Limiting RNA polymerase II (Pol II) at various stages of the transcription cycle is critical for gene regulation, which often occurs during the elongation stage at promoter proximal pause sites and in gene bodies. To determine the distribution of Pol II along genes, I used nascent transcript analysis as a general method. First, I identified the precise positions of Pol II pausing near promoters using a genome-wide nuclear run-on, called Precision Run-On sequencing (PRO-seq) in Drosophila embryonic cells. Using this, I revealed how the position of pausing is associated with initiation and promoter DNA elements. To further dissect the precise dynamics of paused Pol II, I probed the stability of paused Pol II and its termination by analyzing steady-state turn-over of the nascent transcript associated with Drosophila Hsp70 promoter. This shows that paused Pol II on Hsp70 is stable for around 5 min and can either terminate or elongate into the gene body, which is consistent with optical measurements of paused Pol II. I also examined how Pol II elongates during the time course of rapid and robust inhibition of pause escape in mouse embryonic stem cells. The analysis of the elongation rates in nearly 1,000 genes showed tight interplay between promoter proximal pausing, early elongation rates, and co-transcriptional splicing at the beginning of the genes. Finally, I demonstrate that the nascent transcriptome analysis methods can be directly extended into mammalian tissues, and show possibility of linking the study of the fundamental mechanism of Pol II into biomedical applications.