Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements

2006 ◽  
Vol 339 (1) ◽  
pp. 99-106 ◽  
Author(s):  
Kuniko Horie-Inoue ◽  
Kenichi Takayama ◽  
Hidemasa U. Bono ◽  
Yasuyoshi Ouchi ◽  
Yasushi Okazaki ◽  
...  
2013 ◽  
Vol 33 (2) ◽  
Author(s):  
Susi Dudazy-Gralla ◽  
Kristina Nordström ◽  
Peter Josef Hofmann ◽  
Dina Abdul Meseh ◽  
Lutz Schomburg ◽  
...  

TRα1 (thyroid hormone receptor α1) is well recognized for its importance in brain development. However, due to the difficulties in predicting TREs (thyroid hormone response elements) in silico and the lack of suitable antibodies against TRα1 for ChIP (chromatin immunoprecipitation), only a few direct TRα1 target genes have been identified in the brain. Here we demonstrate that mice expressing a TRα1–GFP (green fluorescent protein) fusion protein from the endogenous TRα locus provide a valuable animal model to identify TRα1 target genes. To this end, we analysed DNA–TRα1 interactions in vivo using ChIP with an anti-GFP antibody. We validated our system using established TREs from neurogranin and hairless, and by verifying additional TREs from known TRα1 target genes in brain and heart. Moreover, our model system enabled the identification of novel TRα1 target genes such as RNF166 (ring finger protein 166). Our results demonstrate that transgenic mice expressing a tagged nuclear receptor constitute a feasible approach to study receptor–DNA interactions in vivo, circumventing the need for specific antibodies. Models like the TRα1–GFP mice may thus pave the way for genome-wide mapping of nuclear receptor-binding sites, and advance the identification of novel target genes in vivo.


2006 ◽  
Vol 20 (3) ◽  
pp. 483-490 ◽  
Author(s):  
Ying Liu ◽  
Xianmin Xia ◽  
Joseph D. Fondell ◽  
Paul M. Yen

Abstract Thyroid hormone receptors (TRs) are ligand-regulated transcription factors that bind to thyroid hormone response elements of target genes. Upon ligand binding, they recruit coactivator complexes that increase histone acetylation and recruit RNA polymerase II (Pol II) to activate transcription. Recent studies suggest that nuclear receptors and coactivators may have temporal recruitment patterns on hormone response elements, yet little is known about the nature of the patterns at multiple endogenous target genes. We thus performed chromatin immunoprecipitation assays to investigate coactivator recruitment and histone acetylation patterns on the thyroid hormone response elements of four endogenous target genes (GH, sarcoplasmic endoplasmic reticulum calcium-adenosine triphosphatase, phosphoenolpyruvate carboxykinase, and cholesterol 7α-hydroxylase) in a rat pituitary cell line that expresses TRs. We found that TRβ, several associated coactivators (steroid receptor coactivator-1, glucocorticoid receptor interacting protein-1, and TR-associated protein 220), and RNA Pol II were rapidly recruited to thyroid hormone response elements as early as 15 min after T3 addition. When the four target genes were compared, we observed differences in the types and temporal patterns of recruited coactivators and histone acetylation. Interestingly, the temporal pattern of RNA Pol II was similar for three genes studied. Our findings suggest that thyroid hormone-regulated target genes may have distinct patterns of coactivator recruitment and histone acetylation that may enable highly specific regulation.


2002 ◽  
Vol 76 (13) ◽  
pp. 6762-6770 ◽  
Author(s):  
Michael L. Farrell ◽  
Janet E. Mertz

ABSTRACT The late genes of SV40 are not expressed at significant levels until after the onset of viral DNA replication. We previously identified two hormone response elements (HREs) in the late promoter that contribute to this delay. Mutants defective in these HREs overexpress late RNA at early, but not late, times after transfection of CV-1PD cells. Overexpression of nuclear receptors (NRs) that recognize these HREs leads to repression of the late promoter in a sequence-specific and titratable manner, resulting in a delay in late gene expression. These observations led to a model in which the late promoter is repressed at early times after infection by NRs, with this repression being relieved by titration of these repressors through simian virus 40 (SV40) genome replication to high copy number. Here, we tested this model in the context of the viral life cycle. SV40 genomes containing mutations in either or both HREs that significantly reduce NR binding without altering the coding of any proteins were constructed. Competition for replication between mutant and wild-type viruses in low-multiplicity coinfections indicated that the +1 HRE offered a significant selective advantage to the virus within a few cycles of infection in African green monkey kidney cell lines CV-1, CV-1P, TC-7, MA-134, and Vero but not in CV-1PD′ cells. Interestingly, the +55 HRE offered a selective disadvantage in MA-134 cells but had no effect in CV-1, CV-1P, TC-7, Vero, and CV-1PD′ cells. Thus, we conclude that these HREs are biologically important to the virus, but in a cell type-specific manner.


2006 ◽  
Vol 7 (Suppl 4) ◽  
pp. S27 ◽  
Author(s):  
Maria Stepanova ◽  
Feng Lin ◽  
Valerie Lin

Endocrinology ◽  
2005 ◽  
Vol 146 (11) ◽  
pp. 4926-4933 ◽  
Author(s):  
Bernd Gloss ◽  
Gisele Giannocco ◽  
Eric A. Swanson ◽  
Anselmo S. Moriscot ◽  
Grazia Chiellini ◽  
...  

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