Evidences of the present of the promoter like elements into the non-coding regions of the human coagulation factor VIII gene

Abstract

Accurate prediction of the Cis-regulatory elements encoded within DNA sequences<br><br>throughout the genomes and in different regions of a gene is a crucial step towards<br><br>understanding the regulatory mechanism of the gene expression. Bearing in mind, the<br><br>complete sequences of the human coagulation factor VIII (hFVIII) gene were investigated to<br><br>identify and characterize promoteric like sequences (PLS) based on in-silico examination. In<br><br>this regard, the sequences of the hFVIII gene as well as protein sequence of the human RNA<br><br>polymerase II (RNAPII) retrieved from Genebank and PDB with accession number<br><br>AY769950 and 2F3I, respectively. Subsequently presence of any promoter areas throughout<br><br>the gene was investigated based on potential transcription start positions by linear<br><br>discriminant function combining characteristics describing functional motifs and<br><br>oligonucleotide composition of these sites using FPROM program and evaluated via Cluspro<br><br>and PatchDock programs and also visualized with Pymol software. Our analysis led to<br><br>revealed 43 regions, containing enhancer-like elements and promoter-like elements<br><br>throughout the hFVIII gene except in the introns 8, 11, 12, 16-20 in four groups including<br><br>really, intronic, exonic and pseudo promoters that are located in the 5'UTR, intronic regions,<br><br>exonic regions and 3'UTR, respectively with independent of the intron length. Moreover,<br><br>assessment the binding affinity of these regions to RNAPII showed suitable connection and<br><br>level of energy even less than really promoter in some case of intronic promoters. Altogether,<br><br>the data obtained in this study has provided further proofs for potentials of the intronic regions<br><br>for regulatory functions as well as promoteric regions with high affinity to RNAPII for<br><br>application as self-promoter in new vector designing. However, experimental analysis of the<br><br>detected regions to examine their potential regulatory functions on a reporter gene is the next<br><br>step to this work.