|
1
|
Indukuri R, Damdimopoulos A, Williams C. An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta. Methods Mol Biol 2022; 2418:203-221. [PMID: 35119668 DOI: 10.1007/978-1-0716-1920-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Estrogen regulates transcription through two nuclear receptors, ERα and ERβ, in a tissue and cellular-dependent manner. Both the receptors bind estrogen and activate transcription through direct or indirect interactions with DNA. Revealing their interactions with the chromatin is key to understanding their transcriptional activities and their biological functions. Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) is a powerful technique to map protein-DNA interactions at precise genomic locations. The genome-wide binding of ERα has been extensively studied. Similar studies of ERβ, however, have been more difficult, in part due to a lack of endogenous expression in cell lines and lack of specific antibodies. In this chapter, we provide an optimized stepwise ChIP protocol for a well-validated ERβ antibody, which is applicable for ChIP-Seq analysis of cell lines with exogenous expression of ERβ.
Collapse
Affiliation(s)
- Rajitha Indukuri
- SciLifeLab, Department of Protein Science, KTH-Royal Institute of Technology, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Core, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cecilia Williams
- SciLifeLab, Department of Protein Science, KTH-Royal Institute of Technology, Solna, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| |
Collapse
|
|
2
|
Sinnott-Armstrong N, Sousa IS, Laber S, Rendina-Ruedy E, Nitter Dankel SE, Ferreira T, Mellgren G, Karasik D, Rivas M, Pritchard J, Guntur AR, Cox RD, Lindgren CM, Hauner H, Sallari R, Rosen CJ, Hsu YH, Lander ES, Kiel DP, Claussnitzer M. A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density. Cell Metab 2021; 33:615-628.e13. [PMID: 33513366 PMCID: PMC7928941 DOI: 10.1016/j.cmet.2021.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/14/2019] [Accepted: 12/31/2020] [Indexed: 02/07/2023]
Abstract
Skeletal and glycemic traits have shared etiology, but the underlying genetic factors remain largely unknown. To identify genetic loci that may have pleiotropic effects, we studied Genome-wide association studies (GWASs) for bone mineral density and glycemic traits and identified a bivariate risk locus at 3q21. Using sequence and epigenetic modeling, we prioritized an adenylate cyclase 5 (ADCY5) intronic causal variant, rs56371916. This SNP changes the binding affinity of SREBP1 and leads to differential ADCY5 gene expression, altering the chromatin landscape from poised to repressed. These alterations result in bone- and type 2 diabetes-relevant cell-autonomous changes in lipid metabolism in osteoblasts and adipocytes. We validated our findings by directly manipulating the regulator SREBP1, the target gene ADCY5, and the variant rs56371916, which together imply a novel link between fatty acid oxidation and osteoblast differentiation. Our work, by systematic functional dissection of pleiotropic GWAS loci, represents a framework to uncover biological mechanisms affecting pleiotropic traits.
Collapse
Affiliation(s)
- Nasa Sinnott-Armstrong
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Stanford University, Stanford 94305 CA, USA
| | - Isabel S Sousa
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Samantha Laber
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Big Data Institute, University of Oxford, Oxford, UK
| | - Elizabeth Rendina-Ruedy
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Simon E Nitter Dankel
- University of Bergen, Bergen 5020, Norway; Mohn Nutrition Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; Hormone Laboratory, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Gunnar Mellgren
- University of Bergen, Bergen 5020, Norway; Mohn Nutrition Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; Hormone Laboratory, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA 02131, USA; Faculty of Medicine of the Galilee, Bar-Ilan University, Safed, Israel
| | - Manuel Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Pritchard
- Department of Genetics, Stanford University, Stanford 94305 CA, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Anyonya R Guntur
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Roger D Cox
- Medical Research Council Harwell, Oxfordshire, UK
| | - Cecilia M Lindgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Big Data Institute, University of Oxford, Oxford, UK
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising 85354, Germany; Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Freising 85354, Germany; Clinical Cooperation Group "Nutrigenomics and Type 2 Diabetes" of the German Center of Diabetes Research, Helmholtz Center Munich, Munich 85764, Germany
| | - Richard Sallari
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clifford J Rosen
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA 02131, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA
| | - Eric S Lander
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA 02131, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA
| | - Melina Claussnitzer
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA; University of Hohenheim, Institute of Nutritional Science, Stuttgart 70599, Germany.
| |
Collapse
|