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Old 10-06-2010, 10:25 PM   #7
malachig
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Location: WashU

Join Date: Aug 2010
Posts: 117
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Those are three pretty big questions. Promoters, splice sites, and splice regulatory elements.

Promoters. I agree with jdanderson that it depends what you mean by promoters. The 'regulation' tracks available in the UCSC genome browser contain many relevant data sets. As mentioned, one strategy is simply to use transcription start sites themselves as an indicator of where promoters likely reside. A second option is to use preexisting experimental data such as the results of RNA-PolII binding assays or epigenetic profiling by ChIP-Seq. For example, various histone modifications (methylation, acetylation) are associated with transcript initiation and these have been profiled for various tissues. Third, bioinformatic prediction of promoter elements is a huge field in itself. Have you considered cisRED: "databases of genome-wide regulatory module and element predictions"? Fourth, if you want to download a list of high quality annotated regulatory elements and their coordinates I would recommend ORegAnno.

Splice sites. Again a huge area of research. There are a wide array of gene discovery and splice site prediction tools that will examine a sequence of genomic DNA and tell you the coordinates of possible splice sites. As others have mentioned, it is probably a lot easier to use the exon-exon connections currently present in known transcript models (which are largely based on full-length cDNA sequencing followed by gapped alignment to a reference genome). For example, to get a comprehensive list of splice sites you could use the Table browser of UCSC. Download in BED format the gene table for UCSC genes, CCDS, Ensembl, Refseq, MGC, and Vega. Merging these BED files and extracting the non-redundant set of splice sites for all exons is a relatively straightforward scripting task.

Splice regulatory elements. This is arguably the most challenging of the three, and an area of very active research. Simply put the regulatory elements that influence splicing beyond the splice sites themselves - i.e. exonic splicing silencers and enhancers (ESSs, ESEs) and intronic splicing silencers and enhancers (ISSs, ISEs) are not well known. The recent advent of RNA-seq technology is arguably going to allow us to really start to perform the experiments needed to begin to characterize these sequences. To learn more about these elements and how they are defined I would recommend 'mechanisms of alternative pre-messenger RNA splicing' by Douglas Black. Some labs with recent publications on the topic of discovering the splicing regulatory code are those of Christopher Burge, Robert Darnell, and Benjamin Blencowe.
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