Abstract
Using a novel computational method, an extensive collection of predicted Rho-independent transcription terminators is derived from 343 prokaryotes, offering insight into their relationship to DNA uptake
Highlights
In many prokaryotes, transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop
Algorithm to search for candidate terminators TransTermHP searches whole prokaryotic genomes for intrinsic terminators of the type depicted in Figure 1: a short, low-energy hairpin followed downstream by a stretch of thymine nucleotides
Due to the difference in stability of a G-U pairing versus the complementary C-A pairing in RNA, the hairpins found on one strand of the genome will, in general, be different from those found on the opposite strand
Summary
Transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop. Detecting such Rho-independent transcription terminators can shed light on the organization of bacterial genomes and can improve genome annotation. Rho-independent ( known as intrinsic) terminators are sequence motifs found in many prokaryotes that cause the transcription of DNA to RNA to stop. These termination signals typically consist of a short, often GC-rich hairpin followed by a sequence enriched in thymine residues [1]. Due to lack of sequence data, previous systems (for example, [4,7]) have tended to focus on E. coli or on only a portion of the nowavailable genomes
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