Figure 4

Transcription termination in S. elongatus. (a) Minimum RNA free energy at the end of transcripts. The minimum free energy of 60-nucleotide RNA fragments with 10-nucleotide spacing was calculated and averaged for all mRNAs (Materials and methods). A drop in minimum free energy at the 3' end is indicative of Rho-independent transcription termination. (b) Distance between TransTermHP bioinformatically predicted terminators and 3' ends. Predicted intrinsic terminators (from TransTermHP [29]) tend to be much closer to the 3' end of transcripts than to random positions occurring at the same frequency as 3' ends. Blue bars show distance from a predicted terminator to the closest 3' end. As a control, we randomized the location of 3' ends in the genome. Grey bars show distance from a predicted terminator to the closest randomized 3' end. (c) Energy distributions of TransTermHP terminators. Not all predicted TransTermHP terminators cause transcription termination. Several terminator-like structures are located in non-transcribed regions or in the middle of transcripts. The free energy of terminators that cause transcription termination tends to be lower than the free energy of those that do not. The P-value is 3.00e-20 by two-sided Wilcoxon rank sum test. (d) Partial transcription termination creates complex transcriptional structures. Positive strand transcription is shown in blue and negative strand transcription in red. The positions of predicted terminators (from TransTermHP) are shown in green, and the position of JGI predicted ORFs are shown in black. Terminators located within transcripts often result in a decrease in the transcription of downstream ORFs.