Thermally driven fluctuations play a critical role in key cellular processes such as transcription of gene expression. On the other hand, while the specific biological role remains unknown, recent spectroscopic studies have shown that biomolecules in aqueous solution also possess collective vibrational modes in the terahertz (THz) frequency region. In this study, thermal effect (temperature increase) and THz radiation effect on transcription by RNA polymerase were statistically analyzed and compared using high-throughput DNA sequencing. The results showed that the temperature increase and the THz radiation appear to act oppositely in multiple processes of transcription, including pausing of RNA elongation and mis-incorporation of non-cognate substrates by the enzyme. We interpret these new results to suggest that the highly controlled enzymatic reaction may utilize not only random thermal fluctuations but also the collective vibrational modes of the biomolecules in the THz region, and the THz radiation might specifically amply the latter.