Module 7: Molecular Computing with RNA Sequences


Transcriptional Control Elements

Introduction module 7 contents RNA Structure back to the index of modules

  • Promoters & enhancers: A very large number of consensus sequences corresponding to the promotion (promoters) and enhancement (enhancers) of transcription have been identified in the DNA of eukaryotic organisms. Promoters are found upstream (ie., 5') to the transcriptional start site whereas enhancers have been mapped both outside of and within transcriptional units (ie., 5', 3' and in the middle). No enhancers have been found to transcriptionally stimulate prokaryotic transcription. A relatively recently identified type of sequence called a "silencer" has been shown to shut off (silence) the transcription of certain eukaryotic genes (eg., murine T cell receptor gamma genes).

    • Databases and search engines on the web

      • Transfac: This is a server dedicated to searching for binding sites (DNA sequences) and the transcription factors that bind at those sites. The transcription factors are classified into 39 classes based on their DNA-binding domains.

      • Eukaryotic Promoter Database (EPD) This is an annotated non-redundant collection of eukaryotic POL II (RNA polymerase II) promoters, for which the transcription start site has been determined experimentally. At this site, one can search for biologically meaningful promoter sequences in a query DNA sequence.

      • PROSCAN: This search engine is designed to find putative eukaryotic Pol II promoter sequences in primary sequence data. At this time, using test promoter and non-promoter sequence test sets, the program recognizes approximately 70% of primate promoter sequences, with a false positive rate of about one in every 14,000 bases. The authors of the site suggest that it is best used to find regions in a primary DNA sequence that might be good candidate regions to further test for promoter functionality.

      • TESS: The Transcription Element Search System (TESS) based at the University of Pennsylvania is similar to the Transfac server with some additional search options.

    • Finding patterns in transcriptional control

      • SIGNAL SCAN: This server finds and lists homologies of published transcriptional element signal sequences with an input DNA sequence. It is probable that the major benefit and use of SIGNAL SCAN is to find out the identity of unknown proteins bound to characterized binding sites in DNA sequences.

Introduction module 7 contents RNA Structure back to the index of modules

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