A Bioinformatics Approach to Finding Transcriptional Regulatory Motifs in Bacteria

Abstract

Differential RNA sequencing has made it possible to determine the transcription start sites (TSS) for many of the genes in a genome. By using the TSS information, this study aimed to take advantage of the relatively simple transcriptional organization in bacteria and determine potential transcription factor binding sites for the cyanobacterium Anabaena sp. PCC 7120. By revealing shared sequences adjacent to known TSS, shared TFBS and unique TFBS were identified. This may make this set of computer applications useful in determining which genes in a given dataset are possibly transcriptionally coregulated. This project made use of the transcriptional map of the cyanobacterium Anabaena sp. PCC 7120 in order to narrow down the areas of the bacterial genome that may contain TFBS. The utilization of transcription start sites in locating TFBS is an additional unique feature of this study. This study culminated in tutorials (as shown in the Appendices) covering the programming involved in this project that may help biology students to begin writing their own computer programs.