1
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Zhang ZH, Yuan CY, Xu M, Wang MF, Feng T, Wang Y, Zheng SF, Zhang HL, Shi GH, Cao DL, Wang ZL, Ye DW. Calycosin inhibits the proliferation and metastasis of renal cell carcinoma through the MAZ/HAS2 signaling pathway. Phytother Res 2024. [PMID: 39120474 DOI: 10.1002/ptr.8295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 06/03/2024] [Accepted: 07/07/2024] [Indexed: 08/10/2024]
Abstract
Calycosin (Caly), a flavonoid compound, demonstrates a variety of beneficial properties. However, the specific mechanisms behind Caly's anticancer effects remain largely unexplored. Network pharmacology was used to explore the potential targets of Caly in renal cancer. Additionally, RNA-seq sequencing was used to detect changes in genes in renal cancer cells after Caly treatment. Validation was carried out through quantitative reverse transcription-PCR and Western blot analysis. The luciferase reporter assay was applied to pinpoint the interaction site between MAZ and HAS2. Furthermore, the immunoprecipitation assay was utilized to examine the ubiquitination and degradation of MAZ. In vivo experiments using cell line-derived xenograft mouse models were performed to assess Calycosin's impact on cancer growth. Network pharmacology research suggests Caly plays a role in promoting apoptosis and inhibiting cell adhesion in renal cancer. In vitro, Caly has been observed to suppress proliferation, colony formation, and metastasis of renal cancer cells while also triggering apoptosis. Additionally, it appears to diminish hyaluronic acid synthesis by downregulating HAS2 expression. MAZ is identified as a transcriptional regulator of HAS2 expression. Calycosin further facilitates the degradation of MAZ via the ubiquitin-proteasome pathway. Notably, Caly demonstrates efficacy in reducing the growth of renal cell carcinoma xenograft tumors in vivo. Our findings indicate that Caly suppresses the proliferation, metastasis, and progression of renal cell carcinoma through its action on the MAZ/HAS2 signaling pathway. Thus, Caly represents a promising therapeutic candidate for the treatment of renal cell carcinoma.
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Affiliation(s)
- Zi-Hao Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Urology, School of Life Medicine, Fudan University Shanghai Cancer Center, Qingdao Institute, Fudan University, Qingdao, China
| | - Cheng-Yue Yuan
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng Xu
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng-Fei Wang
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tao Feng
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Urology, School of Life Medicine, Fudan University Shanghai Cancer Center, Qingdao Institute, Fudan University, Qingdao, China
| | - Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sheng-Feng Zheng
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Urology, School of Life Medicine, Fudan University Shanghai Cancer Center, Qingdao Institute, Fudan University, Qingdao, China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zi-Liang Wang
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Urology, School of Life Medicine, Fudan University Shanghai Cancer Center, Qingdao Institute, Fudan University, Qingdao, China
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2
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Bhargavan B, Chhunchha B, Kubo E, Singh DP. DNA methylation as an epigenetic mechanism in the regulation of LEDGF expression and biological response in aging and oxidative stress. Cell Death Discov 2024; 10:296. [PMID: 38909054 PMCID: PMC11193803 DOI: 10.1038/s41420-024-02076-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024] Open
Abstract
The physiological quantum of stress-inducible transcriptional protein, Lens Epithelium-Derived Growth Factor (LEDGF), is vital for the maintenance of cellular physiology. Erratic epigenetic reprogramming in response to oxidative stress or with advancing age is found to be a major cause in the gene silencing, leading to pathobiologies. Using aging human (h) eye lens/lens epithelial cells (LECs) coupled with redox-active Peroxiredoxin 6 (Prdx6)-deficient (Prdx6-/-) mLECs as model systems, herein, we showed that in aging/oxidative stress, the human LEDGF gene was regulated by unique methylation patterns of CGs nucleotides within and around the Sp1 binding site(s) of CpG island of the LEDGF promoter (-170 to -27nts). The process caused the repression of LEDGF and its target, Hsp27, resulting in reactive oxygen species (ROS) amplification and cellular insults. This phenomenon was opposed to the unmethylated promoter in LECs. Clinically, we observed that the loss of LEDGF in the Prdx6-/- mLECs or aging lenses/LECs, correlating with increased expression of DNMT1, DNMT3a, and DNMT3b along with the methyl CpG binding protein 2 (MeCP2). Upon oxidative stress, the expression of these molecules was increased with the dramatic reduction in LEDGF expression. While demethylating agent, 5-Aza deoxycytidine (5-AzaC) transposed the aberrant methylation status, and revived LEDGF and Hsp27 expression. Mechanistically, the chloramphenicol acetyltransferase (CAT) reporter gene driven by the LEDGF promoter (-170/ + 35) and ChIP assays uncovered that 5-AzaC acted on GC/Sp1 sites to release LEDGF transcription. The data argued, for the first time, that de novo methylation of CGs around and within Sp1 sites of the CpG island directly disrupted Sp1 activity, which ensued in LEDGF repression and its biological functions. The findings should improve our understanding of cellular insults-associated with aberrant DNMTs-mediated LEDGF's activity, and can offer strategies for therapeutic intervention to halt aging/oxidative stress-induced abnormalities.
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Affiliation(s)
- Biju Bhargavan
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bhavana Chhunchha
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Eri Kubo
- Department of Ophthalmology, Kanazawa Medical University, Ishikawa, 9200293, Japan
| | - Dhirendra P Singh
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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3
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Xiao T, Li X, Felsenfeld G. The Myc-associated zinc finger protein epigenetically controls expression of interferon-γ-stimulated genes by recruiting STAT1 to chromatin. Proc Natl Acad Sci U S A 2024; 121:e2320938121. [PMID: 38635637 PMCID: PMC11046693 DOI: 10.1073/pnas.2320938121] [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: 12/13/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
The MYC-Associated Zinc Finger Protein (MAZ) plays important roles in chromatin organization and gene transcription regulation. Dysregulated expression of MAZ causes diseases, such as glioblastoma, breast cancer, prostate cancer, and liposarcoma. Previously, it has been reported that MAZ controls the proinflammatory response in colitis and colon cancer via STAT3 signaling, suggesting that MAZ is involved in regulating immunity-related pathways. However, the molecular mechanism underlying this regulation remains elusive. Here, we investigate the regulatory effect of MAZ on interferon-gamma (IFN-γ)-stimulated genes via STAT1, a protein that plays an essential role in immune responses to viral, fungal, and mycobacterial pathogens. We demonstrate that about 80% of occupied STAT1-binding sites colocalize with occupied MAZ-binding sites in HAP1/K562 cells after IFN-γ stimulation. MAZ depletion significantly reduces STAT1 binding in the genome. By analyzing genome-wide gene expression profiles in the RNA-Seq data, we show that MAZ depletion significantly suppresses a subset of the immune response genes, which include the IFN-stimulated genes IRF8 and Absent in Melanoma 2. Furthermore, we find that MAZ controls expression of the immunity-related genes by changing the epigenetic landscape in chromatin. Our study reveals an important role for MAZ in regulating immune-related gene expression.
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Affiliation(s)
- Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH
| | - Xin Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH
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Pan H, Guo Z, Lv P, Hu K, Wu T, Lin Z, Xue Y, Zhang Y, Guo Z. Proline/serine-rich coiled-coil protein 1 inhibits macrophage inflammation and delays atherosclerotic progression by binding to Annexin A2. Clin Transl Med 2023; 13:e1220. [PMID: 36932468 PMCID: PMC10023832 DOI: 10.1002/ctm2.1220] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Atherosclerosis (AS), the main pathological basis of life-threatening cardiovascular disease, is essentially caused by chronic macrophage inflammation. Overexpression of proline/serine-rich coiled-coil protein 1 (PSRC1) reduces macrophage inflammatory responses and delays AS development. However, the exact mechanism of PSRC1 is unclear. METHODS Proteins interacting with PSRC1 were screened by proteomics in RAW264.7 cells, followed by RT-qPCR, immunoprecipitation and immunofluorescence to explore the specific mechanistic pathways affecting inflammation. CRISPR-Cas9 constructs for PSRC1-/- ApoE-/- (DKO) mice and high-fat diet-fed ApoE-/- and DKO mice were used for AS models for in vivo experiments. Upstream transcription factors of PSRC1 were predicted by ATAC-seq, ChIP-seq and UCSC, and the regulatory mechanism was verified by ChIP-qPCR and dual luciferase assays. Peripheral blood serum and monocytes were collected from coronary artery disease (CAD) patients and non-CAD patients. RESULTS Increased binding of ANXA2 to PSRC1 in macrophages under oxidized low-density lipoprotein stimulation and decreased release of ANXA2 to the extracellular compartment were observed. Knockdown of ANXA2 in AS model mice delayed AS progression. Knockdown of ANXA2 in DKO mice reversed the AS-promoting effect of PSRC1 knockdown. Mechanistically, ANXA2 promotes STAT3 phosphorylation, which in turn promotes inflammatory responses. In addition, SP1 is a PSRC1 upstream repressive transcription factor, and the SP1 inhibitor mithramycin (Mith) elevated PSRC1 expression and exerted anti-AS effects in AS model mice. Patients with CAD had considerably greater serum levels of ANXA2 than those without CAD, and Mith reduced the secretion of ANXA2 in peripheral blood monocytes of CAD patients. CONCLUSION In macrophages, PSRC1 can interact with ANXA2 to inhibit its extracellular release and delay AS development. SP1 is an upstream transcription factor of PSRC1 and inhibits the transcription of PSRC1. The SP1 inhibitor Mith can elevate PSRC1 levels and slow AS progression while reducing ANXA2 release from monocytes in CAD patients. Mith is expected to be a new agent for AS treatment.
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Affiliation(s)
- Hangyu Pan
- Department of CardiologyState Key Laboratory of Organ Failure ResearchNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zhongzhou Guo
- Department of PharmacyZhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Ping Lv
- Department of Cardiovascular SurgeryNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Kexin Hu
- Department of CardiologyState Key Laboratory of Organ Failure ResearchNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Tongwei Wu
- Department of Medicine UltrasonicsNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zixiang Lin
- Department of CardiologyShenzhen HospitalHuazhong University of Science and Technology UnionShenzhenChina
| | - Yazhi Xue
- Department of General PracticeNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Yanan Zhang
- Department of CardiologyState Key Laboratory of Organ Failure ResearchNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zhigang Guo
- Department of CardiologyHuiqiao Medical CenterNanfang HospitalSouthern Medical UniversityGuangzhouChina
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5
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Zheng C, Wu H, Jin S, Li D, Tan S, Zhu X. Roles of Myc-associated zinc finger protein in malignant tumors. Asia Pac J Clin Oncol 2022; 18:506-514. [PMID: 35098656 DOI: 10.1111/ajco.13748] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022]
Abstract
As an important transcription factor that is widely expressed in most tissues of the human body, Myc-associated zinc finger protein (MAZ) has been reported highly expressed in many malignant tumors and thought to be a promising therapeutic target for cancer treatment. In this review, we aim to offer a comprehensive understanding of MAZ regulation in malignant tumors. The carboxy terminal of MAZ protein contains six C2H2 zinc fingers, and its regulation of transcription is based on the interaction between the GC-rich DNA binding sites of target genes and its carboxy-terminal zinc finger motifs. MAZ protein has been found to activate or inhibit the transcriptional initiation process of many target genes, as well as play an important role in the transcriptional termination process of some target genes, so MAZ poses dual regulatory functions in the initiation and termination process of gene transcription. Through the transcriptional regulation of c-myc and Ras gene family, MAZ poses an important role in the occurrence and development of breast cancer, pancreatic cancer, prostate cancer, glioblastoma, neuroblastoma, and other malignant tumors. Our review shows a vital role of MAZ in many malignant tumors and provides novel insight for cancer diagnosis and treatment.
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Affiliation(s)
- Chuanjun Zheng
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Hongmei Wu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Song Jin
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Di Li
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Shengkui Tan
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaonian Zhu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
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6
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McDermott A, Kim K, Kasper S, Ho SM, Leung YK. The androgen receptor inhibits transcription of GPER1 by preventing Sp1 and Sp3 from binding to the promoters in prostate cancer cells. Oncotarget 2022; 13:46-60. [PMID: 35018219 PMCID: PMC8741193 DOI: 10.18632/oncotarget.28169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/08/2021] [Indexed: 12/01/2022] Open
Abstract
G-1, a GPER1 agonist, was shown to inhibit the growth of castration-resistant mouse xenografts but not their parental androgen-dependent tumors. It is currently unknown how the androgen receptor (AR) represses GPER1 expression. Here, we found that two GPER1 mRNA variants (GPER1v2 and GPER1v4) were transcriptionally repressed, not via transcript destabilization, by the androgen-activated AR. Although no AR binding was found in all active promoters near GPER1, data from promoter assays suggested that both variants' promoters were inhibited by androgen treatment. Site-directed mutagenesis on Sp1/Sp3 binding sites revealed their role in supporting the basal expression of GPER1. Knockdown of Sp1 and Sp3 together but not separately repressed GPER1 expression whereas overexpression of both Sp1 and Sp3 together was required to alleviate AR repression of GPER1. Based on the chromatin immunoprecipitation data, Sp3 was found to bind to the promoters prior to the binding of Sp1 and RNA polymerase II. However, the binding of all three transcription factors was inhibited by DHT treatment. Concordantly, DHT treatment induced nuclear interactions between AR and Sp1 or Sp3. Taken together, these results indicate that AR represses transcription of GPER1 by binding to Sp1 and Sp3 independently to prevent their transactivation of the GPER1 promoters.
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Affiliation(s)
- Austin McDermott
- Department of Environmental Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - KyoungHyun Kim
- Department of Environmental Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Susan Kasper
- Department of Environmental Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shuk-Mei Ho
- Department of Environmental Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Yuet-Kin Leung
- Department of Environmental Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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7
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Yaşar P, Kars G, Yavuz K, Ayaz G, Oğuztüzün Ç, Bilgen E, Suvacı Z, Çetinkol ÖP, Can T, Muyan M. A CpG island promoter drives the CXXC5 gene expression. Sci Rep 2021; 11:15655. [PMID: 34341443 PMCID: PMC8329181 DOI: 10.1038/s41598-021-95165-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5' untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5'-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G-C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.
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Affiliation(s)
- Pelin Yaşar
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
- Epigenetics and Stem Cell Biology Laboratory, Single Cell Dynamics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
| | - Gizem Kars
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Kerim Yavuz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Gamze Ayaz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Çerağ Oğuztüzün
- Department of Computer Engineering, Bilkent University, Ankara, 06800, Turkey
| | - Ecenaz Bilgen
- Department of Chemistry, Middle East Technical University, Ankara, 06800, Turkey
| | - Zeynep Suvacı
- Department of Chemistry, Middle East Technical University, Ankara, 06800, Turkey
| | | | - Tolga Can
- Department of Computer Engineering, Middle East Technical University, Ankara, 06800, Turkey
| | - Mesut Muyan
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
- Cansyl Laboratories, Middle East Technical University, Ankara, 06800, Turkey.
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8
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Barbagallo C, Di Maria A, Alecci A, Barbagallo D, Alaimo S, Colarossi L, Ferro A, Di Pietro C, Purrello M, Pulvirenti A, Ragusa M. VECTOR: An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma. Genes (Basel) 2021; 12:genes12071004. [PMID: 34210067 PMCID: PMC8305227 DOI: 10.3390/genes12071004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults and, although its genetic background has been extensively studied, little is known about the contribution of non-coding RNAs (ncRNAs) to its pathogenesis. Indeed, its competitive endogenous RNA (ceRNA) regulatory network comprising microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and mRNAs has been insufficiently explored. Thanks to UM findings from The Cancer Genome Atlas (TCGA), it is now possible to statistically elaborate these data to identify the expression relationships among RNAs and correlative interaction data. In the present work, we propose the VECTOR (uVeal mElanoma Correlation NeTwORk) database, an interactive tool that identifies and visualizes the relationships among RNA molecules, based on the ceRNA model. The VECTOR database contains: (i) the TCGA-derived expression correlation values of miRNA-mRNA, miRNA-lncRNA and lncRNA-mRNA pairs combined with predicted or validated RNA-RNA interactions; (ii) data of sense-antisense sequence overlapping; (iii) correlation values of Transcription Factor (TF)-miRNA, TF-lncRNA, and TF-mRNA pairs associated with ChiPseq data; (iv) expression data of miRNAs, lncRNAs and mRNAs both in UM and physiological tissues. The VECTOR web interface can be queried, by inputting the gene name, to retrieve all the information about RNA signaling and visualize this as a graph. Finally, VECTOR provides a very detailed picture of ceRNA networks in UM and could be a very useful tool for researchers studying RNA signaling in UM. The web version of Vector is freely available at the URL reported at the end of the Introduction.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Antonio Di Maria
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Adriana Alecci
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Lorenzo Colarossi
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), 95029 Catania, Italy;
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
- Correspondence:
| | - Marco Ragusa
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
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9
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Shi X, Radhakrishnan S, Wen J, Chen JY, Chen J, Lam BA, Mills RE, Stranger BE, Lee C, Setlur SR. Association of CNVs with methylation variation. NPJ Genom Med 2020; 5:41. [PMID: 33062306 PMCID: PMC7519119 DOI: 10.1038/s41525-020-00145-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/04/2020] [Indexed: 12/03/2022] Open
Abstract
Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.
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Affiliation(s)
- Xinghua Shi
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA.,Present Address: Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122 USA
| | - Saranya Radhakrishnan
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Jia Wen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA
| | - Jin Yun Chen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Junjie Chen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA.,Present Address: Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122 USA
| | - Brianna Ashlyn Lam
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Barbara E Stranger
- Department of Pharmacology, Northwestern University, Chicago, Illinois 60611 USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032 USA.,Department of Life Sciences, Ewha Womans University, Seoul, 03760 South Korea.,Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Sunita R Setlur
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
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10
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Schlag K, Steinhilber D, Karas M, Sorg BL. Analysis of proximal ALOX5 promoter binding proteins by quantitative proteomics. FEBS J 2020; 287:4481-4499. [PMID: 32096311 DOI: 10.1111/febs.15259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/15/2019] [Accepted: 02/23/2020] [Indexed: 01/01/2023]
Abstract
5-Lipoxygenase (5-LO) is the initial enzyme in the biosynthesis of leukotrienes, which are mediators involved in pathophysiological conditions such as asthma and certain cancer types. Knowledge of proteins involved in 5-LO pathway regulation, including gene regulatory proteins, is needed to evaluate all options for therapeutic intervention in these diseases. Here, we present a mass spectrometric screening of ALOX5 promoter-interacting proteins, obtained by DNA pulldown and label-free quantitative mass spectrometry. Protein preparations from myeloid and B-lymphocytic cell lines were screened for promoter DNA interactors. Through statistical analysis, 66 proteins were identified as specific ALOX5 promotor binding proteins. Among those, the 15 most likely candidates for a prominent role in ALOX5 gene regulation are the known ALOX5 interactors Sp1 and Sp3, the related factor Sp2, two Krüppel-like factors (KLF13 and KLF16) and six other zinc finger proteins (MAZ, PRDM10, VEZF1, ZBTB7A, ZNF281 and ZNF579). Intriguingly, we also identified two helicases (BLM and DHX36) and the proteins hnRNPD and hnRNPK, which are, together with the protein MAZ, known to interact with DNA G-quadruplex structures. As G-quadruplexes are implicated in gene regulation, spectroscopic and antibody-based methods were used to confirm their presence within the GC-rich sequence of the ALOX5 promoter. In summary, we have systematically characterized the interactome of the ALOX5 promoter, identifying several zinc finger proteins as novel potential ALOX5 gene regulators. Further, we have shown that the ALOX5 promoter can form DNA G-quadruplex structures, which may play a functional role in ALOX5 gene regulation.
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Affiliation(s)
- Katharina Schlag
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Bernd L Sorg
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
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11
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Revealing the alternative promoter usage of SAF/MAZ gene by bichromatic fluorescent reporter construct. Biosci Rep 2019; 39:BSR20171668. [PMID: 30610159 PMCID: PMC6340948 DOI: 10.1042/bsr20171668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 12/20/2018] [Accepted: 12/31/2018] [Indexed: 11/17/2022] Open
Abstract
The large-scale identification of putative alternative promoters study shows more than 52% of human genes are regulated by alternative promoters. The human myc-associated zinc finger protein (SAF/MAZ) gene have SAF-1 and SAF-3 variants transcripted from two transcription start sites (TSSs). By using SAF/MAZ promoter as a model, we set up an approach to probe how the alternative promoters are regulated in real time. We have constructed the bichromatic fluorescent reporter driven by SAF/MAZ 5'-proximal promoter plasmids from which transactivation status of SAF-1 and SAF-3 alternative promoter could be monitored by EGFP and DsRed expression respectively. The results showed that the SAF-3 expression is regulated by alternative promoters. When the bichromatic fluorescent reporter was driven by -1692/+277 or -1401/+277 SAF/MAZ promoter the dominant expression of SAF-3 would be observed in comparison with SAF-1 expression. We also identified that Elk-1 is an inhibitory transcription factor for SAF-3 expression. The temporal diversity of SAF-1 and SAF-3 expressions can be observed via bichromatic fluorescent reporters. These imply that the bichromatic fluorescent reporter driven by alternative promoter construct might be a useful tool for decoding the temporal regulatory repertoire of alternative promoter in human genes.
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12
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Congras A, Caillet N, Torossian N, Quelen C, Daugrois C, Brousset P, Lamant L, Meggetto F, Hoareau-Aveilla C. Doxorubicin-induced loss of DNA topoisomerase II and DNMT1- dependent suppression of MiR-125b induces chemoresistance in ALK-positive cells. Oncotarget 2018; 9:14539-14551. [PMID: 29581862 PMCID: PMC5865688 DOI: 10.18632/oncotarget.24465] [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: 11/11/2017] [Accepted: 11/20/2017] [Indexed: 12/04/2022] Open
Abstract
Systemic anaplastic large-cell lymphoma (ALCL) is a childhood T cell neoplasm defined by the presence or absence of translocations that lead to the ectopic expression of anaplastic lymphoma kinase (ALK), with nucleophosmin-ALK (NPM-ALK) fusions being the most common. Polychemotherapy involving doxorubicin is the standard first-line treatment but for the 25 to 35% of patients who relapse and develop resistance the prognosis remains poor. We studied the potential role of the microRNA miR-125b in the development of resistance to doxorubicin in NPM-ALK(+) ALCL. Our results show that miR-125b expression is repressed in NPM-ALK(+) cell lines and patient samples through hypermethylation of its promoter. NPM-ALK activity, in cooperation with DNA topoisomerase II (Topo II) and DNA methyltransferase 1 (DNMT1), is responsible for miR-125b repression through DNA hypermethylation. MiR-125b repression was reversed by the inhibition of DNMTs with decitabine or the inhibition of DNA topoisomerase II with either doxorubicin or etoposide. In NPM-ALK(+) cell lines, doxorubicin treatment led to an increase in miR-125b levels by inhibiting the binding of DNMT1 to the MIR125B1 promoter and downregulating the pro-apoptotic miR-125b target BAK1. Reversal of miR-125b silencing, increased miR-125b levels and reduced BAK1 expression also led to a lower efficacy of doxorubicin, suggestive of a pharmacoresistance mechanism. In line with this, miR-125b repression and increased BAK1 expression correlated with early relapse in human NPM-ALK(+) ALCL primary biopsies. Collectively our findings suggest that miR-125b could be used to predict therapeutic outcome in NPM-ALK(+) ALCL.
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Affiliation(s)
- Annabelle Congras
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
| | - Nina Caillet
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
| | - Nouritza Torossian
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France
| | - Cathy Quelen
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
| | - Camille Daugrois
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France
| | - Pierre Brousset
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Institut Carnot Lymphome-CALYM, 31024, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31024, Toulouse, France.,European Research Initiative on ALK-related malignancies (ERIA) (http://www.erialcl.net/).,Equipe Labelisée LIGUE 2017
| | - Laurence Lamant
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Institut Carnot Lymphome-CALYM, 31024, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31024, Toulouse, France.,European Research Initiative on ALK-related malignancies (ERIA) (http://www.erialcl.net/).,Equipe Labelisée LIGUE 2017
| | - Fabienne Meggetto
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Institut Carnot Lymphome-CALYM, 31024, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31024, Toulouse, France.,European Research Initiative on ALK-related malignancies (ERIA) (http://www.erialcl.net/).,Equipe Labelisée LIGUE 2017
| | - Coralie Hoareau-Aveilla
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
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13
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16p11.2 transcription factor MAZ is a dosage-sensitive regulator of genitourinary development. Proc Natl Acad Sci U S A 2018; 115:E1849-E1858. [PMID: 29432158 DOI: 10.1073/pnas.1716092115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genitourinary (GU) birth defects are among the most common yet least studied congenital malformations. Congenital anomalies of the kidney and urinary tract (CAKUTs) have high morbidity and mortality rates and account for ∼30% of structural birth defects. Copy number variation (CNV) mapping revealed that 16p11.2 is a hotspot for GU development. The only gene covered collectively by all of the mapped GU-patient CNVs was MYC-associated zinc finger transcription factor (MAZ), and MAZ CNV frequency is enriched in nonsyndromic GU-abnormal patients. Knockdown of MAZ in HEK293 cells results in differential expression of several WNT morphogens required for normal GU development, including Wnt11 and Wnt4. MAZ knockdown also prevents efficient transition into S phase, affects transcription of cell-cycle regulators, and abrogates growth of human embryonic kidney cells. Murine Maz is ubiquitously expressed, and a CRISPR-Cas9 mouse model of Maz deletion results in perinatal lethality with survival rates dependent on Maz copy number. Homozygous loss of Maz results in high penetrance of CAKUTs, and Maz is haploinsufficient for normal bladder development. MAZ, once thought to be a simple housekeeping gene, encodes a dosage-sensitive transcription factor that regulates urogenital development and contributes to both nonsyndromic congenital malformations of the GU tract as well as the 16p11.2 phenotype.
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14
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Yu ZH, Lun SM, He R, Tian HP, Huang HJ, Wang QS, Li XQ, Feng YM. Dual function of MAZ mediated by FOXF2 in basal-like breast cancer: Promotion of proliferation and suppression of progression. Cancer Lett 2017; 402:142-152. [DOI: 10.1016/j.canlet.2017.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/03/2017] [Accepted: 05/24/2017] [Indexed: 11/16/2022]
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15
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Hewett SJ, Shi J, Gong Y, Dhandapani K, Pilbeam C, Hewett JA. Spontaneous Glutamatergic Synaptic Activity Regulates Constitutive COX-2 Expression in Neurons: OPPOSING ROLES FOR THE TRANSCRIPTION FACTORS CREB (cAMP RESPONSE ELEMENT BINDING) PROTEIN AND Sp1 (STIMULATORY PROTEIN-1). J Biol Chem 2016; 291:27279-27288. [PMID: 27875294 DOI: 10.1074/jbc.m116.737353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 11/10/2016] [Indexed: 11/06/2022] Open
Abstract
Burgeoning evidence supports a role for cyclooxygenase metabolites in regulating membrane excitability in various forms of synaptic plasticity. Two cyclooxygenases, COX-1 and COX-2, catalyze the initial step in the metabolism of arachidonic acid to prostaglandins. COX-2 is generally considered inducible, but in glutamatergic neurons in some brain regions, including the cerebral cortex, it is constitutively expressed. However, the transcriptional mechanisms by which this occurs have not been elucidated. Here, we used quantitative PCR and also analyzed reporter gene expression in a mouse line carrying a construct consisting of a portion of the proximal promoter region of the mouse COX-2 gene upstream of luciferase cDNA to characterize COX-2 basal transcriptional regulation in cortical neurons. Extracts from the whole brain and from the cerebral cortex, hippocampus, and olfactory bulbs exhibited high luciferase activity. Moreover, constitutive COX-2 expression and luciferase activity were detected in cortical neurons, but not in cortical astrocytes, cultured from wild-type and transgenic mice, respectively. Constitutive COX-2 expression depended on spontaneous but not evoked excitatory synaptic activity and was shown to be N-methyl-d-aspartate receptor-dependent. Constitutive promoter activity was reduced in neurons transfected with a dominant-negative cAMP response element binding protein (CREB) and was eliminated by mutating the CRE-binding site on the COX-2 promoter. However, mutation of the stimulatory protein-1 (Sp1)-binding site resulted in an N-methyl-d-aspartate receptor-dependent enhancement of COX-2 promoter activity. Basal binding of the transcription factors CREB and Sp1 to the native neuronal COX-2 promoter was confirmed. In toto, our data suggest that spontaneous glutamatergic synaptic activity regulates constitutive neuronal COX-2 expression via Sp1 and CREB protein-dependent transcriptional mechanisms.
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Affiliation(s)
- Sandra J Hewett
- From the Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, New York 13210,
| | - Jingxue Shi
- From the Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, New York 13210
| | - Yifan Gong
- From the Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, New York 13210
| | - Krishnan Dhandapani
- the Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, Georgia 30912, and
| | - Carol Pilbeam
- the Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - James A Hewett
- From the Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, New York 13210,
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16
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Zhang W, Spector TD, Deloukas P, Bell JT, Engelhardt BE. Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements. Genome Biol 2015; 16:14. [PMID: 25616342 PMCID: PMC4389802 DOI: 10.1186/s13059-015-0581-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 01/02/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific methylation levels is critical to enable genome-wide analyses, but current approaches tackle average methylation within a locus and are often limited to specific genomic regions. RESULTS We characterize genome-wide DNA methylation patterns, and show that correlation among CpG sites decays rapidly, making predictions solely based on neighboring sites challenging. We built a random forest classifier to predict methylation levels at CpG site resolution using features including neighboring CpG site methylation levels and genomic distance, co-localization with coding regions, CpG islands (CGIs), and regulatory elements from the ENCODE project. Our approach achieves 92% prediction accuracy of genome-wide methylation levels at single-CpG-site precision. The accuracy increases to 98% when restricted to CpG sites within CGIs and is robust across platform and cell-type heterogeneity. Our classifier outperforms other types of classifiers and identifies features that contribute to prediction accuracy: neighboring CpG site methylation, CGIs, co-localized DNase I hypersensitive sites, transcription factor binding sites, and histone modifications were found to be most predictive of methylation levels. CONCLUSIONS Our observations of DNA methylation patterns led us to develop a classifier to predict DNA methylation levels at CpG site resolution with high accuracy. Furthermore, our method identified genomic features that interact with DNA methylation, suggesting mechanisms involved in DNA methylation modification and regulation, and linking diverse epigenetic processes.
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Affiliation(s)
- Weiwei Zhang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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17
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Beishline K, Azizkhan-Clifford J. Sp1 and the 'hallmarks of cancer'. FEBS J 2015; 282:224-58. [PMID: 25393971 DOI: 10.1111/febs.13148] [Citation(s) in RCA: 369] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/26/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
Abstract
For many years, transcription factor Sp1 was viewed as a basal transcription factor and relegated to a role in the regulation of so-called housekeeping genes. Identification of Sp1's role in recruiting the general transcription machinery in the absence of a TATA box increased its importance in gene regulation, particularly in light of recent estimates that the majority of mammalian genes lack a TATA box. In this review, we briefly consider the history of Sp1, the founding member of the Sp family of transcription factors. We review the evidence suggesting that Sp1 is highly regulated by post-translational modifications that positively and negatively affect the activity of Sp1 on a wide array of genes. Sp1 is over-expressed in many cancers and is associated with poor prognosis. Targeting Sp1 in cancer treatment has been suggested; however, our review of the literature on the role of Sp1 in the regulation of genes that contribute to the 'hallmarks of cancer' illustrates the extreme complexity of Sp1 functions. Sp1 both activates and suppresses the expression of a number of essential oncogenes and tumor suppressors, as well as genes involved in essential cellular functions, including proliferation, differentiation, the DNA damage response, apoptosis, senescence and angiogenesis. Sp1 is also implicated in inflammation and genomic instability, as well as epigenetic silencing. Given the apparently opposing effects of Sp1, a more complete understanding of the function of Sp1 in cancer is required to validate its potential as a therapeutic target.
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Affiliation(s)
- Kate Beishline
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
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18
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Fang Q, Yang W, Li H, Hu W, Chen L, Jiang S, Dong K, Song Q, Wang C, Chen S, Liu F, Jia W. Negative regulation of DsbA-L gene expression by the transcription factor Sp1. Diabetes 2014; 63:4165-71. [PMID: 25024375 PMCID: PMC4237990 DOI: 10.2337/db14-0182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Disulfide-bond A oxidoreductase-like protein (DsbA-L) possesses beneficial effects such as promoting adiponectin multimerization and stability, increasing insulin sensitivity, and enhancing energy metabolism. The expression level of DsbA-L is negatively correlated with obesity in mice and humans, but the underlying mechanisms remain unknown. To address this question, we generated reporter gene constructs containing the promoter sequence of the mouse DsbA-L gene. Deletion analysis showed that the proximal promoter of mouse DsbA-L is located between -186 and -34 bp relative to the transcription start site. In silico analysis identified a putative Sp1 transcription factor binding site in the first intron of the DsbA-L gene. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis indicated that Sp1 bound to this intron region in vitro and in intact cells. Overexpression of Sp1 or suppressing Sp1 expression by siRNA reduced or increased DsbA-L promoter activity, respectively. The binding activity of Sp1 was gradually decreased during 3T3-L1 cell differentiation and was significantly increased in adipose tissues of obese mice. Our results identify Sp1 as an inhibitor of DsbA-L gene transcription, and the Sp1-mediated inhibition of DsbA-L gene expression may provide a mechanism underlying obesity-induced adiponectin downregulation and insulin resistance.
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Affiliation(s)
- Qichen Fang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Wenjing Yang
- Department of Medicine, Medical School of Soochow University, Suzhou, China
| | - Huating Li
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Wenxiu Hu
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Lihui Chen
- Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, Second Xiangya Hospital, Central South University, Changsha, China
| | - Shan Jiang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Kun Dong
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Qianqian Song
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Chen Wang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Shuo Chen
- Department of Developmental Dentistry, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Feng Liu
- Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, Second Xiangya Hospital, Central South University, Changsha, China Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Weiping Jia
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China
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19
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Takahashi H, Rikimaru K, Komatsu M, Uemoto Y, Suzuki K. Association between Motilin Receptor Gene Haplotypes and Growth Traits in Japanese Hinai-dori Crossbred Chickens. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:316-23. [PMID: 25049957 PMCID: PMC4093263 DOI: 10.5713/ajas.2013.13500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/16/2013] [Accepted: 10/10/2013] [Indexed: 12/29/2022]
Abstract
We previously identified quantitative trait loci (QTL) for body weight and average daily gain in a common region between ADL0198 (chr 1: 171.7 Mb) and ABR0287 (chr 1: 173.4 Mb) on chicken chromosome 1 in an F2 resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Motilin receptor (MLNR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the MLNR gene and investigated its association with growth traits in a Hinai-dori F2 intercross population. All the exons of the MLNR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the F2 population, a mismatch amplification mutation assay was performed. Three haplotypes (Haplotypes 1–3) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 2, and 3) were examined in order to identify associations between MLNR haplotypes and growth traits. The data showed that Haplotype 1 was superior to Haplotype 2 and 3 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age in female in F2 females. It was concluded that MLNR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.
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Affiliation(s)
- Hideaki Takahashi
- Akita Prefectural Livestock Experiment Station, Daisen 019-1701, Japan
| | - Kazuhiro Rikimaru
- Akita Prefectural Livestock Experiment Station, Daisen 019-1701, Japan
| | - Megumi Komatsu
- Akita Prefectural Livestock Experiment Station, Daisen 019-1701, Japan
| | - Yoshinobu Uemoto
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
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20
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Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5′-GCGC-3′. Bioorg Med Chem 2013; 21:5436-41. [DOI: 10.1016/j.bmc.2013.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/27/2022]
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21
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Castro IC, Breiling A, Luetkenhaus K, Ceteci F, Hausmann S, Kress S, Lyko F, Rudel T, Rapp UR. MYC-induced epigenetic activation of GATA4 in lung adenocarcinoma. Mol Cancer Res 2012; 11:161-72. [PMID: 23239811 DOI: 10.1158/1541-7786.mcr-12-0414-t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human lung cancer is a disease with high incidence and accounts for most cancer-related deaths in both men and women. Metastasis is a common event in non-small cell lung carcinoma (NSCLC), diminishing the survival chance of the patients with this type of tumor. It has been shown that MYC is involved in the development of metastasis from NSCLC, but the mechanism underlying this switch remained to be identified. Here, we focus on GATA4 as a MYC target in the development of metastasis with origin in lung adenocarcinoma, the most common type of NSCLC. Epigenetic alterations at the GATA4 promoter level were observed after MYC expression in lung adenocarcinoma in vivo and in vitro. Such alterations include site-specific demethylation that accompanies the displacement of the MYC-associated zinc finger protein (MAZ) from the GATA4 promoter, which leads to GATA4 expression. Histone modification analysis of the GATA4 promoter revealed a switch from repressive histone marks to active histone marks after MYC binding, which corresponds to active GATA4 expression. Our results thus identify a novel epigenetic mechanism by which MYC activates GATA4 leading to metastasis in lung adenocarcinoma, suggesting novel potential targets for the development of antimetastatic therapy.
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Affiliation(s)
- Inês C Castro
- Biocenter, Department of Microbiology, University of Würzburg, Würzburg, Germany
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Xu W, Zhu Q, Wu Z, Guo H, Wu F, Mashausi DS, Zheng C, Li D. A Novel Evolutionarily Conserved Element Is a General Transcriptional Repressor of p21WAF1/CIP1. Cancer Res 2012; 72:6236-46. [DOI: 10.1158/0008-5472.can-12-1236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Han YW, Matsumoto T, Yokota H, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Harada Y, Sugiyama H. Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants. Nucleic Acids Res 2012; 40:11510-7. [PMID: 23042247 PMCID: PMC3526260 DOI: 10.1093/nar/gks897] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan.
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24
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Singh DP, Bhargavan B, Chhunchha B, Kubo E, Kumar A, Fatma N. Transcriptional protein Sp1 regulates LEDGF transcription by directly interacting with its cis-elements in GC-rich region of TATA-less gene promoter. PLoS One 2012; 7:e37012. [PMID: 22615874 PMCID: PMC3353957 DOI: 10.1371/journal.pone.0037012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/11/2012] [Indexed: 02/02/2023] Open
Abstract
LEDGF/p75 interacts with DNA/protein to regulate gene expression and function. Despite the recognized diversity of function of LEDGF/p75, knowledge of its transregulation is in its infancy. Here we report that LEDGF/p75 gene is TATA-less, contains GC-rich cis elements and is transcriptionally regulated by Sp1 involving small ubiquitin-like modifier (Sumo1). Using different cell lines, we showed that Sp1 overexpression increased the level of LEDGF/p75 protein and mRNA expression in a concentration-dependent fashion. In contrast, RNA interference depletion of intrinsic Sp1 or treatment with artemisinin, a Sp1 inhibitor, reduced expression of LEDGF/p75, suggesting Sp1-mediated regulation of LEDGF/p75. In silico analysis disclosed three evolutionarily conserved, putative Sp1 sites within LEDGF/p75 proximal promoter (−170/+1 nt). DNA-binding and transactivation assays using deletion and point mutation constructs of LEDGF/p75 promoter-CAT revealed that all Sp1 sites (−50/−43, −109/−102 and −146/−139) differentially regulate LEDGF/p75. Cotransfection studies with Sp1 in Drosophila cells that were Sp1-deficient, showed increased LEDGF/p75 transcription, while in lens epithelial cells (LECs) promoter activity was inhibited by artemisinin. These events were correlated with levels of endogenous Sp1-dependent LEDGF/p75 expression, and higher resistance to UVB-induced cell death. ChIP and transactivation assays showed that Sumoylation of Sp1 repressed its transcriptional activity as evidenced through its reduced binding to GC-box and reduced ability to activate LEDGF/p75 transcription. As whole, results revealed the importance of Sp1 in regulating expression of LEDGF/p75 gene and add to our knowledge of the factors that control LEDGF/p75 within cellular microenvironments, potentially providing a foundation for LEDGF/p75 expression-based transcription therapy.
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Affiliation(s)
- Dhirendra P Singh
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
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25
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G4-DNA formation in the HRAS promoter and rational design of decoy oligonucleotides for cancer therapy. PLoS One 2011; 6:e24421. [PMID: 21931711 PMCID: PMC3169596 DOI: 10.1371/journal.pone.0024421] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 08/09/2011] [Indexed: 12/12/2022] Open
Abstract
HRAS is a proto-oncogene involved in the tumorigenesis of urinary bladder cancer. In the HRAS promoter we identified two G-rich elements, hras-1 and hras-2, that fold, respectively, into an antiparallel and a parallel quadruplex (qhras-1, qhras-2). When we introduced in sequence hras-1 or hras-2 two point mutations that block quadruplex formation, transcription increased 5-fold, but when we stabilized the G-quadruplexes by guanidinium phthalocyanines, transcription decreased to 20% of control. By ChIP we found that sequence hras-1 is bound only by MAZ, while hras-2 is bound by MAZ and Sp1: two transcription factors recognizing guanine boxes. We also discovered by EMSA that recombinant MAZ-GST binds to both HRAS quadruplexes, while Sp1-GST only binds to qhras-1. The over-expression of MAZ and Sp1 synergistically activates HRAS transcription, while silencing each gene by RNAi results in a strong down-regulation of transcription. All these data indicate that the HRAS G-quadruplexes behave as transcription repressors. Finally, we designed decoy oligonucleotides mimicking the HRAS quadruplexes, bearing (R)-1-O-[4-(1-Pyrenylethynyl) phenylmethyl] glycerol and LNA modifications to increase their stability and nuclease resistance (G4-decoys). The G4-decoys repressed HRAS transcription and caused a strong antiproliferative effect, mediated by apoptosis, in T24 bladder cancer cells where HRAS is mutated.
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26
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Wang Q, Zhou Y, Weiss HL, Chow CW, Evers BM. NFATc1 regulation of TRAIL expression in human intestinal cells. PLoS One 2011; 6:e19882. [PMID: 21603612 PMCID: PMC3095616 DOI: 10.1371/journal.pone.0019882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/06/2011] [Indexed: 12/22/2022] Open
Abstract
TNF-related apoptosis-inducing ligand (TRAIL; Apo2) has been shown to promote intestinal cell differentiation. Nuclear factor of activated T cells (NFAT) participates in the regulation of a variety of cellular processes, including differentiation. Here, we examined the role of NFAT in the regulation of TRAIL in human intestinal cells. Treatment with a combination of phorbol 12-myristate 13-acetate (PMA) plus the calcium ionophore A23187 (Io) increased NFAT activation and TRAIL expression; pretreatment with the calcineurin inhibitor cyclosporine A (CsA), an antagonist of NFAT signaling, diminished NFAT activation and TRAIL induction. In addition, knockdown of NFATc1, NFATc2, NFATc3, and NFATc4 blocked PMA/Io increased TRAIL protein expression. Expression of NFATc1 activated TRAIL promoter activity and increased TRAIL mRNA and protein expression. Deletion of NFAT binding sites from the TRAIL promoter did not significantly abrogate NFATc1-increased TRAIL promoter activity, suggesting an indirect regulation of TRAIL expression by NFAT activation. Knockdown of NFATc1 increased Sp1 transcription factor binding to the TRAIL promoter and, importantly, inhibition of Sp1, by chemical inhibition or RNA interference, increased TRAIL expression. These studies identify a novel mechanism for TRAIL regulation by which activation of NFATc1 increases TRAIL expression through negative regulation of Sp1 binding to the TRAIL promoter.
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Affiliation(s)
- Qingding Wang
- Department of Surgery, The University of Kentucky, Lexington, Kentucky, United States of America
- Markey Cancer Center, The University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuning Zhou
- Markey Cancer Center, The University of Kentucky, Lexington, Kentucky, United States of America
| | - Heidi L. Weiss
- Markey Cancer Center, The University of Kentucky, Lexington, Kentucky, United States of America
| | - Chi-Wing Chow
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - B. Mark Evers
- Department of Surgery, The University of Kentucky, Lexington, Kentucky, United States of America
- Markey Cancer Center, The University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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Cogoi S, Paramasivam M, Membrino A, Yokoyama KK, Xodo LE. The KRAS promoter responds to Myc-associated zinc finger and poly(ADP-ribose) polymerase 1 proteins, which recognize a critical quadruplex-forming GA-element. J Biol Chem 2010; 285:22003-16. [PMID: 20457603 DOI: 10.1074/jbc.m110.101923] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The murine KRAS promoter contains a G-rich nuclease hypersensitive element (GA-element) upstream of the transcription start site that is essential for transcription. Pulldown and chromatin immunoprecipitation assays demonstrate that this GA-element is bound by the Myc-associated zinc finger (MAZ) and poly(ADP-ribose) polymerase 1 (PARP-1) proteins. These proteins are crucial for transcription, because when they are knocked down by short hairpin RNA, transcription is down-regulated. This is also the case when the poly(ADP-ribosyl)ation activity of PARP-1 is inhibited by 3,4-dihydro-5-[4-(1-piperidinyl) butoxyl]-1(2H) isoquinolinone. We found that MAZ specifically binds to the duplex and quadruplex conformations of the GA-element, whereas PARP-1 shows specificity only for the G-quadruplex. On the basis of fluorescence resonance energy transfer melting and polymerase stop assays we saw that MAZ stabilizes the KRAS quadruplex. When the capacity of folding in the GA-element is abrogated by specific G --> T or G --> A point mutations, KRAS transcription is down-regulated. Conversely, guanidine-modified phthalocyanines, which specifically interact with and stabilize the KRAS G-quadruplex, push the promoter activity up to more than double. Collectively, our data support a transcription mechanism for murine KRAS that involves MAZ, PARP-1 and duplex-quadruplex conformational changes in the promoter GA-element.
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Affiliation(s)
- Susanna Cogoi
- Department of Biomedical Science and Technology, University of Udine, School of Medicine, Piazzale Kolbe 4, 33100 Udine, Italy
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Yang R, Amir J, Liu H, Chaqour B. Mechanical strain activates a program of genes functionally involved in paracrine signaling of angiogenesis. Physiol Genomics 2008; 36:1-14. [PMID: 18854370 DOI: 10.1152/physiolgenomics.90291.2008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Studies were performed to examine the extent to which mechanical stimuli mediate control of angiogenesis in bladder cells both in vitro and in vivo. Differential gene expression between control nonstretched and cyclically stretched bladder smooth muscle cells was assessed using oligonucleotide microarrays and pathway analysis by the web tool Fast Assignment and Transference of Information (FatiGO). Data showed that a substantial proportion (33 of 86) of mechanically responsive genes were angiogenesis-related and include cytokines, growth-related factors, adhesion proteins, and matricellular, signal transduction, extracellular matrix (ECM), and inflammatory molecules. Integrative knowledge of protein-protein interactions revealed that 12 mechano-sensitive gene-encoded proteins have interacting partner(s) in the vascular system confirming their potential role in paracrine regulation of angiogenesis. Angiogenic genes include matricellular proteins such as Cyr61/CCN1, CTGF/CCN2 and tenascin C, components of the VEGF and IGF systems, ECM proteins such as type I collagen and proteoglycans, and matrix metalloproteinases. In an in vivo model of bladder overdistension, 5 of 11 mechano-responsive angiogenic genes, independently tested by real-time PCR, were upregulated as a result of pressure overload including Cyr61/CCN1, CTGF/CCN2, MCP-1, VEGF-A, MMP-1, and midkine. Meanwhile, the molecular anatomy of angiogenic gene promoters reveals the presence of GA box-binding for the myc-associated zinc finger protein, MAZ, often found adjacent to binding sites for mechano-responsive transcription factors (e.g., NF-kappaB), suggesting that the coordinated activity of these factors may induce selective angiogenic gene transcription. These data suggest that mechanical control of angiogenic genes is an integral part of the adaptive and plasticity responses to mechanical overload.
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Affiliation(s)
- Ru Yang
- Department of Anatomy and Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203-2098, USA
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29
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Wierstra I. Sp1: emerging roles--beyond constitutive activation of TATA-less housekeeping genes. Biochem Biophys Res Commun 2008; 372:1-13. [PMID: 18364237 DOI: 10.1016/j.bbrc.2008.03.074] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 03/17/2008] [Indexed: 01/21/2023]
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30
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Bartoszewski R, Rab A, Twitty G, Stevenson L, Fortenberry J, Piotrowski A, Dumanski JP, Bebok Z. The mechanism of cystic fibrosis transmembrane conductance regulator transcriptional repression during the unfolded protein response. J Biol Chem 2008; 283:12154-65. [PMID: 18319256 DOI: 10.1074/jbc.m707610200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The unfolded protein response (UPR) aids cellular recovery by increasing the capacity and decreasing the protein load of the endoplasmic reticulum (ER). Although the main pathways of the UPR are known, the mechanisms of UPR-associated transcriptional repression have not been explored in mammalian cells. Previous studies indicate that endogenous cystic fibrosis transmembrane conductance regulator (CFTR) mRNA levels and protein maturation efficiency decrease when the UPR is activated. In the present study, we demonstrate that inhibition of CFTR expression under ER stress leads to reduced cAMP-activated chloride secretion in epithelial monolayers, an indication of diminished CFTR function. Moreover, ER stress and the UPR obliterate endogenous DeltaF508 CFTR mRNA expression in CFPAC-1 cells without affecting recombinant DeltaF508 CFTR mRNA levels or mRNA half-life. These results emphasize that transcriptional repression of CFTR under ER stress, in concert with decreased CFTR maturation efficiency, leads to diminished function. Using human CFTR promoter reporter constructs, we confined the ER stress-associated CFTR transcriptional repression to the minimal promoter. Chromatin immunoprecipitation assays established the binding of the UPR-activated ATF6 transcription factor to this region during ER stress, which links the repression to the UPR. Methylation-specific PCR (MSP) revealed hypermethylation of CpG sites inside and in the vicinity of the MAZ transcription factor binding region of CFTR, demonstrating methylation-dependent repression. Using pharmacological inhibitors, we show that both DNA methylation and histone deacetylation contribute to CFTR transcriptional inhibition. These studies provide novel insight into the mechanism of gene repression during the mammalian UPR.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Cell Biology, University of Alabama, Birmingham, Alabama 35294-0005, USA
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31
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Palumbo SL, Memmott RM, Uribe DJ, Krotova-Khan Y, Hurley LH, Ebbinghaus SW. A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity. Nucleic Acids Res 2008; 36:1755-69. [PMID: 18252774 PMCID: PMC2330228 DOI: 10.1093/nar/gkm1069] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The c-myb promoter contains multiple GGA repeats beginning 17 bp downstream of the transcription initiation site. GGA repeats have been previously shown to form unusual DNA structures in solution. Results from chemical footprinting, circular dichroism and RNA and DNA polymerase arrest assays on oligonucleotides representing the GGA repeat region of the c-myb promoter demonstrate that the element is able to form tetrad:heptad:heptad:tetrad (T:H:H:T) G-quadruplex structures by stacking two tetrad:heptad G-quadruplexes formed by two of the three (GGA)(4) repeats. Deletion of one or two (GGA)(4) motifs destabilizes this secondary structure and increases c-myb promoter activity, indicating that the G-quadruplexes formed in the c-myb GGA repeat region may act as a negative regulator of the c-myb promoter. Complete deletion of the c-myb GGA repeat region abolishes c-myb promoter activity, indicating dual roles of the c-myb GGA repeat element as both a transcriptional repressor and an activator. Furthermore, we demonstrated that Myc-associated zinc finger protein (MAZ) represses c-myb promoter activity and binds to the c-myb T:H:H:T G-quadruplexes. Our findings show that the T:H:H:T G-quadruplex-forming region in the c-myb promoter is a critical cis-acting element and may repress c-myb promoter activity through MAZ interaction with G-quadruplexes in the c-myb promoter.
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Affiliation(s)
- SunMi L Palumbo
- Arizona Cancer Center, University of Arizona, 1515 N. Campbell Ave., Tucson, AZ 85724-5024, USA
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Kovacevic-Grujicic N, Yokoyama K, Stevanovic M. Trans-activation of the human SOX3 promoter by MAZ in NT2/D1 cells. ARCH BIOL SCI 2008. [DOI: 10.2298/abs0803379k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In this study, we examine the role of three highly conserved putative binding sites for Myc-associated zinc finger protein (MAZ) in regulation of the human SOX3 gene expression. Electrophoretic mobility shift and supershift assays indicate that complexes formed at two out of three MAZ sites of the human SOX3 promoter involve ubiquitously expressed MAZ protein. Furthermore, in cotransfection experiments we demonstrate that MAZ acts as a positive regulator of SOX3 gene transcription in both undifferentiated and RA-differentiated NT2/D1 cells. Although MAZ increased both basal and RA-induced promoter activity, our results suggest that MAZ does not contribute to RA inducibility of the SOX3 promoter during neuronal differentiation of NT2/D1 cells.
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Affiliation(s)
| | - Kazunari Yokoyama
- Gene Engineering Division, RIKEN BioResource Center Koyadai, Tsukuba Ibaraki, Japan
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Wang HY, Chang HT, Pai TW, Wu CI, Lee YH, Chang YH, Tai HL, Tang CY, Chou WY, Chang MDT. Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome. BMC Mol Biol 2007; 8:89. [PMID: 17927842 PMCID: PMC2174947 DOI: 10.1186/1471-2199-8-89] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 10/11/2007] [Indexed: 11/24/2022] Open
Abstract
Background Human eosinophil-derived neurotoxin (edn) and eosinophil cationic protein (ecp) are members of a subfamily of primate ribonuclease (rnase) genes. Although they are generated by gene duplication event, distinct edn and ecp expression profile in various tissues have been reported. Results In this study, we obtained the upstream promoter sequences of several representative primate eosinophil rnases. Bioinformatic analysis revealed the presence of a shared 34-nucleotide (nt) sequence stretch located at -81 to -48 in all edn promoters and macaque ecp promoter. Such a unique sequence motif constituted a region essential for transactivation of human edn in hepatocellular carcinoma cells. Gel electrophoretic mobility shift assay, transient transfection and scanning mutagenesis experiments allowed us to identify binding sites for two transcription factors, Myc-associated zinc finger protein (MAZ) and SV-40 protein-1 (Sp1), within the 34-nt segment. Subsequent in vitro and in vivo binding assays demonstrated a direct molecular interaction between this 34-nt region and MAZ and Sp1. Interestingly, overexpression of MAZ and Sp1 respectively repressed and enhanced edn promoter activity. The regulatory transactivation motif was mapped to the evolutionarily conserved -74/-65 region of the edn promoter, which was guanidine-rich and critical for recognition by both transcription factors. Conclusion Our results provide the first direct evidence that MAZ and Sp1 play important roles on the transcriptional activation of the human edn promoter through specific binding to a 34-nt segment present in representative primate eosinophil rnase promoters.
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Affiliation(s)
- Hsiu-Yu Wang
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China.
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Hua P, Xu H, Uno JK, Lipko MA, Dong J, Kiela PR, Ghishan FK. Sp1 and Sp3 mediate NHE2 gene transcription in the intestinal epithelial cells. Am J Physiol Gastrointest Liver Physiol 2007; 293:G146-53. [PMID: 17379926 DOI: 10.1152/ajpgi.00443.2006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Our previous studies have identified a minimal Sp1-driven promoter region (nt -36/+116) directing NHE2 expression in mouse renal epithelial cells. However, this minimal promoter region was not sufficient to support active transcription of NHE2 gene in the intestinal epithelial cells, suggesting the need for additional upstream regulatory elements. In the present study, we used nontransformed rat intestinal epithelial (RIE) cells as a model to identify the minimal promoter region and transcription factors necessary for the basal transcription of rat NHE2 gene in the intestinal epithelial cells. We identified a region within the rat NHE2 gene promoter located within nt -67/-43 upstream of transcription initiation site as indispensable for the promoter function in intestinal epithelial cells. Mutations at nt -56/-51 not only abolished the DNA-protein interaction in this region, but also completely abolished NHE2 gene promoter activity in RIE cells. Supershift assays revealed that Sp1 and Sp3 interact with this promoter region, but, contrary to the minimal promoter indispensable for renal expression of NHE2, both transcription factors expressed individually in Drosophila SL2 cells activated rat NHE2 gene promoter. Moreover, Sp1 was a weaker transactivator and when coexpressed in SL2 cells it reduced Sp3-mediated NHE2 basal promoter activity. Furthermore, DNase I footprinting confirmed that nt -58/-51 is protected by nuclear protein from RIE cells. We conclude that the mechanism of basal control of rat NHE2 gene promoter activity is different in the renal and intestinal epithelium, with Sp3 being the major transcriptional activator of NHE2 gene transcription in the intestinal epithelial cells.
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Affiliation(s)
- Ping Hua
- Department of Pediatrics, Steele Memorial Children's Research Center, 1501 N. Campbell Ave., Tucson, AZ 85724, USA
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Laenen K, Haegeman G, Vanhoenacker P. Structure of the human 5-HT7 receptor gene and characterization of its promoter region. Gene 2007; 391:252-63. [PMID: 17321075 DOI: 10.1016/j.gene.2007.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 01/08/2007] [Accepted: 01/08/2007] [Indexed: 10/23/2022]
Abstract
The molecular mechanism regulating serotonin 5-HT(7) receptor expression is still unclear. In this study we provide evidence that transcription of the 5-HT(7) gene is at least partly regulated by Sp1 and Sp3. We isolated and sequenced >3000 bp of the upstream sequences and identified by RACE a number of transcriptional initiation sites over a region of 300 bp upstream of the coding region. This region has a high GC content, but contains no obvious TATA or a CAAT box. Besides a Sp1/Sp3 consensus motif, regulatory elements for AP2, Egr-1 and MAZ are also present. Transient transfection assays using deletion variants indicated that the GC-rich region is essential for full promoter activity. The role of Sp1 in this was confirmed by transient overexpression of both wild type Sp1 or dominant-negative forms. By gel shift and supershift analyses, targeting the Sp1 consensus sequence and the GC-rich region just upstream of the transcription initiation sites, binding of Sp1 and Sp3 was demonstrated. Both in vitro as well as in vivo experiments, using a cell line which endogenously expresses the 5-HT(7) receptor, indicated that mithramycin A, an inhibitor of Sp1/3 transcription factor binding, was able to inhibit 5-HT(7) promoter activity. Taken together these results support the essential role of Sp factors in regulating 5-HT(7) promoter activity.
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Affiliation(s)
- Koen Laenen
- Laboratory of Eukaryotic Gene Expression and Signal Transduction (LEGEST), Department of Molecular Biology, Ghent University, UGent, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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Estève PO, Chin HG, Pradhan S. Molecular Mechanisms of Transactivation and Doxorubicin-mediated Repression of survivin Gene in Cancer Cells. J Biol Chem 2007; 282:2615-25. [PMID: 17124180 DOI: 10.1074/jbc.m606203200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human maintenance DNA cytosine methyltransferase (DNMT1) regulates gene expression in a methylation-dependent and -independent manner. Anti-apoptotic survivin gene down-regulation is mediated by p53 recruitment of DNMT1 to its promoter. Survivin inhibits programmed cell death, regulates cell division, and is expressed in cancer cells. The survivin gene promoter is CG-rich containing several Sp1 canonical, Sp1-like, cell cycle-dependent element/cell cycle gene homology region, and p53-binding sites. Here we demonstrate that Sp1 transcription factor(s) play a role in transcriptional activation of the survivin promoter in Drosophila and human cells. Sp1 inhibition in vivo by mithramycin A leads to down-regulation of a luciferase reporter driven by the human survivin promoter in transfected cells. Mithramycin A or Sp1-specific short interfering RNA down-regulated the endogenous survivin gene expression, confirming Sp1 as the primary determinant for transcriptional activation. Furthermore, immobilized DNMT1 ligand bound to seven consensus amino acids corresponding to the N-terminal region of the Sp class of transcription factors in a phage display analysis. In the co-immunoprecipitation assay, the endogenous Sp1 or Sp3 pulled down DNMT1 and methyltransferase activity. Similarly, a glutathione S-transferase pulldown assay between DNMT1 and Sp1 demonstrates a direct interaction between the two proteins. Fluorescent fusions of DNMT1 and Sp1 co-localized in the mammalian nucleus, thus supporting binary complex formation between both the proteins. The kinetics of survivin promoter occupancy via chromatin immunoprecipitation following doxorubicin treatment show the presence of Sp1 and gradual accumulation of transcriptional repressors p53, DNMT1, histone methyltransferase G9a, and HDAC1 onto the promoter along with histone H3K9me2. These data suggest that the Sp1 transcription factor acts as a platform for recruitment of transcriptional repressors.
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37
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Bae JS, Kim SH, Ye YM, Yoon HJ, Suh CH, Nahm DH, Park HS. Significant association of FcepsilonRIalpha promoter polymorphisms with aspirin-intolerant chronic urticaria. J Allergy Clin Immunol 2006; 119:449-56. [PMID: 17125826 DOI: 10.1016/j.jaci.2006.10.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 09/27/2006] [Accepted: 10/03/2006] [Indexed: 11/22/2022]
Abstract
BACKGROUND Although the mechanism that underlies aspirin hypersensitivity is not completely understood, an IgE-mediated response was reported for a patient with aspirin-intolerant chronic urticaria (AICU). OBJECTIVE We investigated whether genetic polymorphisms on the alpha-chain of the high-affinity IgE receptor (FcepsilonRIalpha) gene were associated with the AICU phenotype. METHODS We genotyped 2 promoter polymorphisms (-344C>T and -95T>C) of FcepsilonRIalpha gene in the Korean population, and the functional effect of the -344C>T polymorphism was analyzed by using a luciferase reporter assay and an electrophoretic mobility shift assay. RESULTS The rare allele frequency of the -344C>T polymorphism was significantly higher in the patients with AICU compared with the other subjects (P= .008 for AICU vs aspirin-tolerant chronic urticaria; P= .03 for AICU vs controls). This polymorphism was also significantly associated with total serum IgE concentrations and a higher rate of atopy in the patients with AICU (P= .01 and .05, respectively). The reporter plasmid that carried the -344T allele exhibited significantly higher promoter activity in a rat mast cell line (RBL-2H3) compared with the promoter activity of the -344C allele (P< .001). We found that transcription factor Myc-associated zinc finger protein preferentially bound the -344C promoter. Moreover, patients with AICU with the heterozygous CT genotype of the -344C>T polymorphism exhibited greater anti-IgE-mediated histamine release compared with those with the homozygous CC genotype. CONCLUSION These results suggest that the -344C>T polymorphism of the FcepsilonRIalpha promoter may be associated with increased expression of FcepsilonRIalpha on mast cells and enhanced release of histamine. CLINICAL IMPLICATIONS The FcepsilonRIalpha -344C>T polymorphism may contribute to the development of AICU.
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Affiliation(s)
- Jin-Sik Bae
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, Korea
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Abstract
Myc regulates to some degree every major process in the cell. Proliferation, growth, differentiation, apoptosis, and metabolism are all under myc control. In turn, these processes feed back to adjust the level of c-myc expression. Although Myc is regulated at every level from RNA synthesis to protein degradation, c-myc transcription is particularly responsive to multiple diverse physiological and pathological signals. These signals are delivered to the c-myc promoter by a wide variety of transcription factors and chromatin remodeling complexes. How these diverse and sometimes disparate signals are processed to manage the output of the c-myc promoter involves chromatin, recruitment of the transcription machinery, post-initiation transcriptional regulation, and mechanisms to provide dynamic feedback. Understanding these mechanisms promises to add new dimensions to models of transcriptional control and to reveal new strategies to manipulate Myc levels.
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Affiliation(s)
- J Liu
- Gene Regulation Section, Laboratory of Pathology, NCI, DCS, Bldg. 10, Rm 2N106, Bethesda, MD 20892-1500, USA
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Kawane T, Mimura J, Fujii-Kuriyama Y, Horiuchi N. Identification of the promoter region of the parathyroid hormone receptor gene responsible for transcriptional suppression by insulin-like growth factor-I. Arch Biochem Biophys 2005; 439:61-9. [PMID: 15950922 DOI: 10.1016/j.abb.2005.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 05/06/2005] [Accepted: 05/08/2005] [Indexed: 01/24/2023]
Abstract
We investigated parathyroid hormone (PTH)/PTH-related protein receptor (PTH1R) gene suppression induced by insulin-like growth factor (IGF)-I using a rat osteoblast-like cell line (UMR-106). Observations were made with PD98059, a specific ERK signaling pathway inhibitor, and UMR-106 cells transfected with dominant negative or constitutively active forms of MAP kinase kinase. IGF-I inhibited PTH1R gene expression via an ERK1/2 MAP kinase pathway. We cloned the 8-kb promoter region of the rat PTH1R gene and characterized the U3 promoter, a major IGF-I-responsive promoter among the two present in rat osteoblasts. The IGF-I-suppressive region was between +1 and +25, identical to the previously described PTH-suppressive region (PTHSR). Gel mobility-shift detected a specific DNA-protein complex decreased by IGF-I. Mutation involving a three base sequence (+1 to +3) among more than 3.5 kb constituting the PTH1R promoter region completely abolished IGF-I action. Thus, IGF-I signaling may act at the osteoblast exon U3 transcription initiation site to repress the transcriptional activity.
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Affiliation(s)
- Tetsuya Kawane
- Section of Biochemistry, Department of Oral Function and Molecular Biology, Ohu University School of Dentistry, Koriyama 963-8611, Japan
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40
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Kavurma MM, Khachigian LM. Vascular smooth muscle cell-specific regulation of cyclin-dependent kinase inhibitor p21WAF1/Cip1 transcription by Sp1 is mediated via distinctcis-acting positive and negative regulatory elements in the proximal p21WAF1/Cip1 promoter. J Cell Biochem 2004; 93:904-16. [PMID: 15389873 DOI: 10.1002/jcb.20238] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Smooth muscle cells (SMC) play a central role in common vascular pathologies such as atherosclerosis and restenosis. Understanding the molecular regulation of SMC proliferation at a transcriptional level may provide important clues for the targeted control of vascular hyperplasia. We recently reported the capacity of the transcription factor Sp1 to down-regulate p21(WAF1/Cip1) production thereby reducing p21(WAF1/Cip1)-cyclin D1-Cdk4 complex formation and inhibiting vascular SMC proliferation (Kavurma and Khachigian [2003] J. Biol. Chem. 278, 32537-32543). We have now localized the Sp1-response elements in the p21(WAF1/Cip1) promoter responsible for p21(WAF1/Cip1) repression in WKY12-22 SMCs. The proximal region of the p21(WAF1/Cip1) promoter contains five distinct Sp1-binding elements that we have termed A, B, C, D, and E. Electrophoretic mobility shift analysis revealed that SMC nuclear Sp1 interacts with all five Sp1-binding sites, and each of these sites is critical for Sp1 repression of the p21(WAF1/Cip1) promoter, since mutation in any one element ablates repression, and in some cases results in activation. In contrast, only elements C, D, and E are bound by Sp1 in endothelial cells. Sp1 overexpression activates the p21(WAF1/Cip1) promoter in this cell type. Furthermore, mutation in any of these five elements is not sufficient to prevent activation of the p21(WAF1/Cip1) promoter by Sp1 in endothelial cells. Surprisingly, double mutations of elements C and E facilitates superactivation by Sp1 in both cell types, whereas triple mutations of C, D, and E inactivate the promoter. These findings demonstrate cell type-specific regulation of p21(WAF1/Cip1) transcription by Sp1 via distinct cis-acting positive and negative regulatory elements in the proximal p21(WAF1/Cip1) promoter.
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Affiliation(s)
- Mary M Kavurma
- The Centre for Vascular Research, Department of Pathology, The University of New South Wales, Australia
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41
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Lee PW, Wu S, Lee YM. Differential Expression of μ-Opioid Receptor Gene in CXBK and B6 Mice by Sp1. Mol Pharmacol 2004. [DOI: 10.1124/mol.66.6.1580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Wu CX, Zhao WP, Kishi H, Dokan J, Jin ZX, Wei XC, Yokoyama KK, Muraguchi A. Activation of mouse RAG-2 promoter by Myc-associated zinc finger protein. Biochem Biophys Res Commun 2004; 317:1096-102. [PMID: 15094381 DOI: 10.1016/j.bbrc.2004.03.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Indexed: 11/24/2022]
Abstract
Recombination activating gene-1 (RAG-1) and RAG-2 are expressed specifically in lymphocytes undergoing the antigen receptor gene rearrangement during the lymphocyte development. Our previous study showed that the -41 to -17 nucleotides (nt) 5' -upstream region of mouse RAG-2 were pre-requisite for the core promoter activity and that Pax-5/c-Myb/LEF-1 protein-protein complex was responsible for its activity in immature B cells. In this study, we show that the -65/-42 sequence, the non-conserved sequence between human and mouse RAG-2 promoter, is necessary for the full promoter activity for mouse RAG-2. Electrophoresis mobility shift assay revealed that Myc-associated zinc finger protein (MAZ) as well as SP1/3 binds a GA box in this region. Using chromatin immunoprecipitation, we show that MAZ binds the RAG-2 promoter region in pre-B cells. Furthermore, we show that MAZ synergistically activates the murine RAG-2 promoter with Pax-5/c-Myb/LEF-1 complex. These results first demonstrate that MAZ participates in activation of mouse RAG-2 promoter.
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Affiliation(s)
- Chun-Xiao Wu
- Department of Immunology, Faculty of Medicine, Toyama Medical and Pharmaceutical University, 2630, Sugitani, Toyama 930-0194, Japan
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43
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Schäffler A, Ehling A, Neumann E, Herfarth H, Paul G, Tarner I, Gay S, Buechler C, Schölmerich J, Müller-Ladner U. Role of specificity protein-1, PPARγ, and pituitary protein transcription factor-1 in transcriptional regulation of the murine CORS-26 promoter. ACTA ACUST UNITED AC 2004; 1678:150-6. [PMID: 15157741 DOI: 10.1016/j.bbaexp.2004.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Revised: 02/10/2004] [Accepted: 02/16/2004] [Indexed: 11/20/2022]
Abstract
The collagenous repeat-containing sequence of 26-kDa protein (CORS-26) was recently described as a new gene that is induced during adipocyte differentiation. Since the transcription factors specificity protein-1 (SP-1) and PPARgamma have been demonstrated to modulate transcriptional activation of adipocytic genes, we investigated the putative role of SP-1 and PPARgamma in the regulation of the murine CORS-26 promoter. Computer-based sequence analysis revealed two putative SP-1 binding sites and binding sites for PPARgamma and Pit-1 within the TATA-box containing promoter. Electrophoretic mobility shift assays (EMSA) with nuclear extracts from 3T3-L1 adipocytes and appropriate promoter fragments demonstrated that SP-1 binds specifically to both SP-1 binding sites. Specificity was demonstrated by (i) the appearance of supershift bands, (ii) competition experiments and, (iii) by using oligonucleotides carrying mutated SP-1 binding sites. Functional promoter activity was analyzed by Luciferase reporter gene assays and SP-1 was shown to exert inhibitory effects on the transcriptional activation of the murine CORS-26 gene. Additionally, specific binding activity of PPARgamma and Pit-1 to the CORS-26 promoter was demonstrated. Taken together, the present data demonstrate the functionality of the proximal murine CORS-26 promoter, which is regulated specifically by two SP-1 binding sites via SP-3-independent repressive effects of SP-1 on transcriptional activation. Pit-1 and PPARgamma can bind specifically to the promoter and might play an additive functional role in gene regulation of murine CORS-26.
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Affiliation(s)
- A Schäffler
- Department of Internal Medicine I, University of Regensburg, Franz-Josef-Strauss-Allee 11, D-93042 Regensburg, Germany.
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44
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Song J, Lu YC, Yokoyama K, Rossi J, Chiu R. Cyclophilin A is required for retinoic acid-induced neuronal differentiation in p19 cells. J Biol Chem 2004; 279:24414-9. [PMID: 15047706 DOI: 10.1074/jbc.m311406200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stable transfectants with expression of small interfering RNA for targeting cyclophilin A (CypA) in p19 cells lose their potential for retinoic acid (RA)-induced neuronal differentiation but not Me(2)SO-induced mesodermal differentiation. This difference suggests that CypA is specifically required for the RA-induced neuronal pathway. In addition to the loss of RA-induced RA receptor beta expression and retinoic acid response element (RARE)-binding activity, a dramatic reduction in RA-induced RARE-mediated luciferase activity in the CypA knockdown cell line suggests that CypA affects RARE-mediated regulation of gene expression. Silent mutation of target sequences confirms the specificity of RNA interference in p19 embryonal carcinoma cells. Collectively, our data reveal that a novel function of CypA is required in the processing of RA-induced neuronal differentiation in p19 embryonal carcinoma cells.
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Affiliation(s)
- Jun Song
- Dental Research Institute, UCLA School of Dentistry, Los Angeles, California 90095, USA
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45
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Fiorenza MT, Bevilacqua A, Canterini S, Torcia S, Pontecorvi M, Mangia F. Early transcriptional activation of the hsp70.1 gene by osmotic stress in one-cell embryos of the mouse. Biol Reprod 2004; 70:1606-13. [PMID: 14766729 DOI: 10.1095/biolreprod.103.024877] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In fertilized mouse eggs, de novo transcription of embryonic genes is first observed during the S phase of the one-cell stage. This transcription, however, is mostly limited to the male pronucleus and possibly uncoupled from translation, making the functional meaning obscure. We found that one-cell mouse embryos respond to the osmotic shock of in vitro isolation with migration of HSF1, the canonical stress activator of mammalian heat shock genes, to pronuclei and by transient transcription of the hsp70.1, but not hsp70.3 and hsp90, heat shock genes. Isolated growing dictyate oocytes also display a nuclear HSF1 localization, but, in contrast with embryos, they transcribe both hsp70.1 and hsp70.3 genes only after heat shock. Intranuclear injection of double-stranded oligodeoxyribonucleotides containing HSE, GAGA box or GC box consensus sequences, and antibodies raised to transcription factors HSF1, HSF2, Drosophila melanogaster GAGA factor, or Sp1 demonstrated that hsp70.1 transcription depends on HSF1 in both oocytes and embryos and that Sp1 is dispensable in oocytes and inhibitory in the embryos. Hsp70.1 thus represents the first endogenous gene so far identified to be physiologically activated and tightly regulated after fertilization in mammals.
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Affiliation(s)
- Maria Teresa Fiorenza
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Psychology, Section of Neuroscience, UniversityLa Sapienza of Rome, 00185 Rome, Italy
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46
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Safe S, Kim K. Nuclear receptor-mediated transactivation through interaction with Sp proteins. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 77:1-36. [PMID: 15196889 DOI: 10.1016/s0079-6603(04)77001-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Stephen Safe
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843-4466, USA
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47
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Khan ZE, Wang TC, Cui G, Chi AL, Dimaline R. Transcriptional regulation of the human trefoil factor, TFF1, by gastrin. Gastroenterology 2003; 125:510-21. [PMID: 12891554 DOI: 10.1016/s0016-5085(03)00908-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS This study aimed to identify gastrin-sensitive genes that may mediate the effects of this hormone on gastric epithelial architecture. METHODS Gastrin-sensitive genes were identified by messenger RNA (mRNA) differential display of the gastric fundus from gastrin-deficient (GAS-KO) or wild-type mice. Gastrin-stimulated expression of the trefoil peptide TFF1 in mouse fundus and in the gastric cancer cell line AGS-G(R) was determined by Northern blot and real-time polymerase chain reaction. Transcriptional regulation of TFF1 in AGS-G(R) cells was studied using promoter-reporter assays and electrophoretic mobility shift assay. Expression of TFF1 and the cholecystokinin(B) receptor in response to gastric mucosal injury was determined by immunohistochemistry. RESULTS mRNA differential display identified TFF1 as a gastrin-regulated gene. TFF1 mRNA was reversibly reduced in GAS-KO mice and increased in a hypergastrinemic transgenic strain versus respective background strains. TFF1 mRNA expression was rapidly and potently induced by gastrin in a gastric cancer cell line that expresses the gastrin/cholecystokinin(B) receptor. Gastrin responsiveness of the human TFF1 promoter mapped to a G-C rich region 300 base pairs upstream of the transcriptional start site. This region bound the transcription factors SP3 and MAZ. Gastrin activated transcription through a Raf-, Mek- and Erk-dependent but Ras-independent pathway. TFF1 expression was induced both directly and by transactivation between neighboring cells. Neither direct nor indirect gastrin-induced TFF1 expression required activation of the epidermal growth factor receptor. CONCLUSIONS Gastrin exerts tonic control of TFF1 expression but also has the potential for rapid up-regulation of this trefoil factor. TFF1 is a potential candidate to counterbalance the proliferative effects of gastrin.
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Affiliation(s)
- Zara E Khan
- Physiological Laboratory, University of Liverpool, Liverpool, England UK
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48
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Barrett TB, Hauger RL, Kennedy JL, Sadovnick AD, Remick RA, Keck PE, McElroy SL, Alexander M, Shaw SH, Kelsoe JR. Evidence that a single nucleotide polymorphism in the promoter of the G protein receptor kinase 3 gene is associated with bipolar disorder. Mol Psychiatry 2003; 8:546-57. [PMID: 12808434 DOI: 10.1038/sj.mp.4001268] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In a genome-wide linkage survey, we have previously shown evidence suggesting that the chromosome 22q12 region contains a susceptibility locus for bipolar disorder (BPD). Two independent family sets yielded lod scores suggestive of linkage at markers in this region near the gene G protein receptor kinase 3 (GRK3). GRK3 is an excellent candidate risk gene for BPD since GRK3 is expressed widely in the brain, and since GRKs play key roles in the homologous desensitization of G protein-coupled receptor signaling. We have also previously shown GRK3 expression to be induced by amphetamine in an animal model of mania using microarray-based expression profiling. To identify possible functional mutations in GRK3, we sequenced the putative promoter region, all 21 exons, and intronic sequence flanking each exon, in 14-22 individuals with BPD. We found six sequence variants in the 5'-UTR/promoter region, but no coding or obvious splice variants. Transmission disequilibrium analyses of one set of 153 families indicated that two of the 5'-UTR/promoter variants are associated with BPD in families of northern European Caucasian ancestry. A supportive trend towards association to one of these two variants (P-5) was then subsequently obtained in an independent sample of 237 families. In the combined sample, the P-5 variant had an estimated allele frequency of 3% in bipolar subjects, and displayed a transmission to non-transmission ratio of 26 : 7.7 (chi(2)=9.6, one-sided P value=0.0019). Altogether, these data support the hypothesis that a dysregulation in GRK3 expression alters signaling desensitization, and thereby predisposes to the development of BPD.
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Affiliation(s)
- T B Barrett
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093-0603, USA
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Wu CG, Forgues M, Siddique S, Farnsworth J, Valerie K, Wang XW. SAGE transcript profiles of normal primary human hepatocytes expressing oncogenic hepatitis B virus X protein. FASEB J 2002; 16:1665-7. [PMID: 12207007 DOI: 10.1096/fj.02-0074fje] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Hepatitis B virus (HBV) is a major risk factor for hepatocellular carcinoma (HCC). HBV encodes an oncogenic HBx gene that functions as a transcriptional coactivator of multiple cellular genes. To understand the role(s) of HBx in the early genesis of HCC, we systematically analyzed gene expression profiles by serial analysis of gene expression (SAGE) in freshly isolated human primary hepatocytes infected with a replication-defective adenovirus containing HBx. A total of 19,501 sequence tags (representing 1443 unique transcripts) were analyzed, which provide a distribution of a transcriptome characteristic of normal hepatocytes and a profile associated with HBx expression. Examples of the targeted genes were confirmed by the Megarray analysis with a significant correlation between quantitative SAGE and Megarray (r = 0.8, P < 0.005). In HBx-expressing hepatocytes, a total of 57 transcripts (3.9%) were induced, and 46 transcripts (3.3%) were repressed by more than fivefold. Interestingly, most of the HBx-up-regulated transcripts can be clustered into three major classes, including genes that encode ribosomal proteins, transcription factors with zinc-finger motifs, and proteins associated with protein degradation pathways. These results suggest that HBx may function as a major regulator in common cellular pathways that, in turn, regulate protein synthesis, gene transcription, and protein degradation.
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Affiliation(s)
- Chuan-Ging Wu
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland 20892-4255, USA
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50
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Saur D, Seidler B, Paehge H, Schusdziarra V, Allescher HD. Complex regulation of human neuronal nitric-oxide synthase exon 1c gene transcription. Essential role of Sp and ZNF family members of transcription factors. J Biol Chem 2002; 277:25798-814. [PMID: 11960979 DOI: 10.1074/jbc.m109802200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Neuronal nitric-oxide synthase (nNOS) is expressed in a variety of human tissues and shows a complex transcriptional regulation with the presence of nine alternative first exons (1a-1i) resulting in nNOS transcripts with differing 5'-untranslated regions. We previously demonstrated that nNOS exon 1c, one of the predominant transcripts in the human gastrointestinal tract, is driven by a separate promoter (Saur, D., Paehge, H., Schusdziarra, V., and Allescher, H. D. (2000) Gastroenterology 118, 849-858). The present study focused on the quantitative expression of nNOS first exon variants in different human tissues and the characterization of the basal nNOS exon 1c promoter. In human brain, skeletal muscle, colon, and TGW-nu-I neuroblastoma cells, first exon expression patterns were analyzed by quantitative real-time reverse transcription-PCR. In these tissues/cells exon 1c was one of the most abundant first exons of nNOS. By transient transfections of TGW-nu-I and HeLa cells with reporter plasmids containing a series of 5' and 3' deletions in the exon 1c regulatory region, the minimal TATA-less promoter was localized within 44 base pairs. Gel mobility shift assays of this cis-regulatory region revealed a high complexity of the basal promoter with a cooperative binding of several transcription factors, like Sp and ZNF family members. When the Sp binding site of the minimal promoter construct was mutated, promoter activity was completely abolished in both cell lines, whereas mutation of the common binding site of ZNF76 and ZNF143 resulted in a decrease of 53% in TGW-nu-I and 37% in HeLa cells. In Drosophila Schneider cells expression of Sp1, the long Sp3 isoform, ZNF76 and ZNF143 potently transactivated the nNOS exon 1c promoter. These results identify the critical regulatory region for the nNOS exon 1c basal promoter and stress the functional importance of multiple protein complexes involving Sp and ZNF families of transcription factors in regulating nNOS exon 1c transcription.
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Affiliation(s)
- Dieter Saur
- Department of Internal Medicine II, Technische Universität München, Germany.
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