Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates

Transcription is regulated at multiple levels, including initiation, elongation, and termination. Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and genome stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase II (RNAPII) speed, RNAPII elongation rate studies have been limited to a relatively small number of long genes or to velocity estimates inferred indirectly from RNAPII occupancy data. Here, we present DRB/TT_chem-seq2, a modified version of the DRB/TT_chem-seq method, to directly measure gene-specific elongation rates of more than 3000 genes. By combining short time point sampling after synchronized RNAPII release into the gene body and a new computational framework to track the distance traveled by RNAPII, we greatly increase the number of genes for which it is possible to obtain elongation rates. Our direct RNAPII elongation rate quantification reveals that elongation rates vary not only among genes but also within genes. Additionally, we describe how specific histone modifications and elongation factor occupancy correlate with subclasses of genes based on their elongation rates. Together, we present a robust and powerful method for RNAPII transcription elongation rate measurement.