Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

Curated 3´ ends for E. coli MG1655 (WT) grown to OD₆₀₀ ~0.4 and 2.0 in LB, and to OD₆₀₀ ~0.4 in minimal (M63) glucose medium. The genomic coordinate of the 3´ end (3´ end position), DNA strand, average RNA-seq read count of the 3´ end of both biological replicates, 3´ end classification (see Materials and methods), the gene annotation for the classification (details), and the sequence surrounding the 3´ end (40 bp upstream and 10 bp downstream, 3´ end nucleotide red and bolded) make up the columns of the table. The data for each growth condition are displayed on a separate tab.

All identified Rho termination regions are represented, defined as regions with at least one genomic coordinate with a significance score <1e⁻⁴. Rho scores were calculated for each genomic position by comparing DirectRNA-seq coverage in windows 800 nt upstream and downstream in the treated (+BCM) and untreated (-BCM) samples (see materials and methods). The 3´ genomic coordinate with the highest Rho score, DNA strand, 3´ end classification (see materials and methods), the gene annotation for the classification (details), the read coverage in the 800 nt windows upstream and downstream the 3´ end position ±BCM, the Rho score, and the p-value from the Fisher’s exact test (significance score) make up the columns of the table. An ‘undefined’ Rho score indicates one that could not be calculated due to zero reads in the -BCM downstream region. A significance score of ‘N/A’ indicates that the significance score was too low to accurately report.

Term-seq identified 3´ ends for E. coli MG1655 (WT) that were between 200 nt upstream of an ORF and the corresponding stop codon. The genomic coordinate of the 3´ end (3´ end position), DNA strand, average RNA-seq read count of the 3´ end of both biological replicates, 3´ end classification (see materials and methods), the gene annotation for the classification (details), the location of the 3´ end relative to an ORF – upstream ORF or internal (ORF classification), and the gene annotation of the associated ORF (upstream ORF/internal details) make up the columns of the table. The data for each growth condition are displayed on a separate tab. For 3´ ends identified in WT E. coli grown to OD₆₀₀ ~0.4 in LB, each 3´ end was also given a Rho score, an assessment of whether it is in a Rho termination region, and an intrinsic terminator score (see materials and methods). The read coverage in 800 nt windows upstream and downstream of each 3´ end position ±BCM from the DirectRNA-seq data, used to calculate Rho scores, is presented. An ‘undefined’ Rho score indicates one that could not be calculated due to zero reads in the ±BCM downstream region. Intrinsic terminator scores > 3.0 are suggestive of intrinsic termination (Chen et al., 2013). An ‘undefined’ intrinsic terminator score indicates one that could not be calculated because the sequence could not be folded into a recognizable secondary structure. Characterized regulatory elements in the LB 0.4 condition are also noted.