Although transcription is one of the most important biological functions of cells, our understanding of its regulation is still limited. In this dissertation, we have studied the transcriptional regulation in prokaryotes in three aspects. First, we investigated the extent to which cis-regulatory elements are conserved during the course of evolution using the LexA regulons in cyanobacteria as an example. We found that in most cyanobacterial genomes analyzed, LexA appears to function as the transcriptional regulator of the key SOS response genes. The loss of lexA in some genomes might lead to the degradation of its binding sites. Second, directional RNA-seq techniques have recently become the workhorse for transcriptome profiling in prokaryotes, however, it is a challenging task to accurately assemble highly labile prokaryotic transcriptomes for further analyses. To fill this gap, we have developed a hidden Markov model based transcriptome assembler which outperforms the state-of-the-art assemblers. Using our tool, we characterized alternative operon structures in E. coli K12 under various growth conditions and growth phases, and found that they are more complex and dynamic than previously anticipated. Lastly, we determined anti-sense and non-coding transcription patterns in E. coli K12 under various growth conditions and time points. We found that a large portion of genes have antisense transcription in a condition-dependent manner. Most antisense transcripts are initiated and restricted to the 5'-end of the gene on the sense strand, and their expression levels are correlated with those of the genes on the sense strand, suggesting that these antisense transcripts might play an important role in transcriptional regulation.
