Chromatin Immunoprecipitation Assays: Analyzing Transcription Factor Binding and Histone Modifications In Vivo

2009 ◽  
pp. 323-339 ◽  
Author(s):  
Smitha Pillai ◽  
Piyali Dasgupta ◽  
Srikumar P. Chellappan
Keyword(s):  
Transcription Factor ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Transcription Factor Binding ◽  
Factor Binding

Tissue-specific histone modification and transcription factor binding in α globin gene expression

Blood ◽  
2007 ◽  
Vol 110 (13) ◽  
pp. 4503-4510 ◽  
Author(s):  
Marco De Gobbi ◽  
Eduardo Anguita ◽  
Jim Hughes ◽  
Jacqueline A. Sloane-Stanley ◽  
Jacqueline A. Sharpe ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Histone Modification ◽  
Histone Modifications ◽  
Globin Gene ◽  
Regulatory Elements ◽  
Transcription Factor Binding ◽  
Telomeric Region ◽  
Globin Genes ◽  
Factor Binding

To address the mechanism by which the human globin genes are activated during erythropoiesis, we have used a tiled microarray to analyze the pattern of transcription factor binding and associated histone modifications across the telomeric region of human chromosome 16 in primary erythroid and nonerythroid cells. This 220-kb region includes the α globin genes and 9 widely expressed genes flanking the α globin locus. This un-biased, comprehensive analysis of transcription factor binding and histone modifications (acetylation and methylation) described here not only identified all known cis-acting regulatory elements in the human α globin cluster but also demonstrated that there are no additional erythroid-specific regulatory elements in the 220-kb region tested. In addition, the pattern of histone modification distinguished promoter elements from potential enhancer elements across this region. Finally, comparison of the human and mouse orthologous regions in a unique mouse model, with both regions coexpressed in the same animal, showed significant differences that may explain how these 2 clusters are regulated differently in vivo.

scholarly journals Genomic Promoter Analysis Predicts Functional Transcription Factor Binding

2008 ◽  
Vol 2008 ◽  
pp. 1-9 ◽  
Author(s):  
J. Sunil Rao ◽  
Suresh Karanam ◽  
Colleen D. McCabe ◽  
Carlos S. Moreno
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Proximal Promoter ◽  
Marginal Effect ◽  
Promoter Sequences ◽  
Factor Binding ◽  
Functional Transcription Factor

Background. The computational identification of functional transcription factor binding sites (TFBSs) remains a major challenge of computational biology. Results. We have analyzed the conserved promoter sequences for the complete set of human RefSeq genes using our conserved transcription factor binding site (CONFAC) software. CONFAC identified 16296 human-mouse ortholog gene pairs, and of those pairs, 9107 genes contained conserved TFBS in the 3 kb proximal promoter and first intron. To attempt to predict in vivo occupancy of transcription factor binding sites, we developed a novel marginal effect isolator algorithm that builds upon Bayesian methods for multigroup TFBS filtering and predicted the in vivo occupancy of two transcription factors with an overall accuracy of 84%. Conclusion. Our analyses show that integration of chromatin immunoprecipitation data with conserved TFBS analysis can be used to generate accurate predictions of functional TFBS. They also show that TFBS cooccurrence can be used to predict transcription factor binding to promoters in vivo.

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