Transcription factor binding sites

It should be possible to extend the DNA microarray-binding experiment to whole-genome analysis of transcription factor binding sites. The authors suggest that a microarray spotted with 12,000 one-kilobase sequences would span the entire Saccharomyces cerevisiae genome (Bulyk et al., 2001). Such an array could be used to characterize the sequence specificity of S. cerevisiae transcription factors. These experiments would be useful for predicting functions of previously uncharacterized transcription... 

Van Lint C, Emiliani S, Ott M, Verdin E (1996a) Transcriptional activation and chromatin remodeling of the HIV-1 promoter in response to histone acetylation. EMBO J 15 1112-1120 Van Lint C, Emiliani S, Verdin E (1996b) The expression of a small fraction of cellular genes is changed in response to histone hyperacetylation. Gene Expr 5 245-53 Van Lint C, Amelia CA, Emiliani S, John M, Jie T, Verdin E (1997) Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for vims infectivity. J Virol 71 6113-6127... 

Vlieghe, D., Sandehn, A., De Bleser, P. J., et al. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34, D95-D97. 

Task Identification of overrepresented transcription factor binding sites (TFBS and modules of TEBS on sequence level). 

Result Transcription factor binding sites for the ER-enriched regions (calculated with RegionMiner and CEAS Tables 7.2 and 7.3). 

Ho Sui SJ et al (2005) oPOSSUM identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res 33 3154-3164. doi 33/10/3154 (pii)10.1093/nar/gki624... 

Lenhard B, Wasserman WW (2002) TFBS computational framework for transcription factor binding site analysis. Biomformatics 18 1135-1136... 

Loots G, Ovcharenko I, Pachter L, Dubchak I, Rubin E. rVISTA for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002 12 832-839. 

Alternately, an analysis of co-regulated genes can identify conserved motifs for novel transcription factor binding sites. This involves identification of a set of co-regulated genes that have similar expression profiles in response to some stimuli. The distal promoters of these genes are then analyzed for sequences that occur more often than would be expected by chance alone. These over-represented sequences are putative binding sites, which can be compared to the consensus sequences of known transcription... 

Transcription factor binding sites for promoter at position - 1931... 

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004 116(4) 499—509. 

Since microarrays are simply spots of DNA arrayed in a known pattern, they also can be used for DNA-DNA hybridization studies. This is the basis for using micro-arrays for comparative DNA hybridizations, single nucleotide polymorphism (SNP) discovery, and chromatin immunoprecipiation followed by microarray chip hybridization (ChIP on chip analyses) to identify transcription factor binding sites (discussed below). 

Prestridge, D. S. (1995). Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol 249, 923-32. 

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