1
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Gopinathan G, Xu Q, Luan X, Diekwisch TGH. CFDP1 regulates the stability of pericentric heterochromatin thereby affecting RAN GTPase activity and mitotic spindle formation. PLoS Biol 2024; 22:e3002574. [PMID: 38630655 PMCID: PMC11023358 DOI: 10.1371/journal.pbio.3002574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 03/02/2024] [Indexed: 04/19/2024] Open
Abstract
The densely packed centromeric heterochromatin at minor and major satellites is comprised of H3K9me2/3 histones, the heterochromatin protein HP1α, and histone variants. In the present study, we sought to determine the mechanisms by which condensed heterochromatin at major and minor satellites stabilized by the chromatin factor CFDP1 affects the activity of the small GTPase Ran as a requirement for spindle formation. CFDP1 colocalized with heterochromatin at major and minor satellites and was essential for the structural stability of centromeric heterochromatin. Loss of CENPA, HP1α, and H2A.Z heterochromatin components resulted in decreased binding of the spindle nucleation facilitator RCC1 to minor and major satellite repeats. Decreased RanGTP levels as a result of diminished RCC1 binding interfered with chromatin-mediated microtubule nucleation at the onset of mitotic spindle formation. Rescuing chromatin H2A.Z levels in cells and mice lacking CFDP1 through knock-down of the histone chaperone ANP32E not only partially restored RCC1-dependent RanGTP levels but also alleviated CFDP1-knockout-related craniofacial defects and increased microtubule nucleation in CFDP1/ANP32E co-silenced cells. Together, these studies provide evidence for a direct link between condensed heterochromatin at major and minor satellites and microtubule nucleation through the chromatin protein CFDP1.
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Affiliation(s)
- Gokul Gopinathan
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Qian Xu
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Xianghong Luan
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Thomas G. H. Diekwisch
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
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2
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Giardoglou P, Deloukas P, Dedoussis G, Beis D. Cfdp1 Is Essential for Cardiac Development and Function. Cells 2023; 12:1994. [PMID: 37566073 PMCID: PMC10417793 DOI: 10.3390/cells12151994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide. A combination of environmental and genetic effectors modulates the risk of developing them. Thus, it is vital to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in Coronary Artery Disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family, and to date, its function and mechanism of action in Cardiovascular Development are still unclear. We utilized zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology, and ease of experimental manipulations. We showed that cfdp1 was expressed during development, and we tested two morpholinos and generated a cfdp1 mutant line. The cfdp1-/- embryos developed arrhythmic hearts and exhibited defective cardiac performance, which led to a lethal phenotype. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process. The cfdp1 zebrafish mutant line provides a valuable tool for unveiling the novel mechanism of regulating cardiac physiology and function. cfdp1 is essential for cardiac development, a previously unreported phenotype most likely due to early lethality in mice. The detected phenotype of bradycardia and arrhythmias is an observation with potential clinical relevance for humans carrying heterozygous CFDP1 mutations and their risk of developing CAD.
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Affiliation(s)
- Panagiota Giardoglou
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Panos Deloukas
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London Medical School, Queen Mary University of London, London E1 4NS, UK;
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Dimitris Beis
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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3
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Araúzo-Bravo MJ, Erichsen L, Ott P, Beermann A, Sheikh J, Gerovska D, Thimm C, Bendhack ML, Santourlidis S. Consistent DNA Hypomethylations in Prostate Cancer. Int J Mol Sci 2022; 24:ijms24010386. [PMID: 36613831 PMCID: PMC9820221 DOI: 10.3390/ijms24010386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/14/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
With approximately 1.4 million men annually diagnosed with prostate cancer (PCa) worldwide, PCa remains a dreaded threat to life and source of devastating morbidity. In recent decades, a significant decrease in age-specific PCa mortality has been achieved by increasing prostate-specific antigen (PSA) screening and improving treatments. Nevertheless, upcoming, augmented recommendations against PSA screening underline an escalating disproportion between the benefit and harm of current diagnosis/prognosis and application of radical treatment standards. Undoubtedly, new potent diagnostic and prognostic tools are urgently needed to alleviate this tensed situation. They should allow a more reliable early assessment of the upcoming threat, in order to enable applying timely adjusted and personalized therapy and monitoring. Here, we present a basic study on an epigenetic screening approach by Methylated DNA Immunoprecipitation (MeDIP). We identified genes associated with hypomethylated CpG islands in three PCa sample cohorts. By adjusting our computational biology analyses to focus on single CpG-enriched 60-nucleotide-long DNA probes, we revealed numerous consistently differential methylated DNA segments in PCa. They were associated among other genes with NOTCH3, CDK2AP1, KLK4, and ADAM15. These can be used for early discrimination, and might contribute to a new epigenetic tumor classification system of PCa. Our analysis shows that we can dissect short, differential methylated CpG-rich DNA fragments and combinations of them that are consistently present in all tumors. We name them tumor cell-specific differential methylated CpG dinucleotide signatures (TUMS).
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Affiliation(s)
- Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Lars Erichsen
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Pauline Ott
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Agnes Beermann
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jamal Sheikh
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Chantelle Thimm
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Marcelo L. Bendhack
- Department of Urology, University Hospital, Positivo University, Curitiba 80420-011, Brazil
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Correspondence:
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4
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Itoh T, Inoue S, Sun X, Kusuda R, Hibi M, Shimizu T. Cfdp1 controls the cell cycle and neural differentiation in the zebrafish cerebellum and retina. Dev Dyn 2021; 250:1618-1633. [PMID: 33987914 DOI: 10.1002/dvdy.371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Although the cell cycle and cell differentiation should be coordinately regulated to generate a variety of neurons in the brain, the molecules that are involved in this coordination still remain largely unknown. In this study, we analyzed the roles of a nuclear protein Cfdp1, which is thought to be involved in chromatin remodeling, in zebrafish neurogenesis. RESULTS Zebrafish cfdp1 mutants maintained the progenitors of granule cells (GCs) in the cerebellum, but showed defects in their differentiation to GCs. cfdp1 mutants showed an increase in phospho-histone 3 (pH 3)-positive cells and apoptotic cells, as well as a delayed cell cycle transition from the G2 to the M phase in the cerebellum. The inhibition of tp53 prevented apoptosis but not GC differentiation in the cfdp1 mutant cerebellum. A similar increase in apoptotic cells and pH 3-positive cells, and defective cell differentiation, were observed in the cfdp1 mutant retina. Although mitotic spindles formed, mitosis was blocked before anaphase in both the cerebellum and retina of cfdp1 mutant larvae. Furthermore, expression of the G2/mitotic-specific cyclin B1 gene increased in the cfdp1 mutant cerebellum. CONCLUSIONS Our findings suggest that Cfdp1 regulates the cell cycle of neural progenitors, thereby promoting neural differentiation in the brain.
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Affiliation(s)
- Tsubasa Itoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Shinsuke Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Xiaoding Sun
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Ryo Kusuda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Masahiko Hibi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Takashi Shimizu
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
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5
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Prozzillo Y, Delle Monache F, Ferreri D, Cuticone S, Dimitri P, Messina G. The True Story of Yeti, the "Abominable" Heterochromatic Gene of Drosophila melanogaster. Front Physiol 2019; 10:1093. [PMID: 31507454 PMCID: PMC6713933 DOI: 10.3389/fphys.2019.01093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/08/2019] [Indexed: 12/21/2022] Open
Abstract
The Drosophila Yeti gene (CG40218) was originally identified by recessive lethal mutation and subsequently mapped to the deep pericentromeric heterochromatin of chromosome 2. Functional studies have shown that Yeti encodes a 241 amino acid protein called YETI belonging to the evolutionarily conserved family of Bucentaur (BCNT) proteins and exhibiting a widespread distribution in animals and plants. Later studies have demonstrated that YETI protein: (i) is able to bind both subunits of the microtubule-based motor kinesin-I; (ii) is required for proper chromosome organization in both mitosis and meiosis divisions; and more recently (iii) is a new subunit of dTip60 chromatin remodeling complex. To date, other functions of YETI counterparts in chicken (CENtromere Protein 29, CENP-29), mouse (Cranio Protein 27, CP27), zebrafish and human (CranioFacial Development Protein 1, CFDP1) have been reported in literature, but the fully understanding of the multifaceted molecular function of this protein family remains still unclear. In this review we comprehensively highlight recent work and provide a more extensive hypothesis suggesting a broader range of YETI protein functions in different cellular processes.
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Affiliation(s)
- Yuri Prozzillo
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Francesca Delle Monache
- "Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Diego Ferreri
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Stefano Cuticone
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Patrizio Dimitri
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Giovanni Messina
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
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6
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Functional analysis of the cfdp1 gene in zebrafish provides evidence for its crucial role in craniofacial development and osteogenesis. Exp Cell Res 2017; 361:236-245. [PMID: 29107067 DOI: 10.1016/j.yexcr.2017.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/20/2022]
Abstract
The CFDP1 proteins have been linked to craniofacial development and osteogenesis in vertebrates, though specific human syndromes have not yet been identified. Alterations of craniofacial development represent the main cause of infant disability and mortality in humans. For this reason, it is crucial to understand the cellular functions and mechanism of action of the CFDP1 protein in model vertebrate organisms. Using a combination of genomic, molecular and cell biology approaches, we have performed a functional analysis of the cfdp1 gene and its encoded protein, zCFDP1, in the zebrafish model system. We found that zCFDP1 is present in the zygote, is rapidly produced after MTZ transition and is highly abundant in the head structures. Depletion of zCFDP1, induced by an ATG-blocking morpholino, produces considerable defects in craniofacial structures and bone mineralization. Together, our results show that zCFDP1 is an essential protein required for proper development and provide the first experimental evidence showing that in vertebrates it actively participates to the morphogenesis of craniofacial territories.
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7
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Sun L, Luk E. Dual function of Swc5 in SWR remodeling ATPase activation and histone H2A eviction. Nucleic Acids Res 2017; 45:9931-9946. [PMID: 28973436 PMCID: PMC5622370 DOI: 10.1093/nar/gkx589] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/29/2017] [Indexed: 12/25/2022] Open
Abstract
The chromatin remodeler SWR deposits histone H2A.Z at promoters and other regulatory sites via an ATP-driven histone exchange reaction that replaces nucleosomal H2A with H2A.Z. Simultaneous binding of SWR to both H2A nucleosome and free H2A.Z induces SWR ATPase activity and engages the histone exchange mechanism. Swc5 is a conserved subunit of the 14-polypeptide SWR complex that is required for the histone exchange reaction, but its molecular role is unknown. We found that Swc5, although not required for substrate binding, is required for SWR ATPase stimulation, suggesting that Swc5 is required to couple substrate recognition to ATPase activation. A biochemical complementation assay was developed to show that a unique, conserved domain at the C-terminus of Swc5, called Bucentaur (BCNT), is essential for the histone exchange activity of SWR, whereas an acidic region at the N-terminus is required for optimal SWR function. In vitro studies showed the acidic N-terminus of Swc5 preferentially binds to the H2A–H2B dimer and exhibits histone chaperone activity. We propose that an auxiliary function of Swc5 in SWR is to assist H2A ejection as H2A.Z is inserted into the nucleosome.
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Affiliation(s)
- Lu Sun
- Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA
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8
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Messina G, Atterrato MT, Prozzillo Y, Piacentini L, Losada A, Dimitri P. The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization. Sci Rep 2017; 7:45022. [PMID: 28367969 PMCID: PMC5377257 DOI: 10.1038/srep45022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The human Cranio Facial Development Protein 1 (Cfdp1) gene maps to chromosome 16q22.2-q22.3 and encodes the CFDP1 protein, which belongs to the evolutionarily conserved Bucentaur (BCNT) family. Craniofacial malformations are developmental disorders of particular biomedical and clinical interest, because they represent the main cause of infant mortality and disability in humans, thus it is important to understand the cellular functions and mechanism of action of the CFDP1 protein. We have carried out a multi-disciplinary study, combining cell biology, reverse genetics and biochemistry, to provide the first in vivo characterization of CFDP1 protein functions in human cells. We show that CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. An RNAi-mediated depletion of CFDP1 in HeLa cells affects chromosome organization, SMC2 condensin recruitment and cell cycle progression. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders.
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Affiliation(s)
- Giovanni Messina
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Maria Teresa Atterrato
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Yuri Prozzillo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Lucia Piacentini
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | | | - Patrizio Dimitri
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
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9
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Expression of human Cfdp1 gene in Drosophila reveals new insights into the function of the evolutionarily conserved BCNT protein family. Sci Rep 2016; 6:25511. [PMID: 27151176 PMCID: PMC4858687 DOI: 10.1038/srep25511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
The Bucentaur (BCNT) protein family is widely distributed in eukaryotes and is characterized by a highly conserved C-terminal domain. This family was identified two decades ago in ruminants, but its role(s) remained largely unknown. Investigating cellular functions and mechanism of action of BCNT proteins is challenging, because they have been implicated in human craniofacial development. Recently, we found that YETI, the D. melanogaster BCNT, is a chromatin factor that participates to H2A.V deposition. Here we report the effects of in vivo expression of CFDP1, the human BCNT protein, in Drosophila melanogaster. We show that CFDP1, similarly to YETI, binds to chromatin and its expression results in a wide range of abnormalities highly reminiscent of those observed in Yeti null mutants. This indicates that CFDP1 expressed in flies behaves in a dominant negative fashion disrupting the YETI function. Moreover, GST pull-down provides evidence indicating that 1) both YETI and CFDP1 undergo homodimerization and 2) YETI and CFDP1 physically interact each other by forming inactive heterodimers that would trigger the observed dominant-negative effect. Overall, our findings highlight unanticipated evidences suggesting that homodimerization mediated by the BCNT domain is integral to the chromatin functions of BCNT proteins.
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10
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Messina G, Celauro E, Atterrato MT, Giordano E, Iwashita S, Dimitri P. The Bucentaur (BCNT) protein family: a long-neglected class of essential proteins required for chromatin/chromosome organization and function. Chromosoma 2014; 124:153-62. [DOI: 10.1007/s00412-014-0503-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/05/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
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11
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Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. J Proteome Res 2012; 11:3520-32. [PMID: 22578083 DOI: 10.1021/pr3002996] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prevalence of diabetes mellitus is increasing dramatically throughout the world, and the disease has become a major public health issue. The most common form of the disease, type 2 diabetes, is characterized by insulin resistance and insufficient insulin production from the pancreatic beta-cell. Since glucose is the most potent regulator of beta-cell function under physiological conditions, identification of the insulin secretory defect underlying type 2 diabetes requires a better understanding of glucose regulation of human beta-cell function. To this aim, a bottom-up LC-MS/MS-based proteomics approach was used to profile pooled islets from multiple donors under basal (5 mM) or high (15 mM) glucose conditions. Our analysis discovered 256 differentially abundant proteins (∼p < 0.05) after 24 h of high glucose exposure from more than 4500 identified in total. Several novel glucose-regulated proteins were elevated under high glucose conditions, including regulators of mRNA splicing (pleiotropic regulator 1), processing (retinoblastoma binding protein 6), and function (nuclear RNA export factor 1), in addition to neuron navigator 1 and plasminogen activator inhibitor 1. Proteins whose abundances markedly decreased during incubation at 15 mM glucose included Bax inhibitor 1 and synaptotagmin-17. Up-regulation of dicer 1 and SLC27A2 and down-regulation of phospholipase Cβ4 were confirmed by Western blots. Many proteins found to be differentially abundant after high glucose stimulation are annotated as uncharacterized or hypothetical. These findings expand our knowledge of glucose regulation of the human islet proteome and suggest many hitherto unknown responses to glucose that require additional studies to explore novel functional roles.
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12
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Bustos-Valenzuela JC, Fujita A, Halcsik E, Granjeiro JM, Sogayar MC. Unveiling novel genes upregulated by both rhBMP2 and rhBMP7 during early osteoblastic transdifferentiation of C2C12 cells. BMC Res Notes 2011; 4:370. [PMID: 21943021 PMCID: PMC3196718 DOI: 10.1186/1756-0500-4-370] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 09/26/2011] [Indexed: 01/24/2023] Open
Abstract
FINDINGS We set out to analyse the gene expression profile of pre-osteoblastic C2C12 cells during osteodifferentiation induced by both rhBMP2 and rhBMP7 using DNA microarrays. Induced and repressed genes were intercepted, resulting in 1,318 induced genes and 704 repressed genes by both rhBMP2 and rhBMP7. We selected and validated, by RT-qPCR, 24 genes which were upregulated by rhBMP2 and rhBMP7; of these, 13 are related to transcription (Runx2, Dlx1, Dlx2, Dlx5, Id1, Id2, Id3, Fkhr1, Osx, Hoxc8, Glis1, Glis3 and Cfdp1), four are associated with cell signalling pathways (Lrp6, Dvl1, Ecsit and PKCδ) and seven are associated with the extracellular matrix (Ltbp2, Grn, Postn, Plod1, BMP1, Htra1 and IGFBP-rP10). The novel identified genes include: Hoxc8, Glis1, Glis3, Ecsit, PKCδ, LrP6, Dvl1, Grn, BMP1, Ltbp2, Plod1, Htra1 and IGFBP-rP10. BACKGROUND BMPs (bone morphogenetic proteins) are members of the TGFβ (transforming growth factor-β) super-family of proteins, which regulate growth and differentiation of different cell types in various tissues, and play a critical role in the differentiation of mesenchymal cells into osteoblasts. In particular, rhBMP2 and rhBMP7 promote osteoinduction in vitro and in vivo, and both proteins are therapeutically applied in orthopaedics and dentistry. CONCLUSION Using DNA microarrays and RT-qPCR, we identified both previously known and novel genes which are upregulated by rhBMP2 and rhBMP7 during the onset of osteoblastic transdifferentiation of pre-myoblastic C2C12 cells. Subsequent studies of these genes in C2C12 and mesenchymal or pre-osteoblastic cells should reveal more details about their role during this type of cellular differentiation induced by BMP2 or BMP7. These studies are relevant to better understanding the molecular mechanisms underlying osteoblastic differentiation and bone repair.
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Affiliation(s)
- Juan C Bustos-Valenzuela
- Chemistry Institute, Department of Biochemistry, Cell and Molecular Therapy Centre (NUCEL), University of São Paulo, Avenida Prof, Lineu Prestes, 748 Bloco 9S, São Paulo, SP 05508-000, Brazil.
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13
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Makeyev AV, Bayarsaihan D. Molecular Basis of Williams-Beuren Syndrome: TFII-I Regulated Targets Involved in Craniofacial Development. Cleft Palate Craniofac J 2011; 48:109-16. [DOI: 10.1597/09-093] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective The aim of this study is to identify gene targets of TFII-I transcription factors involved in craniofacial development. Design Recent findings in individuals with Williams-Beuren syndrome who show facial dysmorphism and cognitive defects have pointed to TFII-I genes ( GTF2I and GTF2IRD1) as the prime candidates responsible for these clinical features. However, TFII-I proteins are multifunctional transcriptional factors regulating a number of genes during development, and how their haploinsufficiency leads to the Williams-Beuren syndrome phenotype is currently unknown. Results Here we report the identification of three genes with a well-established relevance to craniofacial development as direct TFII-I targets. These genes, craniofacial development protein 1 ( Cfdp1), Sec23 homolog A ( Sec23a), and nuclear receptor binding SET domain protein 1 ( Nsd1), contain consensus TFII-I binding sites in their proximal promoters; the chromatin immunoprecipitation analysis showed that TFII-I transcription factors are recruited to these sites in vivo. Conclusions The results suggest that transcriptional regulation of these genes by TFII-I proteins could provide a possible genotype-phenotype link in Williams-Beuren syndrome.
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Affiliation(s)
- Aleksandr V. Makeyev
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, Connecticut
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, Connecticut
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Luan X, Ito Y, Zhang Y, Diekwisch TGH. Characterization of the mouse CP27 promoter and NF-Y mediated gene regulation. Gene 2010; 460:8-19. [PMID: 20388536 PMCID: PMC2892892 DOI: 10.1016/j.gene.2010.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 03/26/2010] [Accepted: 03/27/2010] [Indexed: 01/02/2023]
Abstract
The cp27 gene is a highly conserved and unique gene with important roles related to craniofacial organogenesis. The present study is a first analysis of the CP27 promoter and its regulation. Here, we have cloned the promoter of the mouse cp27 gene, examined its transcriptional activity, and identified transcription factor binding sites in the proximal promoter region. Two major transcription start sites were mapped adjacent to exon 1. Promoter function analysis of the 5' flanking region by progressive 5' deletion mutations localized transcription repression elements between -1993bp and -969bp and several positive elements between -968bp and the preferred transcription start site. EMSA and functional studies indicated two function-cooperative CCAAT boxes and identified the NF-Y transcription factor as the CCAAT activator controlling transactivation of the CP27 promoter. In addition, this study demonstrated that for its effective binding and function, NF-Y required not only the minimal DNA segment length identified by deletion studies, but also a defined nucleotide sequence in the distal 3' flanking region of the CP27 proximal promoter CCAAT box. These results provide a basis for our understanding of the specific regulation of the cp27 gene in the NF-Y-mediated gene transcription network.
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Affiliation(s)
- Xianghong Luan
- The Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, 801 South Paulina Street, Chicago, Il 60612, USA
| | - Yoshihiro Ito
- The Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, 801 South Paulina Street, Chicago, Il 60612, USA
| | - Youbin Zhang
- The Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, 801 South Paulina Street, Chicago, Il 60612, USA
| | - Thomas G. H. Diekwisch
- The Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, 801 South Paulina Street, Chicago, Il 60612, USA
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15
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Dimitri P, Caizzi R, Giordano E, Carmela Accardo M, Lattanzi G, Biamonti G. Constitutive heterochromatin: a surprising variety of expressed sequences. Chromosoma 2009; 118:419-35. [PMID: 19412619 DOI: 10.1007/s00412-009-0211-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
Abstract
The organization of chromosomes into euchromatin and heterochromatin is amongst the most important and enigmatic aspects of genome evolution. Constitutive heterochromatin is a basic yet still poorly understood component of eukaryotic chromosomes, and its molecular characterization by means of standard genomic approaches is intrinsically difficult. Although recent evidence indicates that the presence of transcribed genes in constitutive heterochromatin is a conserved trait that accompanies the evolution of eukaryotic genomes, the term heterochromatin is still considered by many as synonymous of gene silencing. In this paper, we comprehensively review data that provide a clearer picture of transcribed sequences within constitutive heterochromatin, with a special emphasis on Drosophila and humans.
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Affiliation(s)
- Patrizio Dimitri
- Laboratorio di Genomica Funzionale e Proteomica di Sistemi modello and Istituto Pasteur-Fondazione Bolognetti, Dipartimento di Genetica e Biologia Molecolare Charles Darwin, Università La Sapienza, 00185, Italy.
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16
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Corradini N, Rossi F, Giordano E, Caizzi R, Verní F, Dimitri P. Drosophila melanogaster as a model for studying protein-encoding genes that are resident in constitutive heterochromatin. Heredity (Edinb) 2006; 98:3-12. [PMID: 17080025 DOI: 10.1038/sj.hdy.6800877] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The organization of chromosomes into euchromatin and heterochromatin is one of the most enigmatic aspects of genome evolution. For a long time, heterochromatin was considered to be a genomic wasteland, incompatible with gene expression. However, recent studies--primarily conducted in Drosophila melanogaster--have shown that this peculiar genomic component performs important cellular functions and carries essential genes. New research on the molecular organization, function and evolution of heterochromatin has been facilitated by the sequencing and annotation of heterochromatic DNA. About 450 predicted genes have been identified in the heterochromatin of D. melanogaster, indicating that the number of active genes is higher than had been suggested by genetic analysis. Most of the essential genes are still unknown at the molecular level, and a detailed functional analysis of the predicted genes is difficult owing to the lack of mutant alleles. Far from being a peculiarity of Drosophila, heterochromatic genes have also been found in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Oryza sativa and Arabidopsis thaliana, as well as in humans. The presence of expressed genes in heterochromatin seems paradoxical because they appear to function in an environment that has been considered incompatible with gene expression. In the future, genetic, functional genomic and proteomic analyses will offer powerful approaches with which to explore the functions of heterochromatic genes and to elucidate the mechanisms driving their expression.
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Affiliation(s)
- N Corradini
- Laboratorio di Genomica Funzionale e Proteomica di Sistemi modello and Dipartimento di Genetica e Biologia Molecolare 'Charles Darwin', Università 'La Sapienza', Piazzale Aldo Moro 5, 00185 Roma, Italy
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17
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Abstract
Growth and development of pig fetuses is dependent on the coordinated expression of multiple genes. Between 21 and 45 days of gestation, fetuses experience increasing growth rates that can result in uterine crowding and increased mortality. We used differential display reverse transcription-PCR (DDRT-PCR) to identify differentially expressed genes in pig fetuses at 21, 35, and 45 days of gestation. Pig cDNAs were identified with homologies to CD3 gamma-subunit, collagen type XIV alpha1, complement component C6, craniofacial developmental protein 1, crystallin-gammaE, DNA binding protein B, epsilon-globin, formin binding protein 2, ribosomal protein L23, small acidic protein, secreted frizzled related protein 2, titin, vitamin D binding protein, and two hypothetical protein products. Two novel expressed sequence tags (ESTs) were also identified. Expression patterns were confirmed for eight genes, and spatiotemporal expression of three genes was evaluated. We identified novel transcriptome changes in fetal pigs during a period of rapid growth. These changes involved genes with a spectrum of proposed functions, including musculoskeletal growth, immune system function, and cellular regulation. This information can ultimately be used to enhance production efficiency through improved pig growth and survival.
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Affiliation(s)
- Stephanie R Wesolowski
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824, USA
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18
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Diekwisch TGH, Berman BJ, Anderton X, Gurinsky B, Ortega AJ, Satchell PG, Williams M, Arumugham C, Luan X, McIntosh JE, Yamane A, Carlson DS, Sire JY, Shuler CF. Membranes, minerals, and proteins of developing vertebrate enamel. Microsc Res Tech 2002; 59:373-95. [PMID: 12430167 DOI: 10.1002/jemt.10218] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Developing tooth enamel is formed as organized mineral in a specialized protein matrix. In order to analyze patterns of enamel mineralization and enamel protein expression in species representative of the main extant vertebrate lineages, we investigated developing teeth in a chondrichthyan, the horn shark, a teleost, the guppy, a urodele amphibian, the Mexican axolotl, an anuran amphibian, the leopard frog, two lepidosauria, a gecko and an iguana, and two mammals, a marsupial, the South American short-tailed gray opossum, and the house mouse. Electron microscopic analysis documented the presence of a distinct basal lamina in all species investigated. Subsequent stages of enamel biomineralization featured highly organized long and parallel enamel crystals in mammals, lepidosaurians, the frog, and the shark, while amorphous mineral deposits and/or randomly oriented crystals were observed in the guppy and the axolotl. In situ hybridization using a full-length mouse probe for amelogenin mRNA resulted in amelogenin specific signals in mouse, opossum, gecko, frog, axolotl, and shark. Using immunohistochemistry, amelogenin and tuftelin enamel proteins were detected in the enamel organ of many species investigated, but tuftelin epitopes were also found in other tissues. The anti-M179 antibody, however, did not react with the guppy and axolotl enameloid matrix. We conclude that basic features of vertebrate enamel/enameloid formation such as the presence of enamel proteins or the mineral deposition along the dentin-enamel junction were highly conserved in vertebrates. There were also differences in terms of enamel protein distribution and mineral organization between the vertebrates lineages. Our findings indicated a correlation between the presence of amelogenins and the presence of long and parallel hydroxyapatite crystals in tetrapods and shark.
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Affiliation(s)
- Thomas G H Diekwisch
- Allan G. Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, Illinois, USA
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19
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Luan X, Diekwisch TGH. CP27 affects viability, proliferation, attachment and gene expression in embryonic fibroblasts. Cell Prolif 2002; 35:207-19. [PMID: 12153613 PMCID: PMC6496629 DOI: 10.1046/j.1365-2184.2002.00238.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2001] [Accepted: 11/27/2001] [Indexed: 11/20/2022] Open
Abstract
CP27 is a gene that has been cloned from an E11 early embryonic library and has been suggested to mediate early organogenesis (Diekwisch et al., 1999, Gene 235, 19). We have hypothesized that CP27 exhibits its effects on organogenesis by affecting individual cell function. Based on the CP27 expression pattern we have selected the CP27 expressing embryonic fibroblast cell line BALB/c 3T3 to determine the effects of CP27 on cell function. CP27 loss of function strategies were performed by adding 5, 12.5 or 25 micro g/ml anti-CP27 antibody to cultured BALB/c 3T3 cells and comparing the results to controls in which identical concentrations of rabbit serum were added to the culture medium. Other controls included an antibody against another extracellular matrix protein amelogenin (negative control) and anti-CP27 antibodies directed against other areas of the CP27 molecule (positive control). Following cell culture, cell viability, apoptosis, cell proliferation, cell shape, cellular attachment and fibronectin matrix production were assayed using MTT colourimetric assay, BrdU staining, morphometry, immunostaining and western blot analysis. Block of CP27 function using an antibody strategy resulted in the following significant changes: (i) reduced viability, (ii) increased number of apoptotic cells, (iii) reduced proliferation, (iv) alterations in cell shape, (v) loss of attachment, and (vi) reduction in fibronectin matrix production. There was also a redistribution in fibronectin matrix organization demonstrated by immunohistochemistry. We conclude that CP27 plays an important role in the maintance of normal cell function and that CP27 block leads to significant changes in cellular behaviour.
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Affiliation(s)
- X Luan
- Brodie Laboratory for Craniofacil Genetics, University of Illinois at Chicago, IL, 60612, USA
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20
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Diekwisch TGH, Luan X. CP27 function is necessary for cell survival and differentiation during tooth morphogenesis in organ culture. Gene 2002; 287:141-7. [PMID: 11992732 DOI: 10.1016/s0378-1119(01)00868-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Thomas G H Diekwisch
- Allan G. Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago College of Dentistry, 801 South Paulina M/C841, Chicago, IL 60612, USA.
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21
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Diekwisch TGH, Luan X, McIntosh JE. CP27 localization in the dental lamina basement membrane and in the stellate reticulum of developing teeth. J Histochem Cytochem 2002; 50:583-6. [PMID: 11897812 DOI: 10.1177/002215540205000416] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
cp27 is a novel gene involved in early vertebrate development that features a distinct protein localization pattern in developing tooth organs. During initial tooth development, CP27 was detected at the epithelial-mesenchymal interface of dental lamina stage tooth organs. At later stages of tooth development, CP27 was localized in the stellate reticulum, the oral mucosa mesenchyme, and alveolar bone. The significant changes in the highly restricted distribution pattern suggest that CP27 might be involved at several different levels during tooth development.
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Affiliation(s)
- Thomas G H Diekwisch
- Allan G. Brodie Laboratory for Craniofacial Genetics, College of Dentistry (M/C 841), The University of Illinois at Chicago, 801 South Paulina, Chicago, IL 60612, USA.
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22
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Iwashita S, Itoh T, Takeda H, Sugimoto Y, Takahashi I, Nobukuni T, Sezaki M, Masui T, Hashimoto K. Gene organization of bovine BCNT that contains a portion corresponding to an endonuclease domain derived from an RTE-1 (Bov-B LINE), non-LTR retrotransposable element: duplication of an intramolecular repeat unit downstream of the truncated RTE-1. Gene 2001; 268:59-66. [PMID: 11368901 DOI: 10.1016/s0378-1119(01)00422-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BCNT (a protein named after Bucentaur or craniofacial development protein 1) has a unique structure in Ruminantia. Bovine BCNT contains a region of the endonuclease domain derived from a truncated RTE-1 (previously called Bov-B LINE), a non-LTR retrotransposable repetitive element, and two repeat units (intramolecular repeat, IR) each with 40 amino acids in the C-terminal region. In contrast the human and mouse BCNT proteins contain one repeat unit and lack the RTE-1-derived portion. The 3' UTR of bovine bcnt cDNA also contains an approximately 300-bp portion homologous to the 3'-part of RTE-1. We examined the bovine bcnt genomic DNA sequence to understand how the bovine bcnt gene has been organized. The sequence of 3' UTR homologous portion was found to more closely resemble the Art2 element than the bovine RTE-1. By PCR screening a bovine/hamster hybrid somatic cell panel, the bovine bcnt gene was mapped to chromosome 18, syntenic human chromosome 16q on which human BCNT is located. The bcnt genomic DNA sequence corresponding to the cDNA downstream of a RTE-1 derived portion reveals that each IR unit is flanked by both 5'-side and 3'-side introns and that 3'-UTR consists of one exon. The alignment of the above sequence with a bovine RTE-1 did not show any significant homology downstream of the endonuclease domain. On the other hand, the alignment of the intron sequences with each other revealed that the six sequential homologous segments ranging in size from 40 to 453 bp existed over a 1 kb long sequence between both the 5'- and 3'-side introns flanking each bovine IR unit. In addition, both the 174-bp of 5'-side intron and 80-bp of 3'-side intron neighboring each 120-bp IR exon are significantly homologous among the two bovine IRs, human IR and mouse IR. These results suggest that a truncated bovine RTE-1 was inserted into the intron upstream of an IR unit of an ancestor bcnt gene and that a duplication of a relatively long region that includes IR occurred in the bovine genome.
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Affiliation(s)
- S Iwashita
- Mitsubishi Kasei Institute of Life Sciences, 194-8511, Tokyo, Japan.
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