scholarly journals A Profile HMM for Recognition of Hormone Response Elements

2006 ◽  
pp. 15-22
Author(s):  
Maria Stepanova ◽  
Feng Lin ◽  
Valerie C. -L. Lin
Keyword(s):  
Hormone Response ◽  
Response Elements ◽  
Hormone Response Elements ◽  
Profile Hmm

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 ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Target Genes ◽  
Hormone Response ◽  
Response Elements ◽  
Hormone Response Elements

scholarly journals Cell Type-Specific Replication of Simian Virus 40 Conferred by Hormone Response Elements in the Late Promoter

2002 ◽  
Vol 76 (13) ◽  
pp. 6762-6770 ◽  
Author(s):  
Michael L. Farrell ◽  
Janet E. Mertz
Keyword(s):  
Simian Virus 40 ◽  
Simian Virus ◽  
Genome Replication ◽  
Hormone Response ◽  
Cell Type ◽  
Late Promoter ◽  
African Green Monkey Kidney ◽  
Response Elements ◽  
Hormone Response Elements ◽  
Cell Type Specific

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.

scholarly journals In silico modelling of hormone response elements

2006 ◽  
Vol 7 (Suppl 4) ◽  
pp. S27 ◽  
Author(s):  
Maria Stepanova ◽  
Feng Lin ◽  
Valerie Lin
Keyword(s):  
In Silico ◽  
Hormone Response ◽  
Response Elements ◽  
Hormone Response Elements ◽  
In Silico Modelling

scholarly journals Different Configurations of Specific Thyroid Hormone Response Elements Mediate Opposite Effects of Thyroid Hormone and GC-1 on Gene Expression

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