Analysis and Comparison of Regulatory Regions Between Oryza Sativa and Non-Plant Eukaryotic Species
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Rawat, Shiva
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Abstract
Deciphering the non-coding regions of the eukaryotic genes continues to be an important transdisciplinary area spanning bioinformatics and experimental biology fields. Upstream of a eukaryotic gene there is a region of regulatory DNA sequences, which serve as genetic switches for modulating its expression. Various computational methods have been implemented to locate specific functionally important genomic elements. Nonetheless, accurately detecting promoters, transcription start sites (TSS), and transcription factor binding sites (TFBS) is a conundrum as even the finest and most sophisticated computational tools produce a significant amount of false positive and false negative predictions. In this study, our objective was to accurately classify regulatory regions in several eukaryotic species and elucidate their roles. Information of several transcription factors (TFs) of rice (O. sativa), their corresponding binding sites and the distribution of these sites near TSSs of rice genome were obtained from (Triska, et al., 2017), (Tatarinova, et al., 2016). For each transcription factor, we determined its orthologues in other species and compared their binding sites to those of O. sativa transcription factors. After mapping the identified TFs to non-plant eukaryote genomes, we discovered their putative binding sites in non-plant eukaryote species, and analyzed the distribution of distances between corresponding TFBS and TSS. We have shown that the genome distributions of orthologous TFBSs in rice (O. sativa), fruit fly (D. melanogaster), two species of rodents (M. musculus and R. norvegicus), as well as humans (H. sapiens) share similar characteristics, thus, proving a conservative nature of TF-TFBS interactions at a genomic scale.
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Keywords
Transcription factor, Binding sites, Sequence motifs, Orthologous, Transcription start site (TSS), Oryza Sativa