Promoter analysis

Regulatory regions, in general, tend to be DNase sensitive, and promoters are particularly DNase sensitive.

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=195093397&c=chr12&g=wgEncodeReg

http://www.scfbio-iitd.res.in/tutorial/promoter.html
Conserved eukaryotic promoter elements Consensus sequence
CAAT box   = GGCCAATCT
TATA box   = TATAA
GC box        = GGGCGG
CAP site      = TAC

http://bip.weizmann.ac.il/toolbox/seq_analysis/promoters.html

EPD - Eukaryotic Promoter Database at EMBL, Heidelberg 

dbTSS - database of Transcriptions Start Sites 

Jaspar - The high-quality transcription factor binding profile database 

PLACE - Database of Plant Cis-acting Regulatory DNA Elements 

PlantCare - a Plant Promoters database 

PlantPromDB - A Database of Plant Promoter Sequences 

SCPD - the Promoter Database of Saccharomyces cerevisiae 

TFD - the IFTI-MIRAGE website 

TransFac - Gene Regulation 

TRED - Transcriptional Regulatory Element Database 

TRRD - Transcription Regulatory Regions Database 

Dragon TF Integrator 

cisRED database holds conserved sequence motifs identified by genome scale motif discovery  

http://www.bios.net/daisy/promoters/239/g1/240.html

PROMOTER ELEMENTS
1. Core promoter - the minimal portion of the promoter required to properly initiate transcription

• Transcription Start Site (TSS)
• Approximately -34
• A binding site for RNA polymerase
• General transcription factor binding sites

2. Proximal promoter - the proximal sequence upstream of the gene that tends to contain primary regulatory elements

• Approximately -250
• Specific transcription factor binding sites                

THE RNA POLYMERASE II CORE PROMOTER

Annual Review of Biochemistry
Vol. 72: 449-479 (Volume publication date July 2003)
DOI: 10.1146/annurev.biochem.72.121801.161520
Stephen T. Smale1 and James T. Kadonaga2
http://www.annualreviews.org/doi/full/10.1146/annurev.biochem.72.121801.161520?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed


Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA.
The evolution of transcriptional regulation in eukaryotes.
Mol Biol Evol. 2003 Sep;20(9):1377-419.
PMID:12777501
Highly recommended for integrating recent data on chromatin modifications with prior knowledge about transcription in eukaryotes. 43 pages long!

Heintzmann ND and Ren B.
The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome.
Cell Mol Life Sci. 2007 Feb; 64(4):386-400. 15 pages long.
PMID: 17171231

http://onlinelibrary.wiley.com/doi/10.1111/j.1471-4159.2006.04111.x/full

TATA-less core promoters, as discovered in the Snca proximal promoter, often initiate from numerous start sites (cluster) that can be distributed over a region of about 50–100 nucleotides (Butler and Kadonaga 2002). In contrast, transcription from TATA core promoters occurs from a single site.


often, alternate promoters are associated with tissue-specific or developmentally-regulated gene expression (Schibler and Sierra 1987; Valdenaire et al. 1994).