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Giacopelli F, Cappato S, Tonachini L, Mura M, Di Lascio S, Fornasari D, Ravazzolo R, Bocciardi R. Identification and characterization of regulatory elements in the promoter of ACVR1, the gene mutated in Fibrodysplasia Ossificans Progressiva. Orphanet J Rare Dis 2013; 8:145. [PMID: 24047559 PMCID: PMC4015442 DOI: 10.1186/1750-1172-8-145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/03/2013] [Indexed: 12/12/2022] Open
Abstract
Background The ACVR1 gene encodes a type I receptor for bone morphogenetic proteins (BMPs). Mutations in the ACVR1 gene are associated with Fibrodysplasia Ossificans Progressiva (FOP), a rare and extremely disabling disorder characterized by congenital malformation of the great toes and progressive heterotopic endochondral ossification in muscles and other non-skeletal tissues. Several aspects of FOP pathophysiology are still poorly understood, including mechanisms regulating ACVR1 expression. This work aimed to identify regulatory elements that control ACVR1 gene transcription. Methods and results We first characterized the structure and composition of human ACVR1 gene transcripts by identifying the transcription start site, and then characterized a 2.9 kb upstream region. This region showed strong activating activity when tested by reporter gene assays in transfected cells. We identified specific elements within the 2.9 kb region that are important for transcription factor binding using deletion constructs, co-transfection experiments with plasmids expressing selected transcription factors, site-directed mutagenesis of consensus binding-site sequences, and by protein/DNA binding assays. We also characterized a GC-rich minimal promoter region containing binding sites for the Sp1 transcription factor. Conclusions Our results showed that several transcription factors such as Egr-1, Egr-2, ZBTB7A/LRF, and Hey1, regulate the ACVR1 promoter by binding to the -762/-308 region, which is essential to confer maximal transcriptional activity. The Sp1 transcription factor acts at the most proximal promoter segment upstream of the transcription start site. We observed significant differences in different cell types suggesting tissue specificity of transcriptional regulation. These findings provide novel insights into the molecular mechanisms that regulate expression of the ACVR1 gene and that could be targets of new strategies for future therapeutic treatments.
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Affiliation(s)
- Francesca Giacopelli
- Department of Neurosciences, Rehabilitation, Ophthalmogy, Genetics, Maternal and Child Health and CEBR, Università degli Studi di Genova, Genova, Italy.
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105
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Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W, Längst G, Benner C, Rehli M. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res 2013; 41:6391-402. [PMID: 23658224 PMCID: PMC3711439 DOI: 10.1093/nar/gkt355] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/03/2013] [Accepted: 04/15/2013] [Indexed: 11/16/2022] Open
Abstract
The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well as computational prediction, we show that PU.1 selects its binding sites primarily based on sequence affinity, which results in the frequent autonomous binding of high affinity sites in DNase I inaccessible regions (25-45% of all occupied sites). Increasing PU.1 concentrations and the availability of cooperative transcription factor interactions during lineage differentiation both decrease affinity thresholds for in vivo binding and fine-tune cell type-specific PU.1 binding, which seems to be largely independent of DNA methylation. Occupied sites were predominantly detected in active chromatin domains, which are characterized by higher densities of PU.1 recognition sites and neighboring motifs for cooperative transcription factors. Our study supports a model of PU.1 binding control that involves motif-binding affinity, PU.1 concentration, cooperativeness with neighboring transcription factor sites and chromatin domain accessibility, which likely applies to all PU.1 expressing cells.
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Affiliation(s)
- Thu-Hang Pham
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia Minderjahn
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christian Schmidl
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Helen Hoffmeister
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sandra Schmidhofer
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wei Chen
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gernot Längst
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Benner
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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106
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Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res 2013; 23:1210-23. [PMID: 23636943 PMCID: PMC3730096 DOI: 10.1101/gr.152306.112] [Citation(s) in RCA: 362] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have integrated and analyzed a large number of data sets from a variety of genomic assays using a novel computational pipeline to provide a global view of estrogen receptor 1 (ESR1; a.k.a. ERα) enhancers in MCF-7 human breast cancer cells. Using this approach, we have defined a class of primary transcripts (eRNAs) that are transcribed uni- or bidirectionally from estrogen receptor binding sites (ERBSs) with an average transcription unit length of ∼3–5 kb. The majority are up-regulated by short treatments with estradiol (i.e., 10, 25, or 40 min) with kinetics that precede or match the induction of the target genes. The production of eRNAs at ERBSs is strongly correlated with the enrichment of a number of genomic features that are associated with enhancers (e.g., H3K4me1, H3K27ac, EP300/CREBBP, RNA polymerase II, open chromatin architecture), as well as enhancer looping to target gene promoters. In the absence of eRNA production, strong enrichment of these features is not observed, even though ESR1 binding is evident. We find that flavopiridol, a CDK9 inhibitor that blocks transcription elongation, inhibits eRNA production but does not affect other molecular indicators of enhancer activity, suggesting that eRNA production occurs after the assembly of active enhancers. Finally, we show that an enhancer transcription “signature” based on GRO-seq data can be used for de novo enhancer prediction across cell types. Together, our studies shed new light on the activity of ESR1 at its enhancer sites and provide new insights about enhancer function.
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Affiliation(s)
- Nasun Hah
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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109
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de la Rica L, Rodríguez-Ubreva J, García M, Islam ABMMK, Urquiza JM, Hernando H, Christensen J, Helin K, Gómez-Vaquero C, Ballestar E. PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation. Genome Biol 2013; 14:R99. [PMID: 24028770 PMCID: PMC4054781 DOI: 10.1186/gb-2013-14-9-r99] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/09/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of monocytes to osteoclasts is a unique terminal differentiation process within the hematopoietic system. This differentiation model is relevant to autoimmune disease and cancer, and there is abundant knowledge on the sets of transcription factors involved. RESULTS Here we focused on DNA methylation changes during osteoclastogenesis. Hypermethylation and hypomethylation changes took place in several thousand genes, including all relevant osteoclast differentiation and function categories. Hypomethylation occurred in association with changes in 5-hydroxymethylcytosine, a proposed intermediate toward demethylation. Transcription factor binding motif analysis revealed an over-representation of PU.1, NF-κB, and AP-1 (Jun/Fos) binding motifs in genes undergoing DNA methylation changes. Among these, only PU.1 motifs were significantly enriched in both hypermethylated and hypomethylated genes; ChIP-seq data analysis confirmed its association to both gene sets. Moreover, PU.1 interacts with both DNMT3b and TET2, suggesting its participation in driving hypermethylation and hydroxymethylation-mediated hypomethylation. Consistent with this, siRNA-mediated PU.1 knockdown in primary monocytes impaired the acquisition of DNA methylation and expression changes, and reduced the association of TET2 and DNMT3b at PU.1 targets during osteoclast differentiation. CONCLUSIONS The work described here identifies key changes in DNA methylation during monocyte-to-osteoclast differentiation and reveals novel roles for PU.1 in this process.
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Affiliation(s)
- Lorenzo de la Rica
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Mireia García
- Rheumatology Service, Bellvitge University Hospital (HUB), L’Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Abul BMMK Islam
- Department of Experimental and Health Sciences, Barcelona Biomedical Research Park, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - José M Urquiza
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Henar Hernando
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Jesper Christensen
- Biotech Research and Innovation Center (BRIC), Center for Epigenetics University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Center (BRIC), Center for Epigenetics University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
| | - Carmen Gómez-Vaquero
- Rheumatology Service, Bellvitge University Hospital (HUB), L’Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona 08908, Spain
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