miRStart, a novel resource of human microRNA TSSs (transcription start sites), systematically incorporates significant datasets derived from TSS-relevant experiments to identify transcription start sites of microRNAs. The distribution patterns of these experimental features within 50 k upstream region of microRNA precursors provides an insight into determining reliable microRNA TSSs. In general, a high-confidence TSS is recommended for each microRNA based on a SVM training model. However, users can customize their preferable microRNA TSSs according to the straightforward display of experimental TSS signals.

 

Published experimental evidences used in miRStart are described as follows:


(1) CAGE (Cap Analysis of Gene Expression) tags: Recognize 5’-end of a gene
(2) TSS Seq tags: More than 300 million 5’-end sequences of human and mouse cDNAs by combining oligo-capping method and Solexa sequencing technology
(3) H3K4me3 enrichment (histone H3 is trimethylated at its lysine 4 residue): Enriched surrounding TSSs

 

Moreover, ESTs and comparative genomics around putative miRNA TSSs are used to provide strong supports for reconfirmation.

 

The following figure demonstrates the concept of miRStart.

 
 

 

       The human miRNA let-7a-1 gives a typical example how miRStart defines TSSs of intergenic miRNA by using experimental evidences mentioned above. In total, there exist 1083 CAGE tags and 208 TSS tags within the 50 kb upstream region of let-7a-1 precursor (Genomic coordinates Chr9: 96938239-96938318 [+]). The aggregation of CAGE tags, TSS tags, and H3K4me3 enrichment appears around the 9000-10000 upstream region of precursor, suggesting that the putative TSS of let-7a-1 may be located between 96928239 and 96929239. It is observed that CAGE tags are strikingly assembled at 96928529, where represents the putative TSS of let-7a-1. As expected, an EST BG326593 initiated from 96928570 nearby putative TSS provides the supporting evidence that the determined TSS is high-confidence. Furthermore, the upstream region immediately adjacent to putative TSS is quite conserved between 44 vertebrate species, which implies that this motif may has promoter activity.