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Neale N, Lona-Durazo F, Ryten M, Gagliano Taliun SA. Leveraging sex-genetic interactions to understand brain disorders: recent advances and current gaps. Brain Commun 2024; 6:fcae192. [PMID: 38894947 PMCID: PMC11184352 DOI: 10.1093/braincomms/fcae192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/11/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
It is established that there are sex differences in terms of prevalence, age of onset, clinical manifestations, and response to treatment for a variety of brain disorders, including neurodevelopmental, psychiatric, and neurodegenerative disorders. Cohorts of increasing sample sizes with diverse data types collected, including genetic, transcriptomic and/or phenotypic data, are providing the building blocks to permit analytical designs to test for sex-biased genetic variant-trait associations, and for sex-biased transcriptional regulation. Such molecular assessments can contribute to our understanding of the manifested phenotypic differences between the sexes for brain disorders, offering the future possibility of delivering personalized therapy for females and males. With the intention of raising the profile of this field as a research priority, this review aims to shed light on the importance of investigating sex-genetic interactions for brain disorders, focusing on two areas: (i) variant-trait associations and (ii) transcriptomics (i.e. gene expression, transcript usage and regulation). We specifically discuss recent advances in the field, current gaps and provide considerations for future studies.
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Affiliation(s)
- Nikita Neale
- Faculty of Medicine, Université de Montréal, Québec, H3C 3J7 Canada
| | - Frida Lona-Durazo
- Faculty of Medicine, Université de Montréal, Québec, H3C 3J7 Canada
- Research Centre, Montreal Heart Institute, Québec, H1T 1C8 Canada
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, 20815 MD, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, Bloomsbury, WC1N 1EH London, UK
| | - Sarah A Gagliano Taliun
- Research Centre, Montreal Heart Institute, Québec, H1T 1C8 Canada
- Department of Medicine & Department of Neurosciences, Faculty of Medicine, Université de Montréal, Québec, H3C 3J7 Canada
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Holland P, Bergenholm D, Börlin CS, Liu G, Nielsen J. Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions. Nucleic Acids Res 2019; 47:4986-5000. [PMID: 30976803 PMCID: PMC6547448 DOI: 10.1093/nar/gkz253] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 01/08/2023] Open
Abstract
Transcription factors (TF) are central to transcriptional regulation, but they are often studied in relative isolation and without close control of the metabolic state of the cell. Here, we describe genome-wide binding (by ChIP-exo) of 15 yeast TFs in four chemostat conditions that cover a range of metabolic states. We integrate this data with transcriptomics and six additional recently mapped TFs to identify predictive models describing how TFs control gene expression in different metabolic conditions. Contributions by TFs to gene regulation are predicted to be mostly activating, additive and well approximated by assuming linear effects from TF binding signal. Notably, using TF binding peaks from peak finding algorithms gave distinctly worse predictions than simply summing the low-noise and high-resolution TF ChIP-exo reads on promoters. Finally, we discover indications of a novel functional role for three TFs; Gcn4, Ert1 and Sut1 during nitrogen limited aerobic fermentation. In only this condition, the three TFs have correlated binding to a large number of genes (enriched for glycolytic and translation processes) and a negative correlation to target gene transcript levels.
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Affiliation(s)
- Petter Holland
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - David Bergenholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Guodong Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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Wang S, Li X, Zhang W, Gao Y, Zhang K, Hao Q, Li W, Wang Z, Li M, Zhang W, Zhang Y, Zhang C. Genome-Wide Investigation of Genes Regulated by ERα in Breast Cancer Cells. Molecules 2018; 23:molecules23102543. [PMID: 30301189 PMCID: PMC6222792 DOI: 10.3390/molecules23102543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/26/2018] [Accepted: 10/03/2018] [Indexed: 01/13/2023] Open
Abstract
Estrogen receptor alpha (ERα), which has been detected in over 70% of breast cancer cases, is a driving factor for breast cancer growth. For investigating the underlying genes and networks regulated by ERα in breast cancer, RNA-seq was performed between ERα transgenic MDA-MB-231 cells and wild type MDA-MB-231 cells. A total of 267 differentially expressed genes (DEGs) were identified. Then bioinformatics analyses were performed to illustrate the mechanism of ERα. Besides, by comparison of RNA-seq data obtained from MDA-MB-231 cells and microarray dataset obtained from estrogen (E2) stimulated MCF-7 cells, an overlap of 126 DEGs was screened. The expression level of ERα was negatively associated with metastasis and EMT in breast cancer. We further verified that ERα might inhibit metastasis by regulating of VCL and TNFRSF12A, and suppress EMT by the regulating of JUNB and ID3. And the relationship between ERα and these genes were validated by RT-PCR and correlation analysis based on TCGA database. By PPI network analysis, we identified TOP5 hub genes, FOS, SP1, CDKN1A, CALCR and JUNB, which were involved in cell proliferation and invasion. Taken together, the whole-genome insights carried in this work can help fully understanding biological roles of ERα in breast cancer.
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Affiliation(s)
- Shuning Wang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Xiaoju Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Wangqian Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Yuan Gao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Kuo Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Qiang Hao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Weina Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Zhaowei Wang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Meng Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Wei Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Yingqi Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Cun Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
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Nicolini A, Ferrari P, Duffy MJ. Prognostic and predictive biomarkers in breast cancer: Past, present and future. Semin Cancer Biol 2018; 52:56-73. [DOI: 10.1016/j.semcancer.2017.08.010] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/14/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
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Neto M, Naval-Sánchez M, Potier D, Pereira PS, Geerts D, Aerts S, Casares F. Nuclear receptors connect progenitor transcription factors to cell cycle control. Sci Rep 2017; 7:4845. [PMID: 28687780 PMCID: PMC5501803 DOI: 10.1038/s41598-017-04936-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/23/2017] [Indexed: 01/31/2023] Open
Abstract
The specification and growth of organs is controlled simultaneously by networks of transcription factors. While the connection between these transcription factors with fate determinants is increasingly clear, how they establish the link with the cell cycle is far less understood. Here we investigate this link in the developing Drosophila eye, where two transcription factors, the MEIS1 homologue hth and the Zn-finger tsh, synergize to stimulate the proliferation of naïve eye progenitors. Experiments combining transcriptomics, open-chromatin profiling, motif analysis and functional assays indicate that these progenitor transcription factors exert a global regulation of the proliferation program. Rather than directly regulating cell cycle genes, they control proliferation through an intermediary layer of nuclear receptors of the ecdysone/estrogen-signaling pathway. This regulatory subnetwork between hth, tsh and nuclear receptors might be conserved from Drosophila to mammals, as we find a significant co-overexpression of their human homologues in specific cancer types.
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Affiliation(s)
- Marta Neto
- CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | | | - Delphine Potier
- School of Medicine, University of Leuven, box 602 3000, Leuven, Belgium
| | - Paulo S Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Dirk Geerts
- Department of Medical Biology L2-109, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Stein Aerts
- School of Medicine, University of Leuven, box 602 3000, Leuven, Belgium.
| | - Fernando Casares
- CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.
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Zeng H, Lu L, Chan NT, Horswill M, Ahlquist P, Zhong X, Xu W. Systematic identification of Ctr9 regulome in ERα-positive breast cancer. BMC Genomics 2016; 17:902. [PMID: 27829357 PMCID: PMC5103509 DOI: 10.1186/s12864-016-3248-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/02/2016] [Indexed: 02/08/2023] Open
Abstract
Background We had previously identified Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), as a key factor regulating a massive ERα target gene expression and ERα-positive breast cancer growth. Furthermore, we have shown that knockdown of Ctr9 reduces ERα protein stability and decreases the occupancy of ERα and RNAPII at a few ERα-target loci. However, it remains to be determined whether Ctr9 controls ERα-target gene expression by regulating the global chromatin occupancy of ERα and RNAPII in the presence of estrogen. Results In this study, we determined the genome-wide ERα and RNAPII occupancy in response to estrogen treatment and/or Ctr9 knockdown by performing chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). We found that loss of Ctr9 dramatically decreases the global occupancy of ERα and RNAPII, highlighting the significance of Ctr9 in regulating estrogen signaling in ERα-positive breast cancer cells. Combining this resource with previously published genomic data sets, we identified a unique subset of ERα and Ctr9 target genes, and further delineated the independent function of Ctr9 from other subunits in PAFc when regulating transcription. Conclusions Our data demonstrated that Ctr9, independent of other PAFc subunits, controls ERα-target gene expression by regulating global chromatin occupancies of ERα and RNAPII. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3248-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Zeng
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Present address: Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Li Lu
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ngai Ting Chan
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mark Horswill
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Wei Xu
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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SERPINA1 is a direct estrogen receptor target gene and a predictor of survival in breast cancer patients. Oncotarget 2016; 6:25815-27. [PMID: 26158350 PMCID: PMC4694868 DOI: 10.18632/oncotarget.4441] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/19/2015] [Indexed: 01/02/2023] Open
Abstract
Of all breast cancer patients, about 70% are ER+ and 10% are ER+/HER2+. The ER+/HER2+ patients have a worse outcome compared to ER+/HER2- patients. Currently there is a lack of effective prognosis biomarkers for the prediction of outcome in ER+/HER2+ patients. Genome-wide differences in ER binding between the endocrine-responsive and endocrine-resistant cells were discovered using ChIP-seq, and combined with gene expression microarray data to identify direct ER target genes. These genes were correlated to survival outcome using publicly available breast cancer patient cohorts. We found the expression of the gene SERPINA1 to have a significant predictive value for the overall survival (OS) of ER+ patients in the TCGA cohort, and validated this finding in the Curtis cohort. SERPINA1 also has a significant predictive value for the OS of ER+/HER2+ patients in the TCGA cohort, with validation in the Bild cohort. The expression of SERPINA1 can be suppressed by fulvestrant and HER2 siRNA. Our results indicate that ER is constitutively activated, resulting in an E2-independent ER binding to the SERPINA1 gene and upregulation of SERPINA1 expression. Importantly, results of survival correlation suggests that high expression of SERPINA1 could be predictive for a better clinical outcome of ER+ and ER+/HER2+ patients.
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Abstract
With the impressive advancement in high-throughput 'omics' technologies over the past two decades, epigenetic mechanisms have emerged as the regulatory interface between the genome and environmental factors. These mechanisms include DNA methylation, histone modifications, ATP-dependent chromatin remodeling and RNA-based mechanisms. Their highly interdependent and coordinated action modulates the chromatin structure controlling access of the transcription machinery and thereby regulating expression of target genes. Given the rather limited proliferative capability of human cardiomyocytes, epigenetic regulation appears to play a particularly important role in the myocardium. The highly dynamic nature of the epigenome allows the heart to adapt to environmental challenges and to respond quickly and properly to cardiac stress. It is now becoming evident that histone-modifying and chromatin-remodeling enzymes as well as numerous non-coding RNAs play critical roles in cardiac development and function, while their dysregulation contributes to the onset and development of pathological cardiac remodeling culminating in HF. This review focuses on up-to-date knowledge about the epigenetic mechanisms and highlights their emerging role in the healthy and failing heart. Uncovering the determinants of epigenetic regulation holds great promise to accelerate the development of successful new diagnostic and therapeutic strategies in human cardiac disease.
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Affiliation(s)
- José Marín-García
- The Molecular Cardiology and Neuromuscular Institute, 75 Raritan Ave., Highland Park, NJ, 08904, USA,
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10
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Drabovich AP, Pavlou MP, Schiza C, Diamandis EP. Dynamics of Protein Expression Reveals Primary Targets and Secondary Messengers of Estrogen Receptor Alpha Signaling in MCF-7 Breast Cancer Cells. Mol Cell Proteomics 2016; 15:2093-107. [PMID: 27067054 DOI: 10.1074/mcp.m115.057257] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 11/06/2022] Open
Abstract
Estrogen receptor alpha (ERα)-mediated proliferation of breast cancer cells is facilitated through expression of multiple primary target genes, products of which induce a secondary response to stimulation. To differentiate between the primary and secondary target proteins of ERα signaling, we measured dynamics of protein expression induced by 17β-estradiol in MCF-7 breast cancer cells. Measurement of the global proteomic effects of estradiol by stable isotope labeling by amino acids in cell culture (SILAC) resulted in identification of 103 estrogen-regulated proteins, with only 40 of the corresponding genes having estrogen response elements. Selected reaction monitoring (SRM) assays were used to validate the differential expression of 19 proteins and measure the dynamics of their expression within 72 h after estradiol stimulation, and in the absence or presence of 4-hydroxytamoxifen, to confirm ERα-mediated signaling. Dynamics of protein expression unambiguously revealed early and delayed response proteins and well correlated with presence or absence of estrogen response elements in the corresponding genes. Finally, we quantified dynamics of protein expression in a rarely studied network of transcription factors with a negative feedback loop (ERα-EGR3-NAB2). Because NAB2 protein is a repressor of EGR3-induced transcription, siRNA-mediated silencing of NAB2 resulted in the enhanced expression of the EGR3-induced protein ITGA2. To conclude, we provided a high-quality proteomic resource to supplement genomic and transcriptomic studies of ERα signaling.
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Affiliation(s)
- Andrei P Drabovich
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada, M5T3L9; §Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada, M5T3L9;
| | - Maria P Pavlou
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada, M5T3L9; ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada, M5T3L9
| | - Christina Schiza
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada, M5T3L9; ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada, M5T3L9
| | - Eleftherios P Diamandis
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada, M5T3L9; §Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada, M5T3L9; ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada, M5T3L9; ‖Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada, M5T3L9
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11
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Buniello A, Ingham NJ, Lewis MA, Huma AC, Martinez-Vega R, Varela-Nieto I, Vizcay-Barrena G, Fleck RA, Houston O, Bardhan T, Johnson SL, White JK, Yuan H, Marcotti W, Steel KP. Wbp2 is required for normal glutamatergic synapses in the cochlea and is crucial for hearing. EMBO Mol Med 2016; 8:191-207. [PMID: 26881968 PMCID: PMC4772953 DOI: 10.15252/emmm.201505523] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023] Open
Abstract
WBP2 encodes the WW domain-binding protein 2 that acts as a transcriptional coactivator for estrogen receptor α (ESR1) and progesterone receptor (PGR). We reported that the loss of Wbp2 expression leads to progressive high-frequency hearing loss in mouse, as well as in two deaf children, each carrying two different variants in the WBP2 gene. The earliest abnormality we detect in Wbp2-deficient mice is a primary defect at inner hair cell afferent synapses. This study defines a new gene involved in the molecular pathway linking hearing impairment to hormonal signalling and provides new therapeutic targets.
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Affiliation(s)
- Annalisa Buniello
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Neil J Ingham
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Morag A Lewis
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Andreea C Huma
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Raquel Martinez-Vega
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Unit 761, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Varela-Nieto
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Unit 761, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Roland A Fleck
- Centre for Ultrastructural Imaging, King's College London, London, UK
| | - Oliver Houston
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Tanaya Bardhan
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Stuart L Johnson
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Huijun Yuan
- Medical Genetics Center, Southwest Hospital Third Military Medical University, Chongqing, China
| | - Walter Marcotti
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Karen P Steel
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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Klinge CM. miRNAs regulated by estrogens, tamoxifen, and endocrine disruptors and their downstream gene targets. Mol Cell Endocrinol 2015; 418 Pt 3:273-97. [PMID: 25659536 PMCID: PMC4523495 DOI: 10.1016/j.mce.2015.01.035] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are short (22 nucleotides), single-stranded, non-coding RNAs that form complimentary base-pairs with the 3' untranslated region of target mRNAs within the RNA-induced silencing complex (RISC) and block translation and/or stimulate mRNA transcript degradation. The non-coding miRBase (release 21, June 2014) reports that human genome contains ∼ 2588 mature miRNAs which regulate ∼ 60% of human protein-coding mRNAs. Dysregulation of miRNA expression has been implicated in estrogen-related diseases including breast cancer and endometrial cancer. The mechanism for estrogen regulation of miRNA expression and the role of estrogen-regulated miRNAs in normal homeostasis, reproduction, lactation, and in cancer is an area of great research and clinical interest. Estrogens regulate miRNA transcription through estrogen receptors α and β in a tissue-specific and cell-dependent manner. This review focuses primarily on the regulation of miRNA expression by ligand-activated ERs and their bona fide gene targets and includes miRNA regulation by tamoxifen and endocrine disrupting chemicals (EDCs) in breast cancer and cell lines.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Biology, Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program. Proc Natl Acad Sci U S A 2015; 112:1380-5. [PMID: 25605944 DOI: 10.1073/pnas.1424228112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Substantial evidence supports the hypothesis that enhancers are critical regulators of cell-type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and repression events remain incompletely understood. Here we report the required actions of LIM domain-binding protein 1 (LDB1)/cofactor of LIM homeodomain protein 2/nuclear LIM interactor, interacting with the enhancer-binding protein achaete-scute complex homolog 1, to mediate looping to target gene promoters and target gene regulation in corticotrope cells. LDB1-mediated enhancer:promoter looping appears to be required for both activation and repression of these target genes. Although LDB1-dependent activated genes are regulated at the level of transcriptional initiation, the LDB1-dependent repressed transcription units appear to be regulated primarily at the level of promoter pausing, with LDB1 regulating recruitment of metastasis-associated 1 family, member 2, a component of the nucleosome remodeling deacetylase complex, on these negative enhancers, required for the repressive enhancer function. These results indicate that LDB1-dependent looping events can deliver repressive cargo to cognate promoters to mediate promoter pausing events in a pituitary cell type.
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14
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Wang S, Tie J, Wang R, Hu F, Gao L, Wang W, Wang L, Li Z, Hu S, Tang S, Li M, Wang X, Nie Y, Wu K, Fan D. SOX2, a predictor of survival in gastric cancer, inhibits cell proliferation and metastasis by regulating PTEN. Cancer Lett 2014; 358:210-219. [PMID: 25543086 DOI: 10.1016/j.canlet.2014.12.045] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/08/2014] [Accepted: 12/19/2014] [Indexed: 01/02/2023]
Abstract
Inconsistent results of SOX2 expression have been reported in gastric cancer (GC). Here, we demonstrated that SOX2 was progressively downregulated during GC development via immunochemistry in 755 human gastric specimens. Low SOX2 levels were associated with pathological stage and clinical outcome. Multivariate analysis indicated that SOX2 protein expression served as an independent prognostic marker for GC. Gain-and loss-of function studies showed the anti-proliferative, anti-metastatic, and pro-apoptotic effects of SOX2 in GC. PTEN was selected as SOX2 targets by cDNA microarray and ChIP-DSL, further identified by luciferase assays, EMSA and ChIP-PCR. PTEN upregulation in response to SOX2-enforced expression suppressed GC malignancy via regulating Akt dephosphorylation. PTEN inhibition reversed SOX2-induced anticancer effects. Moreover, concordant positivity of SOX2 and PTEN proteins in nontumorous tissues but lost in matched GC specimens predicted a worse patient prognosis. Thus, SOX2 proved to be a new marker for evaluating GC outcome.
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Affiliation(s)
- Simeng Wang
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jun Tie
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Rui Wang
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Fengrong Hu
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Liucun Gao
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wenlan Wang
- Department of Aerospace Hygiene and Health Service, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Lifeng Wang
- Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zengshan Li
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Sijun Hu
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Shanhong Tang
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Mengbin Li
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xin Wang
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Yongzhan Nie
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Kaichun Wu
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Daiming Fan
- State key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
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Diao S, Yang DM, Dong R, Wang LP, Wang JS, Du J, Wang SL, Fan Z. Enriched trimethylation of lysine 4 of histone H3 of WDR63 enhanced osteogenic differentiation potentials of stem cells from apical papilla. J Endod 2014; 41:205-11. [PMID: 25498833 DOI: 10.1016/j.joen.2014.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/14/2014] [Accepted: 09/29/2014] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Dental tissue-derived mesenchymal stem cells (MSCs) are a reliable cell source for dental tissue regeneration. However, the molecular mechanisms underlying their directed differentiation remain unclear, thus limiting their use. Trimethylation of lysine 4 of histone H3 (H3K4Me3) correlates with gene activation and osteogenic differentiation. We used stem cells from apical papilla (SCAPs) to investigate the effects of genomic changes in H3K4Me3 modification at gene promoter regions on MSC osteogenic differentiation. METHODS ChIP-on-chip assays were applied to compare the H3K4Me3 profiles at gene promoter regions of undifferentiated and differentiated SCAPs. Alkaline phosphatase activity assay, alizarin red staining, quantitative analysis of calcium, the expressions of osteogenesis-related genes, and transplantation in nude mice were used to investigate the osteogenic differentiation potentials of SCAPs. RESULTS In differentiated SCAPs, 119 gene promoters exhibited >2-fold increases of H3K4Me3; in contrast, the promoter regions of 21 genes exhibited >2-fold decreases of H3K4Me3. On the basis of enriched H3K4Me3 and up-regulated gene expression on the osteogenic differentiation of SCAPs, WDR63 may be a potential regulator for mediating SCAP osteogenic differentiation. Through gain-of-function and loss-of-function studies, we discovered that WDR63 enhances alkaline phosphatase activity, mineralization, and the expression of BSP, OSX, and RUNX2 in vitro. In addition, transplant experiments in nude mice confirmed that SCAP osteogenesis is triggered by activated WDR63. CONCLUSIONS These results indicate that WDR63 is a positive enhancer for SCAP osteogenic differentiation and suggest that activation of WDR63 signaling might improve tissue regeneration mediated by MSCs of dental origin.
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Affiliation(s)
- Shu Diao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China; Department of Pediatric Dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Dong-Mei Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China; Department of Pediatric Dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Rui Dong
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Li-Ping Wang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Jin-Song Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China; Department of Biochemistry and Molecular Biology, Capital Medical University School of Basic Medical Sciences, Beijing, China
| | - Juan Du
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China; Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Song-Lin Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China; Department of Biochemistry and Molecular Biology, Capital Medical University School of Basic Medical Sciences, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.
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Biased, non-equivalent gene-proximal and -distal binding motifs of orphan nuclear receptor TR4 in primary human erythroid cells. PLoS Genet 2014; 10:e1004339. [PMID: 24811540 PMCID: PMC4014424 DOI: 10.1371/journal.pgen.1004339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 03/17/2014] [Indexed: 02/04/2023] Open
Abstract
We previously reported that TR2 and TR4 orphan nuclear receptors bind to direct repeat (DR) elements in the ε- and γ-globin promoters, and act as molecular anchors for the recruitment of epigenetic corepressors of the multifaceted DRED complex, thereby leading to ε- and γ-globin transcriptional repression during definitive erythropoiesis. Other than the ε- and γ-globin and the GATA1 genes, TR4-regulated target genes in human erythroid cells remain unknown. Here, we identified TR4 binding sites genome-wide using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) as human primary CD34+ hematopoietic progenitors differentiated progressively to late erythroid precursors. We also performed whole transcriptome analyses by RNA-seq to identify TR4 downstream targets after lentiviral-mediated TR4 shRNA knockdown in erythroid cells. Analyses from combined ChIP-seq and RNA-seq datasets indicate that DR1 motifs are more prevalent in the proximal promoters of TR4 direct target genes, which are involved in basic biological functions (e.g., mRNA processing, ribosomal assembly, RNA splicing and primary metabolic processes). In contrast, other non-DR1 repeat motifs (DR4, ER6 and IR1) are more prevalent at gene-distal TR4 binding sites. Of these, approximately 50% are also marked with epigenetic chromatin signatures (such as P300, H3K27ac, H3K4me1 and H3K27me3) associated with enhancer function. Thus, we hypothesize that TR4 regulates gene transcription via gene-proximal DR1 sites as TR4/TR2 heterodimers, while it can associate with novel nuclear receptor partners (such as RXR) to bind to distant non-DR1 consensus sites. In summary, this study reveals that the TR4 regulatory network is far more complex than previously appreciated and that TR4 regulates basic, essential biological processes during the terminal differentiation of human erythroid cells. Sequential genome-wide binding studies investigated by deep sequencing (ChIP-seq) represent a powerful tool for investigating the temporal sequence of gene activation and repression events that take place as cells differentiate. Here, we report the binding of an “orphan” nuclear receptor (one for which no ligand has been identified) to its cognate genomic regulatory sites and perform the functional analysis to validate its downstream targets as precursor cells differentiate from very early human hematopoietic progenitors into red blood cells. We discovered that when this receptor is bound at gene proximal promoters, it recognizes a different DNA sequence than when it binds to more distant regulatory sites (enhancers and silencers). Since this receptor can either activate or repress specific target genes, the data suggest the intriguing possibility that the two different modes of DNA recognition may reflect association of the receptor with different partner molecules when regulating gene expression from proximal or distal sequences.
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Chen H, Lu S, Zhou J, Bai Z, Fu H, Xu X, Yang S, Jiao B, Sun Y. An integrated approach for the identification of USF1-centered transcriptional regulatory networks during liver regeneration. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:415-23. [PMID: 24686121 DOI: 10.1016/j.bbagrm.2014.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/08/2014] [Accepted: 03/19/2014] [Indexed: 01/20/2023]
Abstract
Liver regeneration after partial hepatectomy (PH) is a synchronized process that is precisely controlled by system-wide transcriptional regulatory networks. To clarify the transcriptional changes and regulatory networks that involve transcription factors (TFs) and their target genes during the priming phase, an advanced mouse oligonucleotide array-based transcription factor assay (MOUSE OATFA), mRNA microarray analysis, bioinformatic analysis and ChIP-on-chip experiments were used. A total of 774 genes were upregulated or downregulated in PH liver samples compared with the sham operation (SH) group. Seventeen TFs showed significant changes in activity in the regenerating livers, some of which have not been extensively studied in previous reports, including upstream stimulatory transcription factor 1 (USF1). The TF signatures from MOUSE OATFA were combined with mRNA expression profiles and ChIP-on-chip analyses to construct experimental transcriptional regulatory networks in regenerating livers. USF1-centered regulatory networks were further confirmed by ChIP assays, revealing some of its target genes and novel coregulatory networks. The combination of MOUSE OATFA with transcriptome profiling and bioinformatic analysis represents a novel paradigm for the comprehensive prediction of transcriptional coregulatory networks during the early phase of liver regeneration.
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Affiliation(s)
- Huan Chen
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Shan Lu
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Jiansheng Zhou
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Zihe Bai
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Hailong Fu
- Department of Anesthesiology, Changzheng Hospital, Second Military Medical University, Shanghai 200433, China
| | - Xiaoping Xu
- School of Pharm. Sichuan University, 3-17 Ren-min-nan Road, Chengdu, Sichuan 610041, China
| | - Shengsheng Yang
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China.
| | - Yimin Sun
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, China; National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Beijing 102206, China.
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Genome-wide activity of unliganded estrogen receptor-α in breast cancer cells. Proc Natl Acad Sci U S A 2014; 111:4892-7. [PMID: 24639548 DOI: 10.1073/pnas.1315445111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Estrogen receptor-α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions that are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in the absence of ligands and its functions on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ERα binds to more than 4,000 chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ERα binding is specifically linked to genes with developmental functions, compared with estrogen-induced binding. Moreover, we found that siRNA-mediated down-regulation of ERα in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Down-regulated mRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ERα down-regulation using shRNA, which caused cell growth arrest, was accompanied by increased H3K27me3 at ERα binding sites. Finally, we found that FOXA1 and AP2γ binding to several sites is decreased upon ERα silencing, suggesting that unliganded ERα participates, together with other factors, in the maintenance of the luminal-specific cistrome in breast cancer cells.
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19
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Yu Y, Wang XY, Sun L, Wang YL, Wan YF, Li XQ, Feng YM. Inhibition of KIF22 suppresses cancer cell proliferation by delaying mitotic exit through upregulating CDC25C expression. Carcinogenesis 2014; 35:1416-25. [PMID: 24626146 DOI: 10.1093/carcin/bgu065] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
KIF22 is a microtubule-dependent molecular motor protein with DNA-binding capacity. It is well known that KIF22 plays a critical role in cell mitosis as a motor protein; however, the role of altered KIF22 expression and its transcriptional regulatory function in cancer development have not yet been defined. This study showed that KIF22 was overexpressed in human cancer tissues, and inhibition of KIF22 significantly led to accumulation of cells in the G2/M phases, resulting in suppression of cancer cell proliferation. The investigation of the molecular mechanisms demonstrated that cell division cycle 25C (CDC25C) is a direct transcriptional target of KIF22, and inhibition of KIF22 increased CDC25C expression and cyclin-dependent kinase 1 (CDK1) activity, resulting in delayed mitotic exit. Phosphorylation of KIF22 was required for its transcriptional regulatory function and the reduction of CDK1 activity. Thus, we conclude that inhibition of KIF22 suppresses cancer cell proliferation by delaying mitotic exit through the transcriptional upregulation of CDC25C.
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Affiliation(s)
- Yue Yu
- Department of Biochemistry and Molecular Biology and
| | - Xiao-Yan Wang
- Department of Biochemistry and Molecular Biology and
| | - Lei Sun
- Department of Biochemistry and Molecular Biology and Key Laboratory of Breast Cancer Prevention and Therapy of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin 300060, China
| | - Yu-Li Wang
- Department of Biochemistry and Molecular Biology and
| | - Yan-Fang Wan
- Department of Biochemistry and Molecular Biology and
| | - Xiao-Qing Li
- Department of Biochemistry and Molecular Biology and Key Laboratory of Breast Cancer Prevention and Therapy of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin 300060, China
| | - Yu-Mei Feng
- Department of Biochemistry and Molecular Biology and Key Laboratory of Breast Cancer Prevention and Therapy of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin 300060, China.
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20
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Liu MH, Cheung E. Estrogen receptor-mediated long-range chromatin interactions and transcription in breast cancer. Mol Cell Endocrinol 2014; 382:624-632. [PMID: 24071518 DOI: 10.1016/j.mce.2013.09.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
Estrogen induces the binding of ERα to thousands of locations in the breast cancer genome, preferring intergenic and distal regions rather than near the promoters of estrogen-regulated genes. With recent technological innovations in mapping and characterization of global chromatin organization, evidence now indicates ERα mediates long-range chromatin interactions to control gene transcription. The principles that govern how ERα communicates with their putative target genes via chromosomal interactions are also beginning to unravel. Herein, we summarize our current knowledge on the functional significance of chromatin looping in estrogen-mediated transcription. ERα collaborative factors and other players that contribute to define the genomic interactions in breast cancer cells will also be discussed. Defects in chromatin organization are emerging key players in diseases such as cancer, thus understanding how ERα-mediated chromatin looping affects genome organization will clarify the receptor's role in estrogen responsive pathways sensitive to defects in chromatin organization.
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Affiliation(s)
- Mei Hui Liu
- Food Science and Technology Programme, Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; Cancer Biology and Pharmacology, Genome Institute of Singapore, A∗STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
| | - Edwin Cheung
- Cancer Biology and Pharmacology, Genome Institute of Singapore, A∗STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore.
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21
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Benner C, Konovalov S, Mackintosh C, Hutt KR, Stunnenberg R, Garcia-Bassets I. Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions. PLoS Genet 2013; 9:e1003906. [PMID: 24244184 PMCID: PMC3820735 DOI: 10.1371/journal.pgen.1003906] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
Genome-wide maps of DNase I hypersensitive sites (DHSs) reveal that most human promoters contain perpetually active cis-regulatory elements between −150 bp and +50 bp (−150/+50 bp) relative to the transcription start site (TSS). Transcription factors (TFs) recruit cofactors (chromatin remodelers, histone/protein-modifying enzymes, and scaffold proteins) to these elements in order to organize the local chromatin structure and coordinate the balance of post-translational modifications nearby, contributing to the overall regulation of transcription. However, the rules of TF-mediated cofactor recruitment to the −150/+50 bp promoter regions remain poorly understood. Here, we provide evidence for a general model in which a series of cis-regulatory elements (here termed ‘cardinal’ motifs) prefer acting individually, rather than in fixed combinations, within the −150/+50 bp regions to recruit TFs that dictate cofactor signatures distinctive of specific promoter subsets. Subsequently, human promoters can be subclassified based on the presence of cardinal elements and their associated cofactor signatures. In this study, furthermore, we have focused on promoters containing the nuclear respiratory factor 1 (NRF1) motif as the cardinal cis-regulatory element and have identified the pervasive association of NRF1 with the cofactor lysine-specific demethylase 1 (LSD1/KDM1A). This signature might be distinctive of promoters regulating nuclear-encoded mitochondrial and other particular genes in at least some cells. Together, we propose that decoding a signature-based, expanded model of control at proximal promoter regions should lead to a better understanding of coordinated regulation of gene transcription. Human cells exploit different mechanisms to coordinate the expression of both protein-coding and non-coding RNAs. Elucidating these mechanisms is essential to understanding normal physiology and disease. In our attempt to identify new regulatory layers acting particularly at proximal promoters, we have computationally analyzed the genomic sequences located from −150 bp to +50 bp relative to the transcriptional start site (TSS), which are often at the center of ‘open’ chromatin regions in human promoters. We have confirmed the presence of a series of cis-regulatory elements (here referred to as ‘cardinal’ motifs) that show a strong preference for these short regions. Interestingly, these elements tend to act independently rather than in fixed combinations. Therefore, we propose that they confer unique regulatory features to the human promoter subsets that contain each of these particular elements. In agreement with this model, we have identified a large repertoire of preferential partnerships between transcription factors recognizing cardinal motifs and their associated proteins (cofactors), thus decoding a signature-based model that distinguishes distinctive regulatory types of promoters based on cardinal motifs. These signatures may underlie a new layer of transcriptional regulation to orchestrate coordinated gene expression in human promoters.
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Affiliation(s)
- Christopher Benner
- The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Sergiy Konovalov
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Carlos Mackintosh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Kasey R. Hutt
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Rieka Stunnenberg
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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22
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Proteomic analysis of coregulators bound to ERα on DNA and nucleosomes reveals coregulator dynamics. Mol Cell 2013; 51:185-99. [PMID: 23850489 DOI: 10.1016/j.molcel.2013.06.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/02/2013] [Accepted: 06/04/2013] [Indexed: 11/21/2022]
Abstract
Chromatin immunoprecipitation studies have mapped protein occupancies at many genomic loci. However, a detailed picture of the complexity of coregulators (CoRs) bound to a defined enhancer along with a transcription factor is missing. To address this, we used biotin-DNA pull-down assays coupled with mass spectrometry-immunoblotting to identify at least 17 CoRs from nuclear extracts bound to 17β-estradiol (E2)-liganded estrogen receptor-α on estrogen response elements (EREs). Unexpectedly, these complexes initially are biochemically stable and contain certain atypical corepressors. Addition of ATP dynamically converts these complexes to an "activated" state by phosphorylation events, primarily mediated by DNA-dependent protein kinase. Importantly, a "natural" ERE-containing enhancer and nucleosomal EREs recruit similar complexes. We further discovered the mechanism whereby H3K4me3 stimulates ERα-mediated transcription as compared with unmodified nucleosomes. H3K4me3 templates promote specific CoR dynamics in the presence of ATP and AcCoA, as manifested by CBP/p300 and SRC-3 dismissal and SAGA and TFIID stabilization/recruitment.
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23
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Karmakar S, Jin Y, Nagaich AK. Interaction of glucocorticoid receptor (GR) with estrogen receptor (ER) α and activator protein 1 (AP1) in dexamethasone-mediated interference of ERα activity. J Biol Chem 2013; 288:24020-34. [PMID: 23814048 PMCID: PMC3745347 DOI: 10.1074/jbc.m113.473819] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The role of glucocorticoids in the inhibition of estrogen (17-β-estradiol (E2))-regulated estrogen receptor (ER)-positive breast cancer cell proliferation is well established. We and others have seen that synthetic glucocorticoid dexamethasone (Dex) antagonizes E2-stimulated endogenous ERα target gene expression. However, how glucocorticoids negatively regulate the ERα signaling pathway is still poorly understood. ChIP studies using ERα- and glucocorticoid receptor (GR)-positive MCF-7 cells revealed that GR occupies several ERα-binding regions (EBRs) in cells treated with E2 and Dex simultaneously. Interestingly, there was little or no GR loading to these regions when cells were treated with E2 or Dex alone. The E2+Dex-dependent GR recruitment is associated with the displacement of ERα and steroid receptor coactivator-3 from the target EBRs leading to the repression of ERα-mediated transcriptional activation. The recruitment of GR to EBRs requires assistance from ERα and FOXA1 and is facilitated by AP1 binding within the EBRs. The GR binding to EBRs is mediated via direct protein-protein interaction between the GR DNA-binding domain and ERα. Limited mutational analyses indicate that arginine 488 located within the C-terminal zinc finger domain of the GR DNA-binding domain plays a critical role in stabilizing this interaction. Together, the results of this study unravel a novel mechanism involved in glucocorticoid inhibition of ERα transcriptional activity and E2-mediated cell proliferation and thus establish a foundation for future exploitation of the GR signaling pathway in the treatment of ER-positive breast cancer.
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Affiliation(s)
- Sudipan Karmakar
- Division of Therapeutic Proteins, Office of Biotechnology Products, Office of Pharmaceutical Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
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24
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Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 2013; 498:516-20. [PMID: 23728302 PMCID: PMC3718886 DOI: 10.1038/nature12210] [Citation(s) in RCA: 730] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 04/22/2013] [Indexed: 12/12/2022]
Abstract
The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNAs (lncRNAs) in mammalian cells, bidirectional ncRNAs are transcribed on enhancers, and are thus referred to as enhancer RNAs (eRNAs). However, it has remained unclear whether these eRNAs are functional or merely a reflection of enhancer activation. Here we report that in human breast cancer cells 17β-oestradiol (E2)-bound oestrogen receptor α (ER-α) causes a global increase in eRNA transcription on enhancers adjacent to E2-upregulated coding genes. These induced eRNAs, as functional transcripts, seem to exert important roles for the observed ligand-dependent induction of target coding genes, increasing the strength of specific enhancer-promoter looping initiated by ER-α binding. Cohesin, present on many ER-α-regulated enhancers even before ligand treatment, apparently contributes to E2-dependent gene activation, at least in part by stabilizing E2/ER-α/eRNA-induced enhancer-promoter looping. Our data indicate that eRNAs are likely to have important functions in many regulated programs of gene transcription.
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Affiliation(s)
- Wenbo Li
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Dimple Notani
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Qi Ma
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
- Graduate Program in Bioinformatics, University of California, San Diego, La Jolla CA, 92093
| | - Bogdan Tanasa
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
- Graduate Program, Kellogg School of Science and Technology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA, 92037
| | - Esperanza Nunez
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Aaron Yun Chen
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Daria Merkurjev
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
- Graduate Program in Bioinformatics, University of California, San Diego, La Jolla CA, 92093
| | - Jie Zhang
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Kenneth Ohgi
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Xiaoyuan Song
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Soohwan Oh
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
- Graduate Program in Biological Sciences, University of California, San Diego, La Jolla CA, 92093
| | - Hong-Sook Kim
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Christopher K. Glass
- Cellular and Molecular Medicine, Dept. of Medicine, University of California, San Diego, La Jolla CA, 92093
| | - Michael G. Rosenfeld
- Howard Hughes Medical Institute, Dept. of Medicine, School of Medicine, University of California, San Diego, La Jolla CA, 92093
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Coughlan N, Thillainadesan G, Andrews J, Isovic M, Torchia J. β-Estradiol-dependent activation of the JAK/STAT pathway requires p/CIP and CARM1. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1463-75. [PMID: 23434684 DOI: 10.1016/j.bbamcr.2013.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 01/15/2013] [Accepted: 02/11/2013] [Indexed: 01/07/2023]
Abstract
The steroid receptor coactivator p/CIP, also known as SRC-3, is an oncogene commonly amplified in breast and ovarian cancers. p/CIP is known to associate with coactivator arginine methyltransferase 1 (CARM1) on select estrogen responsive genes. We have shown, using a ChIP-on-chip approach, that in response to stimulation with 17β-estradiol (E2), the p/CIP/CARM1 complex is recruited to 204 proximal promoters in MCF-7 cells. Many of the complex target genes have been previously implicated in signaling pathways related to oncogenesis. Jak2, a member of the Jak/Stat signaling cascade, is one of the direct E2-dependent targets of the p/CIP/CARM1 complex. Following E2-treatment, histone modifications at the Jak2 promoter are reflective of a transcriptionally permissive gene, and modest changes in RNA and protein expression lead us to suggest that an additional factor(s) may be required for a more notable transcriptional and functional response. Bioinformatic examination of the 204 proximal promoter sequences of p/CIP/CARM1 targets supports the idea that transcription factor crosstalk is likely the favored mechanism of E2-dependent p/CIP/CARM1 complex recruitment. This data may have implications towards understanding the oncogenic role of p/CIP in breast cancer and ultimately allow for the identification of new prognostic indicators and/or viable therapeutic targets.
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Affiliation(s)
- N Coughlan
- Dept. of Oncology, The University of Western Ontario, Canada
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26
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Zhang Y, Hu Z, Qin H, Wei X, Cheng K, Liu F, Wu R, Zou H. Highly Efficient Extraction of Cellular Nucleic Acid Associated Proteins in Vitro with Magnetic Oxidized Carbon Nanotubes. Anal Chem 2012; 84:10454-62. [DOI: 10.1021/ac302695u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yi Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Hu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjie Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren’an Wu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Vinckevicius A, Chakravarti D. Chromatin immunoprecipitation: advancing analysis of nuclear hormone signaling. J Mol Endocrinol 2012; 49:R113-23. [PMID: 22872135 PMCID: PMC3839787 DOI: 10.1530/jme-12-0016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Recent decades have been filled with groundbreaking research in the field of endocrine hormone signaling. Pivotal events like the isolation and purification of the estrogen receptor, the cloning of glucocorticoid receptor cDNA, or dissemination of nuclear hormone receptor (NHR) DNA binding sequences are well recognized for their contributions. However, the novel genome-wide and gene-specific information obtained over the last decade describing NHR association with chromatin, cofactors, and epigenetic modifications, as well as their role in gene regulation, has been largely facilitated by the adaptation of the chromatin immunoprecipitation (ChIP) technique. Use of ChIP-based technologies has taken the field of hormone signaling from speculating about the transcription-enabling properties of acetylated chromatin and putative transcription (co-)factor genomic occupancy to demonstrating the detailed, stepwise mechanisms of factor binding and transcriptional initiation; from treating hormone-induced transcription as a steady-state event to understanding its dynamic and cyclic nature; from looking at the DNA sequences recognized by various DNA-binding domains in vitro to analyzing the cell-specific genome-wide pattern of nuclear receptor binding and interpreting its physiological implications. Not only have these events propelled hormone research, but, as some of the pioneering studies, have also contributed tremendously to the field of molecular endocrinology as a whole. In this review, we give a brief summary of some of the most important discoveries in hormone signaling using ChIP and other derivative techniques and speculate on what the future may hold.
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Affiliation(s)
- Aurimas Vinckevicius
- Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 4-119, Chicago, Illinois 60611, USA
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28
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Lin HY, Yin Y, Zhang JX, Xuan H, Zheng Y, Zhan SS, Zhu YX, Han X. Identification of direct forkhead box O1 targets involved in palmitate-induced apoptosis in clonal insulin-secreting cells using chromatin immunoprecipitation coupled to DNA selection and ligation. Diabetologia 2012; 55:2703-2712. [PMID: 22810813 DOI: 10.1007/s00125-012-2643-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/11/2012] [Indexed: 01/10/2023]
Abstract
AIMS/HYPOTHESIS The transcription factor, forkhead box (FOX)O1, is involved in fatty acid-induced apoptosis in pancreatic beta cells, but the precise mechanism is poorly understood. We aimed to identify which direct downstream targets of FOXO1 are involved in palmitate-induced apoptosis in the pancreatic beta cell line MIN6. METHODS Chromatin immunoprecipitation (ChIP) coupled to a DNA selection and ligation technique (ChIP-DSL) was used to identify the direct targets of FOXO1. The mRNA level was examined by real-time PCR assay. The ChIP-DSL results were verified using ChIP-PCR and luciferase assay, respectively. The cell apoptosis rate was determined by TUNEL assay and by scoring cells with pycnotic nuclei. RESULTS We identified 189 target genes and selected 106 targets for expression analysis in MIN6 cells treated with palmitate. The results showed that six genes were significantly upregulated and four were downregulated. Binding of FOXO1 to the promoters was determined by ChIP-PCR and confirmed by luciferase assay. Among the ten up- and downregulated genes, mRNA expression of A930038C07Rik was significantly decreased and that of Ppa1 was increased in 8-week-old db/db mice. The apoptosis assay showed that overproduction of the protein 'RIKEN cDNA A930038C07' (A930038C07Rik) drastically enhanced palmitate-induced apoptosis, while pyrophosphatase (inorganic) 1 (PPA1) partially protected the cells from apoptosis. Knockdown of PPA1, moreover, significantly increased apoptosis. CONCLUSIONS/INTERPRETATION We identified for the first time FOXO1 targets in MIN6 cells treated with palmitate, thus revealing the important roles of A930038C07Rik and PPA1 in palmitate-induced cell apoptosis. These results shed light on the mechanisms of palmitate-induced apoptosis in pancreatic beta cells.
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Affiliation(s)
- H Y Lin
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Y Yin
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - J X Zhang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - H Xuan
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Y Zheng
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - S S Zhan
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Y X Zhu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - X Han
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China.
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Genome-wideChIP-DSLprofiling of promoter methylation patterns associated with cancer and stem cell differentiation. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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30
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Gu GM, Wang JK. [DNA-binding profiles of mammalian transcription factors]. YI CHUAN = HEREDITAS 2012; 34:950-68. [PMID: 22917900 DOI: 10.3724/sp.j.1005.2012.00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The differential gene expression is the molecular base of development and responses to stimuli of organisms. Transcription factors (TFs) play important regulatory roles in this kind of differential gene expression. Therefore, to elucidate how these TFs regulate the complex differential gene expression, it is necessary to identify all target genes of them and construct the gene transcription regulatory network controlled by them. DNA binding is a key step for TFs regulating gene transcription. Therefore, in order to identify their target genes, it is indispensable to identify all possible DNA sequences that can be recognized and bound by TFs at the molecular level of their interactions with DNA, i.e., construction of the DNA-binding profiles of TFs. In recent years, along with the development of DNA microarray and high-throughput DNA sequencing techniques, there appeared some revolutionary new techniques for constructing DNA-binding profiles of TFs, which greatly promotes studies in this field. These techniques include ChIP-chip and ChIP-Seq for constructing in vivo DNA-binding profiles of TFs, dsDNA microarray, SELEX-SAGE, Bind-n-Seq, MMP-SELEX, EMSA-Seq, and HiTS-FLIP for constructing in vitro DNA-binding profiles of TFs. This paper reviewed these techniques.
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Affiliation(s)
- Guang-Ming Gu
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China.
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31
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Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA. Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Hum Mol Genet 2012; 21:2194-204. [PMID: 22328084 DOI: 10.1093/hmg/dds034] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The ongoing requirement in adult heart for transcription factors with key roles in cardiac development is not well understood. We recently demonstrated that TBX20, a transcriptional regulator required for cardiac development, has key roles in the maintenance of functional and structural phenotypes in adult mouse heart. Conditional ablation of Tbx20 in adult cardiomyocytes leads to a rapid onset and progression of heart failure, with prominent conduction and contractility phenotypes that lead to death. Here we describe a more comprehensive molecular characterization of the functions of TBX20 in adult mouse heart. Coupling genome-wide chromatin immunoprecipitation and transcriptome analyses (RNA-Seq), we identified a subset of genes that change expression in Tbx20 adult cardiomyocyte-specific knockout hearts which are direct downstream targets of TBX20. This analysis revealed a dual role for TBX20 as both a transcriptional activator and a repressor, and that each of these functions regulates genes with very specialized and distinct molecular roles. We also show how TBX20 binds to its targets genome-wide in a context-dependent manner, using various cohorts of co-factors to either promote or repress distinct genetic programs within adult heart. Our integrative approach has uncovered several novel aspects of TBX20 and T-box protein function within adult heart. Sequencing data accession number (http://www.ncbi.nlm.nih.gov/geo): GSE30943.
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Affiliation(s)
- Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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32
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Shen C, Huang Y, Liu Y, Wang G, Zhao Y, Wang Z, Teng M, Wang Y, Flockhart DA, Skaar TC, Yan P, Nephew KP, Huang TH, Li L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC SYSTEMS BIOLOGY 2011; 5:67. [PMID: 21554733 PMCID: PMC3117732 DOI: 10.1186/1752-0509-5-67] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 05/09/2011] [Indexed: 12/27/2022]
Abstract
BACKGROUND Estrogens regulate diverse physiological processes in various tissues through genomic and non-genomic mechanisms that result in activation or repression of gene expression. Transcription regulation upon estrogen stimulation is a critical biological process underlying the onset and progress of the majority of breast cancer. Dynamic gene expression changes have been shown to characterize the breast cancer cell response to estrogens, the every molecular mechanism of which is still not well understood. RESULTS We developed a modulated empirical Bayes model, and constructed a novel topological and temporal transcription factor (TF) regulatory network in MCF7 breast cancer cell line upon stimulation by 17β-estradiol stimulation. In the network, significant TF genomic hubs were identified including ER-alpha and AP-1; significant non-genomic hubs include ZFP161, TFDP1, NRF1, TFAP2A, EGR1, E2F1, and PITX2. Although the early and late networks were distinct (<5% overlap of ERα target genes between the 4 and 24 h time points), all nine hubs were significantly represented in both networks. In MCF7 cells with acquired resistance to tamoxifen, the ERα regulatory network was unresponsive to 17β-estradiol stimulation. The significant loss of hormone responsiveness was associated with marked epigenomic changes, including hyper- or hypo-methylation of promoter CpG islands and repressive histone methylations. CONCLUSIONS We identified a number of estrogen regulated target genes and established estrogen-regulated network that distinguishes the genomic and non-genomic actions of estrogen receptor. Many gene targets of this network were not active anymore in anti-estrogen resistant cell lines, possibly because their DNA methylation and histone acetylation patterns have changed.
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Affiliation(s)
- Changyu Shen
- Center for Computational Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Pandya-Jones A. Pre-mRNA splicing during transcription in the mammalian system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:700-17. [PMID: 21823230 DOI: 10.1002/wrna.86] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Splicing of RNA polymerase II transcripts is a crucial step in gene expression and a key generator of mRNA diversity. Splicing and transcription have generally been studied in isolation, although in vivo pre-mRNA splicing occurs in concert with transcription. The two processes appear to be functionally connected because a number of variables that regulate transcription have been identified as also influencing splicing. However, the mechanisms that couple the two processes are largely unknown. This review highlights the observations that implicate splicing as occurring during transcription and describes the evidence supporting functional interactions between the two processes. I discuss postulated models of how splicing couples to transcription and consider the potential impact that such coupling might have on exon recognition. WIREs RNA 2011 2 700-717 DOI: 10.1002/wrna.86 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles (UCLA), USA.
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Stratmann A, Haendler B. The histone demethylase JARID1A regulates progesterone receptor expression. FEBS J 2011; 278:1458-69. [DOI: 10.1111/j.1742-4658.2011.08058.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Ying W, Wang S, Shi J, Sun Y. ER-/ER+ breast cancer cell lines exhibited different resistance to paclitaxel through pulse selection. Med Oncol 2011; 29:495-502. [PMID: 21399998 DOI: 10.1007/s12032-011-9889-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 02/25/2011] [Indexed: 12/31/2022]
Abstract
In this study, we established two PTX-resistant breast cancer cell lines, 231 TIM10 and MCF-7 TIM10, from ER-negative MDA-MB-231 cells and ER-positive MCF-7 cells by pulse selection, respectively. We found that 231 TIM10 variants acquired higher drug resistance than MCF-7 TIM10 variants by the pulse selection, although ER-positive MCF-7 cells were not as sensitive as ER-negative MDA-MB-231 to the initial pulses with PTX. 231 TIM10 had 11.9-fold greater resistance (RI = 11.9) than the parental MDA-MB-231 cells, while MCF-7 TIM10 got 5.5-fold resistance (RI = 5.5) when compared with the parental MCF-7 cells. In the presence of 5nM PTX, 231 TIM10 cells formed colonies, but no colony formed when MCF-7 TIM10 cells were cultured in the same condition. These data have two implications. First, the ER expression state might be an important determinant for the response of breast cancer cells to paclitaxel treatment. Second, ER-negative and ER-positive breast cancer cells develop drug-resistance phenotype with distinctive mechanisms. Our work not only established useful models for studying the paclitaxel resistance but also provides interesting clues to understand the mechanisms underlying the drug resistance of ER-negative and ER-positive breast cancer cells.
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Affiliation(s)
- Wei Ying
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 210029 Nanjing, People's Republic of China
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9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature 2011; 470:264-8. [PMID: 21307941 PMCID: PMC3079517 DOI: 10.1038/nature09753] [Citation(s) in RCA: 476] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 12/16/2010] [Indexed: 02/07/2023]
Abstract
Genome wide association studies (GWAS) have identified SNPs in the 9p21 gene desert associated with coronary artery disease (CAD)1–4 and Type 2 diabetes (T2D)5–7. Despite evidence for a role of the associated interval in neighboring gene regulation8–10, the biological underpinnings of these genetic associations to CAD or T2D have not yet been explained. Here we identify 33 enhancers in 9p21; the interval is the second densest gene-desert for predicted enhancers and 6 times denser than the whole genome (p<6.55 10−33). The CAD risk alleles of SNPs rs10811656/rs10757278 are located in one of these enhancers and disrupt a binding site for STAT1. Lymphoblastoid cell lines (LCL) homozygous for the CAD risk haplotype exhibit no binding of STAT1, and in LCL homozygous for the CAD non-risk haplotype binding of STAT1 inhibits CDKN2BAS expression, which is reversed by siRNA knock-down of STAT1. Using a new, open-ended approach to detect long-distance interactions (3D-DSL), we find that in human vascular endothelium cells (HUVEC) the enhancer interval containing the CAD locus physically interacts with the CDKN2A/B locus, the MTAP gene and an interval downstream of INFA21. In HUVEC, IFNγ activation strongly affects the structure of the chromatin and the transcriptional regulation in the 9p21 locus, including STAT1 binding, long-range enhancer interactions and altered expression of neighboring genes. Our findings establish a link between CAD genetic susceptibility and the response to inflammatory signaling in a vascular cell type and thus demonstrate the utility of GWAS findings to direct studies to novel genomic loci and biological processes important for disease etiology.
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Schlesinger J, Schueler M, Grunert M, Fischer JJ, Zhang Q, Krueger T, Lange M, Tönjes M, Dunkel I, Sperling SR. The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. PLoS Genet 2011; 7:e1001313. [PMID: 21379568 PMCID: PMC3040678 DOI: 10.1371/journal.pgen.1001313] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 01/18/2011] [Indexed: 12/15/2022] Open
Abstract
The transcriptome, as the pool of all transcribed elements in a given cell, is regulated by the interaction between different molecular levels, involving epigenetic, transcriptional, and post-transcriptional mechanisms. However, many previous studies investigated each of these levels individually, and little is known about their interdependency. We present a systems biology study integrating mRNA profiles with DNA–binding events of key cardiac transcription factors (Gata4, Mef2a, Nkx2.5, and Srf), activating histone modifications (H3ac, H4ac, H3K4me2, and H3K4me3), and microRNA profiles obtained in wild-type and RNAi–mediated knockdown. Finally, we confirmed conclusions primarily obtained in cardiomyocyte cell culture in a time-course of cardiac maturation in mouse around birth. We provide insights into the combinatorial regulation by cardiac transcription factors and show that they can partially compensate each other's function. Genes regulated by multiple transcription factors are less likely differentially expressed in RNAi knockdown of one respective factor. In addition to the analysis of the individual transcription factors, we found that histone 3 acetylation correlates with Srf- and Gata4-dependent gene expression and is complementarily reduced in cardiac Srf knockdown. Further, we found that altered microRNA expression in Srf knockdown potentially explains up to 45% of indirect mRNA targets. Considering all three levels of regulation, we present an Srf-centered transcription network providing on a single-gene level insights into the regulatory circuits establishing respective mRNA profiles. In summary, we show the combinatorial contribution of four DNA–binding transcription factors in regulating the cardiac transcriptome and provide evidence that histone modifications and microRNAs modulate their functional consequence. This opens a new perspective to understand heart development and the complexity cardiovascular disorders. An evolutionary conserved orchestra of transcription factors controls cardiac development and function. More recently the contributions of epigenetic and post-transcriptional mechanisms like histone modifications and microRNAs have been identified. The interplay between these regulatory mechanisms is still an open question. However, perturbations of the cardiac transcriptome, triggered by all three levels of regulation, are underlying cardiovascular disease such as congenital heart malformations. Here, we show the impact of the interdependencies of four key transcription factors (Gata4, Mef2a, Nkx2.5, and Srf) and the contribution of activating histone modifications and microRNAs on the cardiac transcriptome. We found that even these non-paralogous transcription factors can partially compensate each other's function. Our data show that histone 3 acetylation correlates with Srf- and Gata4- dependent gene activation. Moreover, we predict a large proportion of indirect Srf targets to be regulated by Srf-dependent microRNAs, which thus might represent an important intermediate layer of regulation. Taken together, we suggest that the different levels regulating cardiac mRNA profiles have a high degree of interdependency and the potential to buffer each other, which presents a starting point to understand the phenotypic variability typically seen in complex cardiovascular disorders.
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Affiliation(s)
- Jenny Schlesinger
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Free University Berlin, Berlin, Germany
| | - Markus Schueler
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marcel Grunert
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jenny J. Fischer
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Qin Zhang
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Sciences and Technology, Northwest A & F University, Yangling, China
| | - Tammo Krueger
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Lange
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martje Tönjes
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ilona Dunkel
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Silke R. Sperling
- Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
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Abstract
Nuclear receptors (NRs) represent a vital class of ligand-activated transcription factors responsible for coordinately regulating the expression of genes involved in numerous biological processes. Transcriptional regulation by NRs is conducted through interactions with multiple coactivator or corepressor complexes that modify the chromatin environment to facilitate or inhibit RNA polymerase II binding and transcription initiation. In recent years, studies have identified specific biological roles for cofactors mediating NR signaling through epigenetic modifications such as acetylation and methylation of histones. Intriguingly, genome-wide analysis of NR and cofactor localization has both confirmed findings from single-gene studies and revealed new insights into the relationships between NRs, cofactors and target genes in determining gene expression. Here, we review recent developments in the understanding of epigenetic regulation by NRs across the genome within the context of the well-established background of cofactor complexes and their roles in histone modification.
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Affiliation(s)
- Christopher D Green
- Chinese Academy of Sciences Key Laboratory of Molecular Developmental Biology, Center for Molecular Systems Biology, Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing, 100101, China
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences–MaxPlanck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
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Resseguie ME, da Costa KA, Galanko JA, Patel M, Davis IJ, Zeisel SH. Aberrant estrogen regulation of PEMT results in choline deficiency-associated liver dysfunction. J Biol Chem 2010; 286:1649-58. [PMID: 21059658 DOI: 10.1074/jbc.m110.106922] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When dietary choline is restricted, most men and postmenopausal women develop multiorgan dysfunction marked by hepatic steatosis (choline deficiency syndrome (CDS)). However, a significant subset of premenopausal women is protected from CDS. Because hepatic PEMT (phosphatidylethanolamine N-methyltransferase) catalyzes de novo biosynthesis of choline and this gene is under estrogenic control, we hypothesized that there are SNPs in PEMT that disrupt the hormonal regulation of PEMT and thereby put women at risk for CDS. In this study, we performed transcript-specific gene expression analysis, which revealed that estrogen regulates PEMT in an isoform-specific fashion. Locus-wide SNP analysis identified a risk-associated haplotype that was selectively associated with loss of hormonal activation. Chromatin immunoprecipitation, analyzed by locus-wide microarray studies, comprehensively identified regions of estrogen receptor binding in PEMT. The polymorphism (rs12325817) most highly linked with the development of CDS (p < 0.00006) was located within 1 kb of the critical estrogen response element. The risk allele failed to bind either the estrogen receptor or the pioneer factor FOXA1. These data demonstrate that allele-specific ablation of estrogen receptor-DNA interaction in the PEMT locus prevents hormone-inducible PEMT expression, conferring risk of CDS in women.
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Affiliation(s)
- Mary E Resseguie
- Department of Nutrition, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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40
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Mittal MK, Singh K, Misra S, Chaudhuri G. SLUG-induced elevation of D1 cyclin in breast cancer cells through the inhibition of its ubiquitination. J Biol Chem 2010; 286:469-79. [PMID: 21044962 DOI: 10.1074/jbc.m110.164384] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
UbcH5c, a member of the UbcH5 family of protein ubiquitin conjugase E2 enzymes, is a critical component of biological processes in human cells, being the initial ubiquitinating enzyme of substrates like IκB, TP53, and cyclin D1. We report here that the metastasis regulator protein SLUG inhibits the expression of UbcH5c directly through chromatin remodeling and thus, among other downstream effects, elevates the level of cyclin D1, thus enhancing the growth rates of breast cancer cells. Overexpression of SLUG in the SLUG-deficient breast cancer cells significantly decreased the levels of mRNA and protein of UbcH5c but only elevated the protein levels of cyclin D1. On the contrary, knockdown of SLUG in SLUG-high breast cancer cells elevated the levels of UbcH5c while decreasing the level of cyclin D1 protein. SLUG is recruited at the E2-box sequence at the UbcH5c gene promoter along with the corepressor CtBP1 and the effector HDAC1 to silence the expression of this gene. Knockdown of UbcH5c in the SLUG-deficient human breast cells elevated the level of cyclin D1 as well as the rates of proliferation and invasiveness of these cells. Whereas the growth rates of the cells are enhanced due to overexpression of SLUG or knockdown of UbcH5c in the breast cancer cells tested, ER(+) cells also acquire resistance to the anti-estrogen 4-hydroxytamoxifen due to the rise of cyclin D1 levels in these cells. This study thus implicates high levels of SLUG and low levels of UbcH5c as a determinant in the progression of metastatic breast cancer.
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Affiliation(s)
- Mukul K Mittal
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208, USA. and
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Abstract
The biological significance of interactions of nuclear proteins with DNA in the context of gene expression, cell differentiation, or disease has immensely been enhanced by the advent of chromatin immunoprecipitation (ChIP). ChIP is a technique whereby a protein of interest is selectively immunoprecipitated from a chromatin preparation to determine the DNA sequences associated with it. ChIP has been widely used to map the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin modifying enzymes on the genome or on a given locus. In spite of its power, ChIP has for a long time remained a cumbersome procedure requiring large numbers of cells. These limitations have sparked the development of modifications to shorten the procedure, simplify sample handling and make ChIP amenable to small numbers of cells. In addition, the combination of ChIP with DNA microarray and high-throughput sequencing technologies has in recent years enabled the profiling of histone modification, histone variants, and transcription factor occupancy on a genome-wide scale. This review highlights the variations on the theme of the ChIP assay, the various detection methods applied downstream of ChIP, and examples of their application.
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Merkl M, Ulbrich SE, Otzdorff C, Herbach N, Wanke R, Wolf E, Handler J, Bauersachs S. Microarray analysis of equine endometrium at days 8 and 12 of pregnancy. Biol Reprod 2010; 83:874-86. [PMID: 20631402 DOI: 10.1095/biolreprod.110.085233] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Establishment and maintenance of pregnancy in equids is only partially understood. To provide new insights into early events of this process, we performed a systematic analysis of transcriptome changes in the endometrium at Days 8 and 12 of pregnancy. Endometrial biopsy samples from pregnant and nonpregnant stages were taken from the same mares. Composition of the collected biopsy samples was analyzed using quantitative stereological techniques to determine proportions of surface and glandular epithelium and blood vessels. Microarray analysis did not reveal detectable changes in gene expression at Day 8, whereas at Day 12 of pregnancy 374 differentially expressed genes were identified, 332 with higher and 42 with lower transcript levels in pregnant endometrium. Expression of selected genes was validated by quantitative real-time RT-PCR. Gene set enrichment analysis, functional annotation clustering, and cocitation analysis were performed to characterize the genes differentially expressed in Day 12 pregnant endometrium. Many known estrogen-induced genes and genes involved in regulation of estrogen signaling were found, but also genes known to be regulated by progesterone and prostaglandin E2. Additionally, differential expression of a number of genes related to angiogenesis and vascular remodeling suggests an important role of this process. Furthermore, genes that probably have conserved functions across species, such as CRYAB, ERRFI1, FGF9, IGFBP2, NR2F2, STC1, and TNFSF10, were identified. This study revealed the potential target genes and pathways of conceptus-derived estrogens, progesterone, and prostaglandin E2 in the equine endometrium probably involved in the early events of establishment and maintenance of pregnancy in the mare.
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Affiliation(s)
- M Merkl
- Clinic for Horses, Center for Clinical Veterinary Medicine, and Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians University of Munich, Munich, Germany
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Shu FJ, Sidell N, Yang D, Kallen CB. The tri-nucleotide spacer sequence between estrogen response element half-sites is conserved and modulates ERalpha-mediated transcriptional responses. J Steroid Biochem Mol Biol 2010; 120:172-9. [PMID: 20403436 PMCID: PMC2891080 DOI: 10.1016/j.jsbmb.2010.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/10/2010] [Accepted: 04/12/2010] [Indexed: 12/17/2022]
Abstract
The estrogen response element (ERE) consensus sequence is AGGTCAnnnTGACCT, where nnn is known as the tri-nucleotide spacer sequence. Studying 1017 high-confidence ERalpha-bound loci, we found that genomic EREs are enriched for spacers composed of C(A/T)G, suggesting that the spacer may influence receptor binding and transcriptional responses. We designed consensus EREs containing variable spacer sequences and compared ERalpha binding in gel shift assays and enhancer function in reporter assays. We found that ERalpha-ERE binding affinity is modulated by the tri-nucleotide spacer sequence and is favored by spacer sequences of CTG>GCC>TTT. Similarly, luciferase reporter assays indicated that the estrogen-stimulated transcriptional response is modulated by the spacer and parallels the gel shift data: CTG>GCC>TTT. Reporter assays demonstrated that the spacer sequence also modulates the sensitivity of EREs to repression engendered by the receptor antagonist hydroxytamoxifen. These experiments indicate that the sequence of the tri-nucleotide spacer is non-random at receptor-bound genomic loci, influences ERalpha-DNA-binding affinity, and modulates transactivation potential of the receptor-ligand-DNA complex. This work has implications for understanding which genomic EREs are targeted by ERalpha, should improve computational prediction of functional EREs within genomic sequences, and describes novel sequence determinants of the estrogen response.
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Affiliation(s)
- Feng-jue Shu
- Department of Gynecology and Obstetrics, Emory University School of Medicine, 1639 Pierce Drive, WMB 4217, Atlanta, GA, USA, 30322
| | - Neil Sidell
- Department of Gynecology and Obstetrics, Emory University School of Medicine, 1639 Pierce Drive, WMB 4217, Atlanta, GA, USA, 30322
- Corresponding Authors: Caleb B. Kallen, Department of Gynecology and Obstetrics, Emory University School of Medicine, 1639 Pierce Drive, WMB 4217, Atlanta, GA 30322. Phone: 404-727-4047, Fax: 404-727-8609, or Neil Sidell, same address, Phone: 404-727-9155, Fax: 404-727-8609,
| | - Danzhou Yang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, USA, 85721
| | - Caleb B. Kallen
- Department of Gynecology and Obstetrics, Emory University School of Medicine, 1639 Pierce Drive, WMB 4217, Atlanta, GA, USA, 30322
- Corresponding Authors: Caleb B. Kallen, Department of Gynecology and Obstetrics, Emory University School of Medicine, 1639 Pierce Drive, WMB 4217, Atlanta, GA 30322. Phone: 404-727-4047, Fax: 404-727-8609, or Neil Sidell, same address, Phone: 404-727-9155, Fax: 404-727-8609,
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Abstract
Many cellular signaling pathways ultimately control specific patterns of gene expression in the nucleus through a variety of signal-regulated transcription factors (TFs), including nuclear hormone receptors (NRs). The advent of genomic technologies for examining signal-regulated transcriptional responses and TF binding on a genomic scale has dramatically increased our understanding of the cellular programs that control hormonal signaling and gene regulation. Studies of TFs, especially NRs, using genomic approaches have revealed novel and unexpected features of hormone-regulated transcription, and a global view is beginning to emerge. In this review, we discuss the genomic methodologies that have been applied to the study of hormone-regulated gene expression, the results that have been obtained from using them, and the future prospects for these approaches. Given the wealth of information about hormone-dependent gene regulation by NRs, we have focused this review on the knowledge gained from genomic studies of their function.
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Affiliation(s)
- Edwin Cheung
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.
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Kocanova S, Kerr EA, Rafique S, Boyle S, Katz E, Caze-Subra S, Bickmore WA, Bystricky K. Activation of estrogen-responsive genes does not require their nuclear co-localization. PLoS Genet 2010; 6:e1000922. [PMID: 20421946 PMCID: PMC2858706 DOI: 10.1371/journal.pgen.1000922] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 03/24/2010] [Indexed: 01/06/2023] Open
Abstract
The spatial organization of the genome in the nucleus plays a role in the regulation of gene expression. Whether co-regulated genes are subject to coordinated repositioning to a shared nuclear space is a matter of considerable interest and debate. We investigated the nuclear organization of estrogen receptor alpha (ERalpha) target genes in human breast epithelial and cancer cell lines, before and after transcriptional activation induced with estradiol. We find that, contrary to another report, the ERalpha target genes TFF1 and GREB1 are distributed in the nucleoplasm with no particular relationship to each other. The nuclear separation between these genes, as well as between the ERalpha target genes PGR and CTSD, was unchanged by hormone addition and transcriptional activation with no evidence for co-localization between alleles. Similarly, while the volume occupied by the chromosomes increased, the relative nuclear position of the respective chromosome territories was unaffected by hormone addition. Our results demonstrate that estradiol-induced ERalpha target genes are not required to co-localize in the nucleus.
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Affiliation(s)
- Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse - UPS, Toulouse, France
- LBME, CNRS, Toulouse, France
| | - Elizabeth A. Kerr
- The Breakthrough Breast Cancer Research Unit, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sehrish Rafique
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Shelagh Boyle
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Elad Katz
- The Breakthrough Breast Cancer Research Unit, Edinburgh, United Kingdom
| | - Stephanie Caze-Subra
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse - UPS, Toulouse, France
- LBME, CNRS, Toulouse, France
| | - Wendy A. Bickmore
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse - UPS, Toulouse, France
- LBME, CNRS, Toulouse, France
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Cicatiello L, Mutarelli M, Grober OMV, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, Zinser C, Chiusano ML, Traini A, De Bortoli M, Weisz A. Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 176:2113-30. [PMID: 20348243 DOI: 10.2353/ajpath.2010.090837] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Luminal-like breast tumor cells express estrogen receptor alpha (ERalpha), a member of the nuclear receptor family of ligand-activated transcription factors that controls their proliferation, survival, and functional status. To identify the molecular determinants of this hormone-responsive tumor phenotype, a comprehensive genome-wide analysis was performed in estrogen stimulated MCF-7 and ZR-75.1 cells by integrating time-course mRNA expression profiling with global mapping of genomic ERalpha binding sites by chromatin immunoprecipitation coupled to massively parallel sequencing, microRNA expression profiling, and in silico analysis of transcription units and receptor binding regions identified. All 1270 genes that were found to respond to 17beta-estradiol in both cell lines cluster in 33 highly concordant groups, each of which showed defined kinetics of RNA changes. This hormone-responsive gene set includes several direct targets of ERalpha and is organized in a gene regulation cascade, stemming from ligand-activated receptor and reaching a large number of downstream targets via AP-2gamma, B-cell activating transcription factor, E2F1 and 2, E74-like factor 3, GTF2IRD1, hairy and enhancer of split homologue-1, MYB, SMAD3, RARalpha, and RXRalpha transcription factors. MicroRNAs are also integral components of this gene regulation network because miR-107, miR-424, miR-570, miR-618, and miR-760 are regulated by 17beta-estradiol along with other microRNAs that can target a significant number of transcripts belonging to one or more estrogen-responsive gene clusters.
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Affiliation(s)
- Luigi Cicatiello
- Department of General Pathology, Second University of Naples, Napoli, Italy
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Lanz RB, Bulynko Y, Malovannaya A, Labhart P, Wang L, Li W, Qin J, Harper M, O'Malley BW. Global characterization of transcriptional impact of the SRC-3 coregulator. Mol Endocrinol 2010; 24:859-72. [PMID: 20181721 DOI: 10.1210/me.2009-0499] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The nuclear receptor and bona fide oncogene, steroid receptor coactivator-3 (SRC-3, AIB1), acts as a master transcriptional regulator of breast cancer by transducing growth signals via the estrogen receptor alpha (ER). In this resource paper, we present the genome-wide localization analysis of SRC-3 chromatin affinity sites in MCF-7 human breast cancer chromatin and compare the cis binding sites to global cartographies for ER and FoxA1. By correlating their gene proximal binding sites to integrated gene expression signatures, and in combination with gene ontology analyses, we provide a functional classification of estradiol-induced gene regulation that further highlights an intricate transcriptional control of interdependent cellular pathways by SRC-3. Furthermore, by presenting proteomics analyses of in vivo SRC-3- and ER-associated proteins, we give strong evidence to support the idea that the interpretative power of SRC-3 in estrogen signaling is mediated through the formation of distinct, cell state-dependent protein complexes. Altogether, we present the first approach in complementary comparative analyses that converges results obtained by three discovery-driven methods (cistromics, transcriptomics, and proteomics) into testable hypotheses, thus providing a valuable resource for follow-up studies that further our understanding of estrogen signaling in human diseases in general and breast cancer in particular.
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Affiliation(s)
- Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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Lo R, Burgoon L, Macpherson L, Ahmed S, Matthews J. Estrogen receptor-dependent regulation of CYP2B6 in human breast cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:469-79. [PMID: 20079471 DOI: 10.1016/j.bbagrm.2010.01.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 12/24/2009] [Accepted: 01/07/2010] [Indexed: 12/27/2022]
Abstract
Estrogen receptor alpha (ERalpha) mediates the biological actions of estrogens and also contributes to the development and progression of breast cancer. To gain a more comprehensive understanding of ERalpha-mediated transcription, we used chromatin immunoprecipitation and promoter focused microarrays (ChIP-chip) to identify ERalpha binding sites in T-47D human breast cancer cells. Transcription factor binding site analysis revealed that the estrogen response element (ERE) was significantly over-represented and was found in 50% of the 243 ERalpha-bound regions identified. Interestingly, multiple ERalpha-bound regions were detected in the upstream regulatory sequences of the CYP2B gene cluster. Because ERalpha has been reported to regulate the expression of other cytochrome P450 enzymes and CYP2B6 is highly expressed in ERalpha-positive breast tumors, we focused on characterizing the ERalpha-dependent regulation of CYP2B6. Reporter gene assays revealed that ERalpha and ERbeta increased CYP2B6-regulated gene expression through a functional ERE located at -1669 to -1657 in the upstream regulatory region of CYP2B6. E2 increased ERalpha and nuclear receptor coactivator 3 (NCoA3) recruitment to the 5'-flanking region of CYP2B6, and increased CYP2B6 mRNA levels in T-47D but not in MCF-7 human breast cancer cells. RNAi-mediated knockdown of ERalpha in the T-47D cells resulted in a significant decrease in CYP2B6 mRNA levels. Taken together, our study provides evidence for cell-type specific transcriptional regulation of the CYP2B6 gene by ERs.
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Affiliation(s)
- Raymond Lo
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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49
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Mason CE, Shu FJ, Wang C, Session RM, Kallen RG, Sidell N, Yu T, Liu MH, Cheung E, Kallen CB. Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements. Nucleic Acids Res 2010; 38:2355-68. [PMID: 20047966 PMCID: PMC2853111 DOI: 10.1093/nar/gkp1188] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10–20% nucleotide deviation from the canonical ERE sequence. We demonstrate that ∼50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.
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Affiliation(s)
- Christopher E Mason
- Department of Human Genetics and the Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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Dai Z, Dai X, Xiang Q, Feng J. Robustness of transcriptional regulatory program influences gene expression variability. BMC Genomics 2009; 10:573. [PMID: 19954511 PMCID: PMC2792230 DOI: 10.1186/1471-2164-10-573] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 12/02/2009] [Indexed: 01/06/2023] Open
Abstract
Background Most genes are not affected when any transcription factor (TF) is knocked out, indicating that they have robust transcriptional regulatory program. Yet the mechanism underlying robust transcriptional regulatory program is less clear. Results Here, we studied the cause and effect of robust transcriptional regulatory program. We found that cooperative TFs in the robust transcriptional regulatory program regulate their common target genes in an activity-redundant fashion, and they are able to compensate for each other's loss. As a result, their target genes are insensitive to their single perturbation. We next revealed that the degree of robustness of transcriptional regulatory program influences gene expression variability. Genes with fragile (unrobust) transcriptional regulatory program under normal growth condition could be readily reprogrammed to significantly modulate gene expression upon changing conditions. They also have high evolutionary rates of gene expression. We further showed that the fragile transcriptional regulatory program is a major source of expression variability. Conclusion We showed that activity-redundant TFs guarantee the robustness of transcriptional regulatory programs, and the fragility of transcriptional regulatory program plays a major role in gene expression variability. These findings reveal the mechanisms underlying robust transcription and expression variability.
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Affiliation(s)
- Zhiming Dai
- Electronic Department, Sun Yat-Sen University, Guangzhou, PR China.
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