Accepted_test

Bioinformatics of transcription initiation in eukaryotes: TATA binding protein (TBP) and TBP binding sites in gene promoters

by Ponomarenko M | Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia

Abstract ID: 782

Event: BGRS-abstracts

Sections: [Sym 1] Section “Genome-wide transcriptomics (differential gene expression)”

Motivation and Aim: One of the largest worldwide scientific projects now is “1000 Genomes”, which has already sequenced the individual genomes of many hundreds of thousands peoples. Their consensus sequence of the most frequent nucleotides to each position of genomic DNA is the reference human genome, difference of which from individual human genomes is single nucleotide polymorphism (SNP). The dbSNP database contains over one hundred of million experimentally proven SNPs.

Methods and Algorithms: Therefore, in this review, we briefly recall how a three-step model of TBP binding to the promoters of human genes was proposed, which was then confirmed experimentally by independent authors. Besides, we will describe how we have next created the Web-service SNP_TATA_Comparator was, and how to use it in practice for genome-wide analysis of SNP within the human gene promoters.

Results: As well, we present the genome-wide knowledge base Human_SNP_DATAdb, which among the all 11,384,651 SNPs within 90 bp proximal promoters of the all 17,079 protein-coding genes pinpoints to 602,547 SNPs altering significantly the TBP-promoter affinity and, thereby, the expression of the human genes under these promoters.

Conclusion: Finally, Human_SNP_DATAdb has 57,612 annotations on how some of the above-said 602,547 candidate SNP-markers of the human gene expression changes can manifest in susceptibility to human diseases according to the PubMed database.