摘要：RNA polymerase II (Pol II) plays an essential role in gene expression. We adapted plant native elongating transcript sequencing and global run on sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site (TSS). Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream the TSS, while Ser5P CTD Pol II associates with spliceosome, and Ser2P CTD Pol II presents a sharp peak within 250 bp downstream of polyadenylation site. Both 5’ pause and 3’ pause of Pol II are important regulatory steps for transcription. Active genes can be classified into three clusters based on different transcription models. In summary, we demonstrated these two methods are suitable to study RNA Pol II dynamics in planta. Although transcription is overall conserved within eukaryotes, there are potential plant specific regulatory mechanisms.