Skip to main content
. 2020 Dec 17;16(12):e9844. doi: 10.15252/msb.20209844

Figure 3. Identification and analysis of M. florum promoters.

Figure 3

  1. Circular representation of the M. florum L1 chromosome enhanced with 5′‐RACE data generated in this study. Outer to inner circle: genomic coordinates (kbp); genes encoded on the positive (blue for coding sequences, turquoise for RNAs) and negative (red for coding sequences, fuchsia for RNAs) DNA strands; raw 5′‐RACE signal (0–1,000 read starts scale) observed at each genomic position for the positive (black) and negative (gray) DNA strands; putative transcription start sites (TSSs) identified on the positive (green) and negative (orange) DNA strands from significant 5′‐RACE peaks.
  2. M. florum promoter motif determined using the MEME software (Bailey & Elkan, 1994) from the DNA sequence located upstream the 605 putative TSSs identified by 5′‐RACE. A total of 422 sites across the genome were included in the motif. The position of the −10 box (TAWAAT) and the extended element (EXT) is indicated.
  3. Venn diagram illustrating the number of TSSs associated with a conserved promoter motif (see panel B) found by MEME, MAST, or both software compared with the total number of putative TSSs passing filters (605). Eight additional putative TSSs were added to the initial set according to the MAST search.
  4. Localization and orientation of TSSs associated with a MEME or MAST promoter motif. p‐gTSS, parallel intergenic TSS; a‐gTSS, antiparallel intergenic TSS; p‐iTSS, parallel internal TSS; a‐iTSS, antiparallel internal TSS. For gTSSs, the orientation was defined according to the closest downstream gene, while the overlapping gene was used in the case of iTSSs.
  5. Relative frequency distribution of the spacing between TSSs and their associated promoter −10 box.
  6. Nucleotide identity at the transcription initiation site (+1) for gTSSs and iTSSs associated with a promoter motif.
  7. Aggregate profile showing the mean RNA‐seq read coverage observed at and around all motif‐associated TSSs identified in this study. The calculated SEM is also shown. The aggregate profile was centered on the TSSs coordinates (relative position 0 bp), indicated by a gray dashed line.