1
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Manuel LL, de los Ángeles César F, Pérez-Silva Nancy B, Celia PL, Elizabeth BR, Gonzalez Rosa O, Antonio GBJ, Jose S. Low-scale production and purification of a biologically active optimized form of the antitumor protein growth arrest specific 1 (GAS1) in a mammalian system for post-translational analysis. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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2
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Gimeno-Valiente F, Riffo-Campos ÁL, Vallet-Sánchez A, Siscar-Lewin S, Gambardella V, Tarazona N, Cervantes A, Franco L, Castillo J, López-Rodas G. ZNF518B gene up-regulation promotes dissemination of tumour cells and is governed by epigenetic mechanisms in colorectal cancer. Sci Rep 2019; 9:9339. [PMID: 31249328 PMCID: PMC6597559 DOI: 10.1038/s41598-019-45411-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 06/04/2019] [Indexed: 12/19/2022] Open
Abstract
Most of colorectal cancer CRC-related death is due to metastasis and the finding of markers for prognosis of invasiveness, constitutes an appealing challenge. Here, after analysing cDNA array containing 43 tumour and 5 normal mucosa samples, we report that the expression of the ZNF518B gene as a whole and that of its two major splicing isoforms are significantly increased in tumours. The canonical isoform was also up-regulated in a patients’ cohort containing 70 tumour and 69 adjacent tissue samples. The effects of silencing ZNF518B on the phenotype of CRC cell lines were then studied. The gene does not affect cell proliferation, but plays a significant role in cell migration and invasiveness and induces changes in the epithelial-to-mesenchymal transition markers, suggesting that ZNF518B favours tumour cell dissemination. To study the regulation of the gene, transcription-related changes in nucleosomal organisation and epigenetic marks around the transcriptional start site were analysed. The positioning of a nucleosome over the transcription start site and the differential presence of the epigenetic marks H3K9ac, H3K27ac, H3K4me3 and H3K9me3 correlate with gene expression. Inhibition of histone deacetylases increases the transcription of ZNF518B, which may be a candidate for invasiveness prognosis in CRC and a target for epigenetic drugs.
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Affiliation(s)
| | - Ángela L Riffo-Campos
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro De Excelencia de Modelación y Computación Científica, Departamento de Anatomía Patológica, Universidad de La Frontera, Temuco, Chile
| | - Azahara Vallet-Sánchez
- Institute of Health Research, INCLIVA, Valencia, Spain.,Department of Cell Biology, Universitat de València, Burjassot, Valencia, Spain
| | - Sofía Siscar-Lewin
- Institute of Health Research, INCLIVA, Valencia, Spain.,Department of Microbial Pathogenicity Mechanisms, Hans-Knoell-Institute, Jena, Germany
| | - Valentina Gambardella
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, University Hospital, Universitat de València, Valencia, Spain
| | - Noelia Tarazona
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, University Hospital, Universitat de València, Valencia, Spain
| | - Andrés Cervantes
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, University Hospital, Universitat de València, Valencia, Spain
| | - Luis Franco
- Institute of Health Research, INCLIVA, Valencia, Spain. .,Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain.
| | - Josefa Castillo
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain
| | - Gerardo López-Rodas
- Institute of Health Research, INCLIVA, Valencia, Spain.,Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain
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3
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Rashad MM, Galal MK, EL-Behairy AM, Gouda EM, Moussa SZ. Maternal exposure to di-n-butyl phthalate induces alterations of c-Myc gene, some apoptotic and growth related genes in pups’ testes. Toxicol Ind Health 2018; 34:744-752. [DOI: 10.1177/0748233718791623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The aim of this study was to investigate the effects of maternal exposure to di-( n-butyl) phthalate (DBP) on testicular development and function in pre-pubertal and post-pubertal male rat offspring. Fourteen pregnant female rats were equally divided into two groups: a control group and a DBP-treated group. During gestation day (GD) 12 to postnatal day (PND) 14, the control group was administered 1 ml/day corn oil, and the DBP-treated group was administered DBP 500 mg/kg/day by oral gavage. On PND 25 (pre-puberty) and PND 60 (post-puberty), blood for serum and the testes were collected from five male offspring of each group. To determine the relationship between the methylation state of the c-Myc promoter and the expression of the c-Myc gene, some apoptotic-related genes, such as p53 and Bax, the anti-apoptotic Bcl-2 gene, and some growth arrest-related genes, such as BRD7 and GAS1, were examined. Compared with the control ( p < 0.05), at pre-puberty, DBP induces c-Myc hyper-methylation with significant downregulation for c-Myc, p53, Bax genes, and significant upregulation for Bcl-2, BRD7, and GAS1, while at post puberty, the methylation state and expression of c-Myc and apoptosis-related genes returned to control levels in the same sequence with the fold change in the expression of BRD7 and GAS1 genes. These findings suggest that DBP induced a transient pre-pubertal increase in c-Myc promoter methylation that may be associated with disruption of both apoptotic and growth mechanisms in the testes.
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Affiliation(s)
- Maha M Rashad
- Biochemistry Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Mona K Galal
- Biochemistry Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Adel M EL-Behairy
- Biochemistry Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Eman M Gouda
- Biochemistry Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Said Z Moussa
- Biochemistry Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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4
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Role of epigenetic factors in the selection of the alternative splicing isoforms of human KRAS in colorectal cancer cell lines. Oncotarget 2018; 9:20578-20589. [PMID: 29755673 PMCID: PMC5945503 DOI: 10.18632/oncotarget.25016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
Mutation-driven activation of KRAS is crucial to cancer development. The human gene yields four mRNA splicing isoforms, 4A and 4B being translated to protein. Their different properties and oncogenic potential have been studied, but the mechanisms deciding the ratio 4A/4B are not known. To address this issue, the expression of the four KRAS isoforms was determined in 9 human colorectal cancer cell lines. HCT116 and SW48 were further selected because they present the highest difference in the ratio 4A/4B (twice as much in HCT116 than in SW48). Chromatin structure was analysed at the exon 4A, characteristic of isoform 4A, at its intronic borders and at the two flanking exons. The low nucleosome occupancy at exon 4A in both cell lines may result in a fast transcriptional rate, which would explain the general lower abundance of isoform 4A, also found in cells and tissues by other authors, but due to its similarity between both cell lines, chromatin structure does not influence alternative splicing. DNA methylation downstream exon 4A significantly differs in HCT116 and SW48 cells, but the CCCTC-binding factor, which affects the processivity of RNA polymerase and the alternative splicing, does not bind the differentially methylated sequences. Quantitative epigenetic analysis at mononucleosomal level revealed significant differences between both cell lines in H3K4me3, H3K27me3, H3K36me3, H3K9ac, H3K27ac and H4K20me1, and the inhibition of some histone-modifying enzymes alters the ratio 4A/4B. It can be concluded that the epigenetic modification of histones has an influence on the selection of isoforms 4A and 4B.
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5
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Bennett-Toomey J, Stocco C. GATA Regulation and Function During the Ovarian Life Cycle. VITAMINS AND HORMONES 2018; 107:193-225. [PMID: 29544631 DOI: 10.1016/bs.vh.2018.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
GATA4 and GATA6 are the sole GATA factors expressed in the ovary during embryonic development and adulthood. Up today, GATA4 and GATA6 are the only transcription factors that have been conditionally deleted during ovarian development and at each major stage of follicle maturation. The evidence from these transgenic mice revealed that GATA4 and GATA6 are crucial for follicles assembly, granulosa cell differentiation, postnatal follicle growth, and luteinization. Thus, conditional knockdown of both factors in the granulosa cells at any stage of development leads to female infertility. GATA targets impacting female reproduction include genes involved in steroidogenesis, hormone signaling, ovarian hormones, extracellular matrix organization, and apoptosis/cell division.
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Affiliation(s)
| | - Carlos Stocco
- College of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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6
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Quezada-Ramírez M, Castañeda-Arellano R, Pérez-Sánchez G, Hernández-Soto J, Segovia J. The Growth arrest specific 1 ( Gas1 ) gene is transcriptionally regulated by NeuroD1 via two distal E-boxes. Exp Cell Res 2018; 363:332-341. [DOI: 10.1016/j.yexcr.2018.01.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 12/13/2022]
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7
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Conceição ALG, Da Silva CT, Badial RM, Valsechi MC, Stuqui B, Gonçalves JD, Jasiulionis MG, De Freitas Calmon M, Rahal P. Downregulation of OCLN and GAS1 in clear cell renal cell carcinoma. Oncol Rep 2017; 37:1487-1496. [PMID: 28184927 DOI: 10.3892/or.2017.5414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/03/2016] [Indexed: 11/05/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of kidney cancer. This carcinoma is histologically characterized by the presence of clear and abundant cytoplasm. In the present study, we sought to identify genes differentially expressed in ccRCC and build a molecular profile of this cancer. We selected genes described in the literature related to cellular differentiation and proliferation. We analyzed the gene and protein expression by quantitative PCR (qPCR) and immunohistochemistry, respectively, and examined possible epigenetic mechanisms that regulate their expression in ccRCC samples and cell lines. Occludin (OCLN) and growth arrest-specific 1 (GAS1) genes were underexpressed in ccRCC, and we report that miR-122 and miR-34a, respectively, may regulate their expression in this cancer. Furthermore, we showed by qPCR and immunohistochemistry that solute carrier family 2 member 1 (SLC2A1) was significantly overexpressed in ccRCC. The set of genes identified in the present study furthers our understanding of the molecular basis and development of ccRCC.
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Affiliation(s)
- André Luis Giacometti Conceição
- Laboratory of Genomic Studies, Department of Biology, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Camila Tainah Da Silva
- Department of Pharmacology, The Federal University of São Paulo (UNIFESP), São Paulo, SP 15054-000, Brazil
| | - Rodolfo Miglioli Badial
- Laboratory of Genomic Studies, Department of Biology, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Marina Curado Valsechi
- Laboratory of Genomic Studies, Department of Biology, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Bruna Stuqui
- Laboratory of Genomic Studies, Department of Biology, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | | | | | - Marilia De Freitas Calmon
- Laboratory of Genomic Studies, Department of Biology, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Paula Rahal
- Laboratory of Genomic Studies, Department of Biology, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
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8
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Histone Post-Translational Modifications and Nucleosome Organisation in Transcriptional Regulation: Some Open Questions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 28639249 DOI: 10.1007/5584_2017_58] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The organisation of chromatin is first discussed to conclude that nucleosomes play both structural and transcription-regulatory roles. The presence of nucleosomes makes difficult the access of transcriptional factors to their target sequences and the action of RNA polymerases. The histone post-translational modifications and nucleosome remodelling are first discussed, from a historical point of view, as mechanisms to remove the obstacles imposed by chromatin structure to transcription. Instead of reviewing the state of the art of the whole field, this review is centred on some open questions. First, some "non-classical" histone modifications, such as short-chain acylations other than acetylation, are considered to conclude that their relationship with the concentration of metabolic intermediaries might make of them a sensor of the physiological state of the cells. Then attention is paid to the interest of studying chromatin organisation and epigenetic marks at a single nucleosome level as a complement to genome-wide approaches. Finally, as a consequence of the above questions, the review focuses on the presence of multiple histone post-translational modifications on a single nucleosome. The methods to detect them and their meaning, with special emphasis on bivalent marks, are discussed.
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9
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Ayala-Sarmiento AE, Estudillo E, Pérez-Sánchez G, Sierra-Sánchez A, González-Mariscal L, Martínez-Fong D, Segovia J. GAS1 is present in the cerebrospinal fluid and is expressed in the choroid plexus of the adult rat. Histochem Cell Biol 2016; 146:325-36. [PMID: 27225491 DOI: 10.1007/s00418-016-1449-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 12/19/2022]
Abstract
Growth arrest specific 1 (GAS1) is a GPI-anchored protein that inhibits proliferation when overexpressed in tumors but during development it promotes proliferation and survival of different organs and tissues. This dual ability is caused by its capacity to interact both by inhibiting the signaling induced by the glial cell line-derived neurotrophic factor and by facilitating the activity of the sonic hedgehog pathway. GAS1 is expressed as membrane bound in different organs and as a secreted form by glomerular mesangial cells. In the developing central nervous system, GAS1 is found in neural progenitors; however, it continues to be expressed in the adult brain. Here, we demonstrate that soluble GAS1 is present in the cerebrospinal fluid (CSF) and it is expressed in the choroid plexus (CP) of the adult rat, the main producer of CSF. Additionally, we confirm the presence of GAS1 in blood plasma and liver of the adult rat, the principal source of blood plasma proteins. The pattern of expression of GAS1 is perivascular in both the CP and the liver. In vitro studies show that the fibroblast cell line NIH/3T3 expresses one form of GAS1 and releases two soluble forms into the supernatant. Briefly, in the present work, we show the presence of GAS1 in adult rat body fluids focusing in the CSF and the CP, and suggest that secreted GAS1 exists as two different isoforms.
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Affiliation(s)
- Alberto E Ayala-Sarmiento
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico
| | - Enrique Estudillo
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico
| | - Gilberto Pérez-Sánchez
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico
| | - Arturo Sierra-Sánchez
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico
| | - Lorenza González-Mariscal
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico
| | - Daniel Martínez-Fong
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico
| | - José Segovia
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN #2508, 07360, Mexico, D.F., Mexico.
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10
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Huang J, Schriefer AE, Yang W, Cliften PF, Rudnick DA. Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition. Epigenetics 2015; 9:1521-31. [PMID: 25482284 DOI: 10.4161/15592294.2014.983371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Liver regeneration has been well studied with hope of discovering strategies to improve liver disease outcomes. Nevertheless, the signals that initiate such regeneration remain incompletely defined, and translation of mechanism-based pro-regenerative interventions into new treatments for hepatic diseases has not yet been achieved. We previously reported the isoform-specific regulation and essential function of zinc-dependent histone deacetylases (Zn-HDACs) during mouse liver regeneration. Those data suggest that epigenetically regulated anti-proliferative genes are deacetylated and transcriptionally suppressed by Zn-HDAC activity or that pro-regenerative factors are acetylated and induced by such activity in response to partial hepatectomy (PH). To investigate these possibilities, we conducted genome-wide interrogation of the liver histone acetylome during early PH-induced liver regeneration in mice using acetyL-histone chromatin immunoprecipitation and next generation DNA sequencing. We also compared the findings of that study to those seen during the impaired regenerative response that occurs with Zn-HDAC inhibition. The results reveal an epigenetic signature of early liver regeneration that includes both hyperacetylation of pro-regenerative factors and deacetylation of anti-proliferative and pro-apoptotic genes. Our data also show that administration of an anti-regenerative regimen of the Zn-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) not only disrupts gene-specific pro-regenerative changes in liver histone deacetylation but also reverses PH-induced effects on histone hyperacetylation. Taken together, these studies offer new insight into and suggest novel hypotheses about the epigenetic mechanisms that regulate liver regeneration.
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Affiliation(s)
- Jiansheng Huang
- a Department of Pediatrics ; Washington University School of Medicine ; St. Louis , MO USA
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11
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Riffo-Campos ÁL, Castillo J, Tur G, González-Figueroa P, Georgieva EI, Rodríguez JL, López-Rodas G, Rodrigo MI, Franco L. Nucleosome-specific, time-dependent changes in histone modifications during activation of the early growth response 1 (Egr1) gene. J Biol Chem 2014; 290:197-208. [PMID: 25378406 DOI: 10.1074/jbc.m114.579292] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Histone post-translational modifications and nucleosome remodeling are coordinate events involved in eukaryotic transcriptional regulation. There are relatively few data on the time course with which these events occur in individual nucleosomes. As a contribution to fill this gap, we first describe the nature and time course of structural changes in the nucleosomes -2, -1, and +1 of the murine Egr1 gene upon induction. To initiate the transient activation of the gene, we used the stimulation of MLP29 cells with phorbol esters and the in vivo activation after partial hepatectomy. In both models, nucleosomes -1 and +1 are partially evicted, whereas nucleosomes +1 and -2 slide downstream during transcription. The sliding of the latter nucleosome allows the EGR1 protein to bind its site, resulting in the repression of the gene. To decide whether EGR1 is involved in the sliding of nucleosome -2, Egr1 was knocked down. In the absence of detectable EGR1, the nucleosome still slides and remains downstream longer than in control cells, suggesting that the product of the gene may be rather involved in the returning of the nucleosome to the basal position. Moreover, the presence of eight epigenetic histone marks has been determined at a mononucleosomal level in that chromatin region. H3S10phK14ac, H3K4me3, H3K9me3, and H3K27me3 are characteristic of nucleosome +1, and H3K9ac and H4K16ac are mainly found in nucleosome -1, and H3K27ac predominates in nucleosomes -2 and -1. The temporal changes in these marks suggest distinct functions for some of them, although changes in H3K4me3 may result from histone turnover.
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Affiliation(s)
- Ángela L Riffo-Campos
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - Josefa Castillo
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - Gema Tur
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - Paula González-Figueroa
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - Elena I Georgieva
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - José L Rodríguez
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - Gerardo López-Rodas
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - M Isabel Rodrigo
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - Luis Franco
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
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12
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Ferrer-Vicens I, Riffo‐Campos ÁL, Zaragozá R, García C, López-Rodas G, Viña JR, Torres L, García-Trevijano ER. In vivo genome-wide binding of Id2 to E2F4 target genes as part of a reversible program in mice liver. Cell Mol Life Sci 2014; 71:3583-97. [PMID: 24573694 PMCID: PMC11113549 DOI: 10.1007/s00018-014-1588-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/30/2014] [Accepted: 02/12/2014] [Indexed: 12/14/2022]
Abstract
The inhibitor of differentiation Id2, a protein lacking the basic DNA-binding domain, is involved in the modulation of a number of biological processes. The molecular mechanisms explaining Id2 pleiotropic functions are poorly understood. Id2 and E2F4 are known to bind simultaneously to c-myc promoter. To study whether Id2 plays a global role on transcriptional regulation, we performed in vivo genome-wide ChIP/chip experiments for Id2 and E2F4 in adult mouse liver. An Id2-containing complex was bound to a common sequence downstream from the TSS on a subset of 442 E2F4 target genes mainly related to cell development and chromatin structure. We found a positive correlation between Id2 protein levels and the expression of E2F4/Id2 targets in fetal and adult liver. Id2 protein stability increased in fetal liver by interaction with USP1 de-ubiquitinating enzyme, which was induced during development. In adult liver, USP1 and Id2 levels dramatically decreased. In differentiated liver tissue, when Id2 concentration was low, E2F4/Id2 was bound to the same region as paused Pol II and target genes remained transcriptionally inactive. Conversely, in fetal liver when Id2 levels were increased, Id2 and Pol II were released from gene promoters and target genes up-regulated. During liver regeneration after partial hepatectomy, we obtained the same results as in fetal liver. Our results suggest that Id2 might be part of a reversible development-related program involved in the paused-ON/OFF state of Pol II on selected genes that would remain responsive to specific stimuli.
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Affiliation(s)
- Ivan Ferrer-Vicens
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Ángela L. Riffo‐Campos
- Facultad de Ciencias Biológicas. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Rosa Zaragozá
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Concha García
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Gerardo López-Rodas
- Facultad de Ciencias Biológicas. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Juan R. Viña
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Luis Torres
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Elena R. García-Trevijano
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
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13
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Bennett J, Baumgarten SC, Stocco C. GATA4 and GATA6 silencing in ovarian granulosa cells affects levels of mRNAs involved in steroidogenesis, extracellular structure organization, IGF-I activity, and apoptosis. Endocrinology 2013; 154:4845-58. [PMID: 24064357 PMCID: PMC3836082 DOI: 10.1210/en.2013-1410] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Knockdown of the transcription factors GATA4 and GATA6 in granulosa cells (GCs) impairs folliculogenesis and induces infertility. To investigate the pathways and genes regulated by these factors, we performed microarray analyses on wild-type GCs or GCs lacking GATA4, GATA6, or GATA4/6 (G4(gcko), G6(gcko), and G4/6(gcko)) after in vivo treatment with equine chorionic gonadotropin. GATA4 deletion affected a greater number of genes than GATA6, which correlates with the subfertility observed in G4(gcko) mice and the normal reproductive function found in G6(gcko) animals. An even greater number of genes were affected by the deletion of both factors. Moreover, the expression of FSH receptor, LH receptor, inhibin α and β, versican, pregnancy-associated plasma protein A, and the regulatory unit 2b of protein kinase A, which are known to be crucial for ovarian function, was greatly affected in double GATA4 and GATA6 knockouts when compared with single GATA-deficient animals. This suggests that GATA4 and GATA6 functionally compensate for each other in the regulation of key ovarian genes. Functional enrichment revealed that ovulation, growth, intracellular signaling, extracellular structure organization, gonadotropin and growth factor actions, and steroidogenesis were significantly regulated in G4/6(gcko) mice. The results of this analysis were confirmed using quantitative polymerase chain reaction, immunohistochemical, and biological assays. Treatment of GCs with cAMP/IGF-I, to bypass FSH and IGF-I signaling defects, revealed that most of the affected genes are direct targets of GATA4/6. The diversity of pathways affected by the knockdown of GATA underscores the important role of these factors in the regulation of GC function.
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Affiliation(s)
- Jill Bennett
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 606012.
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Zhang WJ, Guo Y. Mechanisms of liver repair following injury. Shijie Huaren Xiaohua Zazhi 2013; 21:3369-3375. [DOI: 10.11569/wcjd.v21.i31.3369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Liver injury caused by a variety of physical or chemical factors is a common disease, and severe or persistent liver injury can ultimately lead to acute liver failure. Its treatment is still a formidable challenge to clinicians. Elucidation of mechanisms underlying liver repair following injury is the cornerstone of treatment of hepatic diseases. Despite many research efforts over the past decades, the mechanisms behind liver repair following injury are still not clear. Recent studies have demonstrated that oval cells and bone marrow stem cells are involved in this complex process. A variety of cells and factors may play a role in different stages of this process. In this paper, we will review mechanisms of liver repair following injury.
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Analysis of Dll4 regulation reveals a combinatorial role for Sox and Notch in arterial development. Proc Natl Acad Sci U S A 2013; 110:11893-8. [PMID: 23818617 DOI: 10.1073/pnas.1300805110] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The mechanisms by which arterial fate is established and maintained are not clearly understood. Although a number of signaling pathways and transcriptional regulators have been implicated in arterio-venous differentiation, none are essential for arterial formation, and the manner in which widely expressed factors may achieve arterial-specific gene regulation is unclear. Using both mouse and zebrafish models, we demonstrate here that arterial specification is regulated combinatorially by Notch signaling and SoxF transcription factors, via direct transcriptional gene activation. Through the identification and characterization of two arterial endothelial cell-specific gene enhancers for the Notch ligand Delta-like ligand 4 (Dll4), we show that arterial Dll4 expression requires the direct binding of both the RBPJ/Notch intracellular domain and SOXF transcription factors. Specific combinatorial, but not individual, loss of SOXF and RBPJ DNA binding ablates all Dll4 enhancer-transgene expression despite the presence of multiple functional ETS binding sites, as does knockdown of sox7;sox18 in combination with loss of Notch signaling. Furthermore, triple knockdown of sox7, sox18 and rbpj also results in ablation of endogenous dll4 expression. Fascinatingly, this combinatorial ablation leads to a loss of arterial markers and the absence of a detectable dorsal aorta, demonstrating the essential roles of SoxF and Notch, together, in the acquisition of arterial identity.
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