. FOXM1 confers resistance to gefitinib in lung adenocarcinoma via a MET/AKT-dependent positive feedback loop. Oncotarget 2018; 7:59245-59259. [PMID: 27494877 PMCID: PMC5312309 DOI: 10.18632/oncotarget.11043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/18/2016] [Indexed: 12/15/2022] Open
Abstract
Gefitinib resistance remains a major problem in the treatment of lung adenocarcinoma. However, the molecular mechanisms of gefitinib resistance are not fully understood. In this study, we characterized the critical role of transcription factor Forkhead box protein M1 (FOXM1) in gefitinib resistance of lung adenocarcinoma cells. In vitro drug sensitivity assays demonstrated that FOXM1 inhibition sensitized PC9/GR and HCC827/GR cells to gefitinib, whereas FOXM1 overexpression enhanced PC9 and HCC827 cell resistance to gefitinib. Increased FOXM1 resulted in the upregulation of hepatocyte growth factor receptor (MET), which led to activation of the protein kinase B (AKT) pathway, whereas knockdown of FOXM1 did the opposite. FOXM1 bound directly to the MET promoter regions and regulated the promoter activities and the expression of MET at the transcriptional level. Moreover, MET/AKT pathway upregulated the expression of FOXM1 in lung adenocarcinoma cells. Inhibition of pAKT by LY294002 or inhibition of pMET by PHA-665752 significantly inhibited the expression of FOXM1 in lung adenocarcinoma cells. Importantly, we further demonstrated that the expression levels of FOXM1, pAKT and MET were significantly increased in lung adenocarcinoma tissues relative to normal lung tissues, and these three biomarkers were concomitantly overexpressed in lung adenocarcinoma tissues. Taken together, our results indicate that FOXM1 promotes acquired resistance to gefitinib of lung adenocarcinoma cells, and FOXM1 crosstalks with MET/AKT signaling to form a positive feedback loop to promote lung adenocarcinoma development.
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Affiliation(s)
- Yu Wang
- Department of Oncology, State Key Discipline of Cell Biology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China.,Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Weiwei Zhang
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Li Wen
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Huiling Yang
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Mingling Wen
- Department of Pharmacy, Affiliated Hospital of Academy of Military Medical Sciences, Beijing, China
| | - Yuyu Yun
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Lisheng Zhao
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
| | - Xiaofei Zhu
- Department of Neurology, Kunming General Hospital, Chinese People's Liberation Army, Kunming, Yunnan, China
| | - Li Tian
- Department of Anesthesiology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Erping Luo
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yu Li
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wenchao Liu
- Department of Oncology, State Key Discipline of Cell Biology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ning Wen
- Institute of Stomatology, Chinese PLA General Hospital, Beijing, China
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182
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Burkett ZD, Day NF, Kimball TH, Aamodt CM, Heston JB, Hilliard AT, Xiao X, White SA. FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch. eLife 2018; 7:30649. [PMID: 29360038 PMCID: PMC5826274 DOI: 10.7554/elife.30649] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/22/2018] [Indexed: 11/26/2022] Open
Abstract
Human speech is one of the few examples of vocal learning among mammals yet ~half of avian species exhibit this ability. Its neurogenetic basis is largely unknown beyond a shared requirement for FoxP2 in both humans and zebra finches. We manipulated FoxP2 isoforms in Area X, a song-specific region of the avian striatopallidum analogous to human anterior striatum, during a critical period for song development. We delineate, for the first time, unique contributions of each isoform to vocal learning. Weighted gene coexpression network analysis of RNA-seq data revealed gene modules correlated to singing, learning, or vocal variability. Coexpression related to singing was found in juvenile and adult Area X whereas coexpression correlated to learning was unique to juveniles. The confluence of learning and singing coexpression in juvenile Area X may underscore molecular processes that drive vocal learning in young zebra finches and, by analogy, humans. Songbirds, much like in humans, have a critical period in youth when they are best at learning vocal communication skills. In birds, this is when they learn a song they will use later in life as a courtship song. In humans, this is when language skills are most easily learned. After this critical period ends, it is much harder for people to learn languages, and for certain bird species to learn their song. When birds sing every morning, the activity of a gene called FoxP2 drops, which causes a coordinated change in the activity of thousands of other genes. It is suspected that FoxP2 – and the changes it causes – could be a part of the molecular basis for vocal learning. FoxP2 is also known to play a role in speech in humans, and both birds and humans have a long and a short version of this gene. Previous research has shown that when the long version of the gene was altered so its activity would no longer decrease when birds were singing, the birds failed to learn their song. Moreover, humans with a mutation in the long version have problems with their speech. However, until now, it was not known if modifications to the short version had the same effect. Burkett et al. investigated whether there was a noticeable pattern in the effects of FoxP2 before and after the critical period in a songbird. The analysis found that during the critical period, a set of genes changed together as young birds learned to sing. This particular pattern disappeared as the birds aged and the critical period ended. Burkett et al. confirmed that when birds had the long version of FoxP2 altered, they were less able to learn. However, changing the short version of FoxP2 had little effect on learning but led to changes in the birds’ song. The genetic pathways identified in the experiments are known to be present in many different species, including humans. Related pathways have also been found to play a role in non-vocal learning in organisms as distantly related as rats and snails. This suggests that they could be acting as a blueprint for learning new skills. Few treatments for language impairments have been developed so far due to poor understanding of the molecular basis for vocal communication. The findings of this study could help to create new treatments for speech problems in people, such as children with autism or people with mutated versions of FoxP2.
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Affiliation(s)
- Zachary Daniel Burkett
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States.,Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, Los Angeles, United States
| | - Nancy F Day
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States
| | - Todd Haswell Kimball
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States.,Physiological Science Master's Degree Program, University of California, Los Angeles, Los Angeles, United States
| | - Caitlin M Aamodt
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States.,Interdepartmental Program in Neuroscience, University of California, Los Angeles, Los Angeles, United States
| | - Jonathan B Heston
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States.,Interdepartmental Program in Neuroscience, University of California, Los Angeles, Los Angeles, United States
| | - Austin T Hilliard
- Department of Biology, Stanford University, Stanford, Stanford, United States
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States.,Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, Los Angeles, United States
| | - Stephanie A White
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States.,Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, Los Angeles, United States.,Interdepartmental Program in Neuroscience, University of California, Los Angeles, Los Angeles, United States
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183
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Johansson P, Klein-Hitpass L, Choidas A, Habenberger P, Mahboubi B, Kim B, Bergmann A, Scholtysik R, Brauser M, Lollies A, Siebert R, Zenz T, Dührsen U, Küppers R, Dürig J. SAMHD1 is recurrently mutated in T-cell prolymphocytic leukemia. Blood Cancer J 2018; 8:11. [PMID: 29352181 PMCID: PMC5802577 DOI: 10.1038/s41408-017-0036-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/05/2017] [Accepted: 10/12/2017] [Indexed: 01/19/2023] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is an aggressive malignancy with a median survival of the patients of less than two years. Besides characteristic chromosomal translocations, frequent mutations affect the ATM gene, JAK/STAT pathway members, and epigenetic regulators. We here performed a targeted mutation analysis for 40 genes selected from a RNA sequencing of 10 T-PLL in a collection of 28 T-PLL, and an exome analysis of five further cases. Nonsynonymous mutations were identified in 30 of the 40 genes, 18 being recurrently mutated. We identified recurrently mutated genes previously unknown to be mutated in T-PLL, which are SAMHD1, HERC1, HERC2, PRDM2, PARP10, PTPRC, and FOXP1. SAMHD1 regulates cellular deoxynucleotide levels and acts as a potential tumor suppressor in other leukemias. We observed destructive mutations in 18% of cases as well as deletions in two further cases. Taken together, we identified additional genes involved in JAK/STAT signaling (PTPRC), epigenetic regulation (PRDM2), or DNA damage repair (SAMHD1, PARP10, HERC1, and HERC2) as being recurrently mutated in T-PLL. Thus, our study considerably extends the picture of pathways involved in molecular pathogenesis of T-PLL and identifies the tumor suppressor gene SAMHD1 with ~20% of T-PLL affected by destructive lesions likely as major player in T-PLL pathogenesis.
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Affiliation(s)
- Patricia Johansson
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany. .,Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
| | - Ludger Klein-Hitpass
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | | | - Bijan Mahboubi
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Anke Bergmann
- Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Kiel, Germany
| | - René Scholtysik
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Martina Brauser
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anna Lollies
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Reiner Siebert
- Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Kiel, Germany.,Institute of Human Genetics, University of Ulm and University Hospital of Ulm, Ulm, Germany
| | - Thorsten Zenz
- Department of Molecular Therapy in Haematology and Oncology, National Center for Tumor Diseases and German Cancer Research Center, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ulrich Dührsen
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jan Dürig
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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184
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Xu H, Huang S, Zhu X, Zhang W, Zhang X. FOXK1 promotes glioblastoma proliferation and metastasis through activation of Snail transcription. Exp Ther Med 2018; 15:3108-3116. [PMID: 29456714 DOI: 10.3892/etm.2018.5732] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/09/2017] [Indexed: 12/12/2022] Open
Abstract
Forkhead box K1 (FOXK1) has been identified to have a crucial function in development and oncogenesis. However, its role in glioblastoma has remained largely elusive and was therefore assessed in the present study. In human glioblastoma multiforme (GBM) tissue samples, FOXK1 was determined to be highly expressed compared with adjacent normal tissue samples. In addition, high levels of FOXK1 were detected in the T98G and LN18 GBM cell lines as compare with those in normal human astrocytes. Of note, high expression of FOXK1 was revealed to be associated with metastasis and tumor size. Loss- and gain-of-function experiments were then performed to determine whether FOXK1 regulates epithelial to mesenchymal transition (EMT) and cell proliferation. Knockdown of FOXK1 significantly suppressed EMT and metastasis of GBM cells, while ectopic expression of FOXK1 promoted them. A luciferase reporter assay and a chromatin immunoprecipitation assay revealed that FOXK1 activated the transcription of Snail. In addition, as the results indicated that FOXK1 promotes GBM cell proliferation, the potential effect of FOXK1 on the cell cycle and apoptosis were further assessed. While FOXK1 had no effect on apoptosis, it promoted cell proliferation via enhancing the S-phase population. In brief, the present study indicated that FOXK1 acts as an oncogene with a key function in glioblastoma cell proliferation and EMT.
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Affiliation(s)
- Haitao Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Shulan Huang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiaonan Zhu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Wangcheng Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiangyang Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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185
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Pellegrini L. Dual Roles of Ctf18-RFC: Loading the Clamp and Angling for the Polymerase. Structure 2018; 26:1-2. [DOI: 10.1016/j.str.2017.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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186
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Maiese K. Novel Treatment Strategies for the Nervous System: Circadian Clock Genes, Non-coding RNAs, and Forkhead Transcription Factors. Curr Neurovasc Res 2018; 15:81-91. [PMID: 29557749 PMCID: PMC6021214 DOI: 10.2174/1567202615666180319151244] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND With the global increase in lifespan expectancy, neurodegenerative disorders continue to affect an ever-increasing number of individuals throughout the world. New treatment strategies for neurodegenerative diseases are desperately required given the lack of current treatment modalities. METHODS Here, we examine novel strategies for neurodegenerative disorders that include circadian clock genes, non-coding Ribonucleic Acids (RNAs), and the mammalian forkhead transcription factors of the O class (FoxOs). RESULTS Circadian clock genes, non-coding RNAs, and FoxOs offer exciting prospects to potentially limit or remove the significant disability and death associated with neurodegenerative disorders. Each of these pathways has an intimate relationship with the programmed death pathways of autophagy and apoptosis and share a common link to the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1) and the mechanistic target of rapamycin (mTOR). Circadian clock genes are necessary to modulate autophagy, limit cognitive loss, and prevent neuronal injury. Non-coding RNAs can control neuronal stem cell development and neuronal differentiation and offer protection against vascular disease such as atherosclerosis. FoxOs provide exciting prospects to block neuronal apoptotic death and to activate pathways of autophagy to remove toxic accumulations in neurons that can lead to neurodegenerative disorders. CONCLUSION Continued work with circadian clock genes, non-coding RNAs, and FoxOs can offer new prospects and hope for the development of vital strategies for the treatment of neurodegenerative diseases. These innovative investigative avenues have the potential to significantly limit disability and death from these devastating disorders.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, Newark, New Jersey 07101
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187
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Enerbäck S, Nilsson D, Edwards N, Heglind M, Alkanderi S, Ashton E, Deeb A, Kokash FEB, Bakhsh ARA, Van't Hoff W, Walsh SB, D'Arco F, Daryadel A, Bourgeois S, Wagner CA, Kleta R, Bockenhauer D, Sayer JA. Acidosis and Deafness in Patients with Recessive Mutations in FOXI1. J Am Soc Nephrol 2017; 29:1041-1048. [PMID: 29242249 DOI: 10.1681/asn.2017080840] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/15/2017] [Indexed: 11/03/2022] Open
Abstract
Maintenance of the composition of inner ear fluid and regulation of electrolytes and acid-base homeostasis in the collecting duct system of the kidney require an overlapping set of membrane transport proteins regulated by the forkhead transcription factor FOXI1. In two unrelated consanguineous families, we identified three patients with novel homozygous missense mutations in FOXI1 (p.L146F and p.R213P) predicted to affect the highly conserved DNA binding domain. Patients presented with early-onset sensorineural deafness and distal renal tubular acidosis. In cultured cells, the mutations reduced the DNA binding affinity of FOXI1, which hence, failed to adequately activate genes crucial for normal inner ear function and acid-base regulation in the kidney. A substantial proportion of patients with a clinical diagnosis of inherited distal renal tubular acidosis has no identified causative mutations in currently known disease genes. Our data suggest that recessive mutations in FOXI1 can explain the disease in a subset of these patients.
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Affiliation(s)
- Sven Enerbäck
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden;
| | - Daniel Nilsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Noel Edwards
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Mikael Heglind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sumaya Alkanderi
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Emma Ashton
- North East Thames Regional Genetic Service Laboratories, London, United Kingdom
| | - Asma Deeb
- Pediatric Services, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Feras E B Kokash
- College of Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Abdul R A Bakhsh
- College of Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - William Van't Hoff
- Great Ormond Street Hospital for Children, National Health Service Foundation Trust, London, United Kingdom
| | - Stephen B Walsh
- University College London Centre for Nephrology, London, United Kingdom
| | - Felice D'Arco
- College of Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Arezoo Daryadel
- Institute of Physiology, University of Zürich, Zurich, Switzerland; and.,National Center for Competence in Research, National Center in Competence in Research Kidney.CH, Zurich, Switzerland
| | - Soline Bourgeois
- Institute of Physiology, University of Zürich, Zurich, Switzerland; and.,National Center for Competence in Research, National Center in Competence in Research Kidney.CH, Zurich, Switzerland
| | - Carsten A Wagner
- Institute of Physiology, University of Zürich, Zurich, Switzerland; and.,National Center for Competence in Research, National Center in Competence in Research Kidney.CH, Zurich, Switzerland
| | - Robert Kleta
- Great Ormond Street Hospital for Children, National Health Service Foundation Trust, London, United Kingdom.,University College London Centre for Nephrology, London, United Kingdom
| | - Detlef Bockenhauer
- Great Ormond Street Hospital for Children, National Health Service Foundation Trust, London, United Kingdom.,University College London Centre for Nephrology, London, United Kingdom
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
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188
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Grabarczyk DB, Silkenat S, Kisker C. Structural Basis for the Recruitment of Ctf18-RFC to the Replisome. Structure 2017; 26:137-144.e3. [PMID: 29225079 DOI: 10.1016/j.str.2017.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/20/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022]
Abstract
Ctf18-RFC is an alternative PCNA loader which plays important but poorly understood roles in multiple DNA replication-associated processes. To fulfill its specialist roles, the Ctf18-RFC clamp loader contains a unique module in which the Dcc1-Ctf8 complex is bound to the C terminus of Ctf18 (the Ctf18-1-8 module). Here, we report the structural and functional characterization of the heterotetrameric complex formed between Ctf18-1-8 and a 63 kDa fragment of DNA polymerase ɛ. Our data reveal that Ctf18-1-8 binds stably to the polymerase and far from its other functional sites, suggesting that Ctf18-RFC could be associated with Pol ɛ throughout normal replication as the leading strand clamp loader. We also show that Pol ɛ and double-stranded DNA compete to bind the same winged-helix domain on Dcc1, with Pol ɛ being the preferred binding partner, thus suggesting that there are two alternative pathways to recruit Ctf18-RFC to sites of replication.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
| | - Sabrina Silkenat
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
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189
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Yang Z, Jiang S, Cheng Y, Li T, Hu W, Ma Z, Chen F, Yang Y. FOXC1 in cancer development and therapy: deciphering its emerging and divergent roles. Ther Adv Med Oncol 2017; 9:797-816. [PMID: 29449899 PMCID: PMC5808840 DOI: 10.1177/1758834017742576] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
Forkhead box C1 (FOXC1) is an essential member of the forkhead box transcription factors and has been highlighted as an important transcriptional regulator of crucial proteins associated with a wide variety of carcinomas. FOXC1 regulates tumor-associated genes and is regulated by multiple pathways that control its mRNA expression and protein activity. Aberrant FOXC1 expression is involved in diverse tumorigenic processes, such as abnormal cell proliferation, cancer stem cell maintenance, cancer migration, and angiogenesis. Herein, we review the correlation between the expression of FOXC1 and tumor behaviors. We also summarize the mechanisms of the regulation of FOXC1 expression and activity in physiological and pathological conditions. In particular, we focus on the pathological processes of cancer targeted by FOXC1 and discuss whether FOXC1 is good or detrimental during tumor progression. Moreover, FOXC1 is highlighted as a clinical biomarker for diagnosis or prognosis in various human cancers. The information reviewed here should assist in experimental designs and emphasize the potential of FOXC1 as a therapeutic target for cancer.
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Affiliation(s)
- Zhi Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences, Northwest University, Xi'an, China Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Shuai Jiang
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yicheng Cheng
- Department of Stomatology, Bayi Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Tian Li
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Wei Hu
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Zhiqiang Ma
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Fulin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an 710069, China
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190
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Choi J, Bachmann AL, Tauscher K, Benda C, Fierz B, Müller J. DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation. Nat Struct Mol Biol 2017; 24:1039-1047. [DOI: 10.1038/nsmb.3488] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/20/2017] [Indexed: 12/20/2022]
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191
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Schneider B, Božíková P, Čech P, Svozil D, Černý J. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes (Basel) 2017; 8:E278. [PMID: 29057824 PMCID: PMC5664128 DOI: 10.3390/genes8100278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/06/2017] [Accepted: 10/13/2017] [Indexed: 01/21/2023] Open
Abstract
We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
| | - Paulína Božíková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
| | - Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic.
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
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192
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Festuccia N, Gonzalez I, Owens N, Navarro P. Mitotic bookmarking in development and stem cells. Development 2017; 144:3633-3645. [DOI: 10.1242/dev.146522] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The changes imposed on the nucleus, chromatin and its regulators during mitosis lead to the dismantlement of most gene regulatory processes. However, an increasing number of transcriptional regulators are being identified as capable of binding their genomic targets during mitosis. These so-called ‘mitotic bookmarking factors’ encompass transcription factors and chromatin modifiers that are believed to convey gene regulatory information from mother to daughter cells. In this Primer, we review mitotic bookmarking processes in development and stem cells and discuss the interest and potential importance of this concept with regard to epigenetic regulation and cell fate transitions involving cellular proliferation.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Nick Owens
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
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193
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Polycomb-like proteins link the PRC2 complex to CpG islands. Nature 2017; 549:287-291. [PMID: 28869966 PMCID: PMC5937281 DOI: 10.1038/nature23881] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 07/25/2017] [Indexed: 12/16/2022]
Abstract
The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and plays essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like proteins (PCLs), including PHF1, MTF2 and PHF19, are PRC2 associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate PRC2’s enzymatic activity or its recruitment to specific genomic loci4–13. Mammalian PRC2 binding sites are enriched in CG content, which correlate with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. In this study, we solved the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We found that the extended homologous (EH) regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a manner completely different from the canonical winged-helix motif-DNA recognition. We further showed that the PCL EH domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic cells. Our research provides the first direct evidence demonstrating that PCLs are critical for PRC2 recruitment to CpG islands, thereby further clarifying their roles in transcriptional regulation in vivo.
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194
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Weinhouse C. Mitochondrial-epigenetic crosstalk in environmental toxicology. Toxicology 2017; 391:5-17. [PMID: 28855114 DOI: 10.1016/j.tox.2017.08.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022]
Abstract
Crosstalk between the nuclear epigenome and mitochondria, both in normal physiological function and in responses to environmental toxicant exposures, is a developing sub-field of interest in environmental and molecular toxicology. The majority (∼99%) of mitochondrial proteins are encoded in the nuclear genome, so programmed communication among nuclear, cytoplasmic, and mitochondrial compartments is essential for maintaining cellular health. In this review, we will focus on correlative and mechanistic evidence for direct impacts of each system on the other, discuss demonstrated or potential crosstalk in the context of chemical insult, and highlight biological research questions for future study. We will first review the two main signaling systems: nuclear signaling to the mitochondria [anterograde signaling], best described in regulation of oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis in response to environmental signals received by the nucleus, and mitochondrial signals to the nucleus [retrograde signaling]. Both signaling systems can communicate intracellular energy needs or a need to compensate for dysfunction to maintain homeostasis, but both can also relay inappropriate signals in the presence of dysfunction in either system and contribute to adverse health outcomes. We will first review these two signaling systems and highlight known or biologically feasible epigenetic contributions to both, then briefly discuss the emerging field of epigenetic regulation of the mitochondrial genome, and finally discuss putative "crosstalk phenotypes", including biological phenomena, such as caloric restriction, maintenance of stemness, and circadian rhythm, and states of disease or loss of function, such as cancer and aging, in which both the nuclear epigenome and mitochondria are strongly implicated.
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Affiliation(s)
- Caren Weinhouse
- Duke Global Health Institute, Duke University, Durham, NC 27708, United States.
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195
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Abstract
Distinct combinations of transcription factors are necessary to elicit cell fate changes in embryonic development. Yet within each group of fate-changing transcription factors, a subset called 'pioneer factors' are dominant in their ability to engage silent, unmarked chromatin and initiate the recruitment of other factors, thereby imparting new function to regulatory DNA sequences. Recent studies have shown that pioneer factors are also crucial for cellular reprogramming and that they are implicated in the marked changes in gene regulatory networks that occur in various cancers. Here, we provide an overview of the contexts in which pioneer factors function, how they can target silent genes, and their limitations at regions of heterochromatin. Understanding how pioneer factors regulate gene expression greatly enhances our understanding of how specific developmental lineages are established as well as how cell fates can be manipulated.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
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196
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Structural and developmental expression of Ss-riok-2, an RIO protein kinase encoding gene of Strongyloides stercoralis. Sci Rep 2017; 7:8693. [PMID: 28821723 PMCID: PMC5562798 DOI: 10.1038/s41598-017-07991-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/03/2017] [Indexed: 01/29/2023] Open
Abstract
RIO kinases are essential atypical protein kinases in diverse prokaryotic and eukaryotic organisms, playing significant roles in yeast and humans. However, little is known about their functions in parasitic nematodes. In the present study, we have isolated and characterized the full-length cDNA, gDNA and a putative promoter of a RIOK-2 protein kinase (Ss-RIOK-2) encoding gene (Ss-riok-2) from Strongyloides stercoralis, a medically important parasitic nematode (Order Rhabditida). A three-dimensional structure (3D) model of Ss-RIOK-2 was generated using the Chaetomium thermophilum RIOK-2 protein kinase (Ct-RIOK-2) crystal structure 4GYG as a template. A docking study revealed some critical sites for ATP binding and metal binding. The putative promoter of Ss-riok-2 contains a number of conserved elements. RNAseq analysis revealed the highest levels of the Ss-riok-2 transcript in free-living females and parasitic females. To identify anatomical patterns of Ss-riok-2 expression in S. stercoralis, we observed expression patterns of a transgene construct encoding green fluorescent protein under the Ss-riok-2 promoter in post free-living S. stercoralis. Expression driven by this promoter predominated in intestinal cells. This study demonstrates significant advancement in molecular and cellular biological study of S. stercoralis and of parasitic nematodes generally, and provides a foundation for further functional genomic studies.
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197
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MicroRNAs as regulators and mediators of forkhead box transcription factors function in human cancers. Oncotarget 2017; 8:12433-12450. [PMID: 27999212 PMCID: PMC5355356 DOI: 10.18632/oncotarget.14015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/07/2016] [Indexed: 02/07/2023] Open
Abstract
Evidence has shown that microRNAs are widely implicated as indispensable components of tumor suppressive and oncogenic pathways in human cancers. Thus, identification of microRNA targets and their relevant pathways will contribute to the development of microRNA-based therapeutics. The forkhead box transcription factors regulate numerous processes including cell cycle progression, metabolism, metastasis and angiogenesis, thereby facilitating tumor initiation and progression. A complex network of protein and non-coding RNAs mediates the expression and activity of forkhead box transcription factors. In this review, we summarize the current knowledge and concepts concerning the involvement of microRNAs and forkhead box transcription factors and describe the roles of microRNAs-forkhead box axis in various disease states including tumor initiation and progression. Additionally, we describe some of the technical challenges in the use of the microRNA-forkhead box signaling pathway in cancer treatment.
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198
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Li J, Dantas Machado AC, Guo M, Sagendorf JM, Zhou Z, Jiang L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen Y. Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site. Biochemistry 2017. [PMID: 28644006 DOI: 10.1021/acs.biochem.7b00211] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). The FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry assays suggested that this region was required for optimal DNA binding. Structure comparison with the FOXA3-DBD bound to DNA revealed more major groove contacts and fewer minor groove contacts in the FOXA2 structure than in the FOXA3 structure. Structure comparison with the FOXO1-DBD bound to DNA showed that different forkhead proteins could induce different DNA conformations upon binding to identical DNA sequences. Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites.
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Affiliation(s)
- Jun Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Ming Guo
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Jared M Sagendorf
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Zhan Zhou
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Longying Jiang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China
| | - Daichao Wu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lingzhi Qu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lin Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Yongheng Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China.,Collaborative Innovation Center for Cancer Medicine , Guangzhou, Guangdong 510060, China
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199
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Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FoxP1. Biophys J 2017; 110:2349-2360. [PMID: 27276253 DOI: 10.1016/j.bpj.2016.04.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/04/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
The forkhead family of transcription factors (Fox) controls gene transcription during key processes such as regulation of metabolism, embryogenesis, and immunity. Structurally, Fox proteins feature a conserved DNA-binding domain known as forkhead. Interestingly, solved forkhead structures of members from the P subfamily (FoxP) show that they can oligomerize by three-dimensional domain swapping, whereby structural elements are exchanged between adjacent subunits, leading to an intertwined dimer. Recent evidence has largely stressed the biological relevance of domain swapping in FoxP, as several disease-causing mutations have been related to impairment of this process. Here, we explore the equilibrium folding and binding mechanism of the forkhead domain of wild-type FoxP1, and of two mutants that hinder DNA-binding (R53H) and domain swapping (A39P), using size-exclusion chromatography, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. Our results show that domain swapping of FoxP1 occurs at micromolar protein concentrations within hours of incubation and is energetically favored, in contrast to classical domain-swapping proteins. Also, DNA-binding mutations do not significantly affect domain swapping. Remarkably, equilibrium unfolding of dimeric FoxP1 follows a three-state N2 ↔ 2I ↔ 2U folding mechanism in which dimer dissociation into a monomeric intermediate precedes protein unfolding, in contrast to the typical two-state model described for most domain-swapping proteins, whereas the A39P mutant follows a two-state N ↔ U folding mechanism consistent with the second transition observed for dimeric FoxP1. Also, the free-energy change of the N ↔ U in A39P FoxP1 is ∼2 kcal⋅mol(-1) larger than the I ↔ U transition of both wild-type and R53H FoxP1. Finally, hydrogen-deuterium exchange mass spectrometry reveals that the intermediate strongly resembles the native state. Our results suggest that domain swapping in FoxP1 is at least partially linked to monomer folding stability and follows an unusual three-state folding mechanism, which might proceed via transient structural changes rather than requiring complete protein unfolding as do most domain-swapping proteins.
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200
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Engineering cell identity: establishing new gene regulatory and chromatin landscapes. Curr Opin Genet Dev 2017; 46:50-57. [PMID: 28667865 DOI: 10.1016/j.gde.2017.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/04/2017] [Accepted: 06/08/2017] [Indexed: 01/14/2023]
Abstract
Cellular reprogramming can be achieved by ectopically expressing transcription factors that directly convert one differentiated cell type into another, bypassing embryonic states. A number of different cell types have been generated by such 'direct lineage reprogramming' methods, but their practical utility has been limited because, in most protocols, the resulting populations are often partially differentiated or incompletely specified. Here, we review mechanisms of lineage reprogramming by pioneer transcription factors, a unique class of transcriptional regulators that has the capacity to engage with silent chromatin to activate target gene regulatory networks. We assess the possible barriers to successful reprogramming in the context of higher-order chromatin landscape, considering how the mechanistic relationship between nuclear organization and cell identity will be crucial to unlocking the full potential of cell fate engineering.
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