We have developed a single-molecule platform to visualize DNA transcription by individual RNA polymerases (RNAPs) over many kilobases. In the meantime, we have developed SEnd-seq, a sequencing method that simultaneously maps both 5’ and 3’ RNA ends in a transcriptome. These novel technologies enable us to gain unprecedented insights into the coordination between RNAPs and their regulatory factors on a crowded genome in both bacterial and eukaryotic systems.