Kinetic measurement of gene-specific RNAPII transcription elongation rates

Transcription is regulated at multiple levels, including initiation, elongation, and termination. Whereas much research has focused on initiation of transcription, regulation of elongation plays an important role not only for transcription dynamics, but also for co-transcriptional RNA processing as the RNAPII elongation rate can influence maturation of the nascent RNA transcript. Despite advances in high-throughput approaches for global identification of RNAPII speed, RNAPII elongation rate studies have been largely limited to a small number of genes. Here, we present DRB/TTchem-seq2, a modified version of DRB/TTchem-seq method, to measure gene-specific elongation rates of more than 3,000 genes. By approximating the distance traveled by RNAPII in certain time intervals using the wave fronts post RNAPII release. Our direct RNAPII elongation rate quantification reveals that elongation rates vary not only among genes but also within genes. Additionally, specific histone modifications and elongation factors are tightly correlated with the elongation rates. Together, we present a robust and powerful method for RNAPII transcription elongation rate measurement. Nascent transcripts following RNA Pol II (RNAPII) stalling and released from promoter-proximal pausing were captured and subsequently sequenced in four different time points (i.e., 5, 10, 15 and 20 minutes) in both U2OS and DLD-1 cells. RNAPII elongation rates were estimated based on the distances traveled by RNAPII in certain time periods for both U2OS and DLD-1 cells.