Pol III transcription initiation preferences on hairpin-encoding DNA coligos. (A) Schematic depiction of a coligo stem-larger loop junction with numbering to distinguish stem and loop nucleotide positions. The dotted line marks the junction location here and in panels B and C. The 5 nt junction window described in the text is from nt 3 to −2. (B) Pol III transcription initiation position preference for each of the six coligos studied. The percentage of reads initiating within the 5 nt junction window is summed and shown in parentheses under the coligo name. Coligo 122 percentage includes initiations with one or two untemplated adenylates (see text). The average percentage of reads initiating within the 5 nt window for the six coligos was 81%. (C) Pol III transcription initiation positions in relation to the stem-larger loop junction for the six coligos studied. Initiation events were concentrated in the 5 nt window from 3 to −2. (D) Transcription initiation nucleotide preference for the six coligos studied. Initiation events took place mainly on template dC and dT positions.
