Four-Nucleotide and Six-Nucleotide Abortive Transcripts Can Inhibit Transcription

Abortive transcripts (ATs) are 2-nucleotide (nt) to 15-nt nascent RNAs that are synthesized and released by RNA polymerase during the transcription initiation period, a phenomenon known as abortive initiation (AI). Abortive initiation occurs in vitro with all characterized RNA polymerase, including bacterial, archaeal, eukaryotic, and bacteriophag. However, the roles of ATs currently remain unknown. In this study, it was found that the 4-nt and 6-nt ATs were produced from a specific gene which could inhibit the transcription of their own gene and of other genes in Escherichia coli. 4-nt ATs displayed the similar abilities to interfere with the transcription of same genes, while different 6-nt ATs showed the varied abilities to interfere with the transcription of same genes. Furthermore, there was no relation between the transcriptional inhibition level and the number of identical sequence sites. The effect of the single-strand DNAs on transcription differed from that of the abortive transcripts. Thus, our finding indicates that AI may be a novel transcriptional regulation mechanism that can prevent excessive transcription and compete for resources for gene expression during the initial transcription period, the transcriptional inhibition mechanism of ATs is most likely not associated with complementary base pairing.