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Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.

Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ - MBio (2014)

Bottom Line: A small number of studies have compared the primary transcriptomes of different bacterial species, but few have compared closely related species with clearly divergent evolutionary histories.We show that a species population history is reflected in its transcriptome and posit relaxed selection as the main driver of an abundance of canonical -10 promoter sites in M. bovis relative to M. marinum.Finally, through comparison of M. bovis and M. tuberculosis, we illustrate that single nucleotide polymorphism (SNP)-driven promoter differences likely underpin many of the transcriptional differences between M. tuberculosis complex lineages.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Cell Biology Centre, The University of Edinburgh, Edinburgh, United Kingdom.

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Related in: MedlinePlus

(A) Line plots show the number of −10 box motifs showing RNAP occupancy at the indicated levels of sequence depth in M. bovis compared with randomly selected genomic sites. The dashed line shows the total number of actual TSS calls made with the available sequence data at each depth. (B) Expansion of TSSs within the upstream regions of orthologous genes in M. bovis. A histogram shows the density of TSSs upstream of orthologs with conserved TSSs (CPTs) in both species. The inset shows the distribution of nonprimary TSSs located within 500 nt of the TSP in both species. **, P < 0.005, Pearson’s chi-squared test.
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fig3: (A) Line plots show the number of −10 box motifs showing RNAP occupancy at the indicated levels of sequence depth in M. bovis compared with randomly selected genomic sites. The dashed line shows the total number of actual TSS calls made with the available sequence data at each depth. (B) Expansion of TSSs within the upstream regions of orthologous genes in M. bovis. A histogram shows the density of TSSs upstream of orthologs with conserved TSSs (CPTs) in both species. The inset shows the distribution of nonprimary TSSs located within 500 nt of the TSP in both species. **, P < 0.005, Pearson’s chi-squared test.

Mentions: To explore the extent to which a genome’s density of −10 boxes correlates with promoter occupancy, we determined the number of consensus −10 sites in M. bovis being filled by at least 10 TEX+ reads, a number which is lower than the cutoff of 20 reads used for actual TSS calls, while maintaining a minimum TEX+/TEX− ratio of at least 2:1. Applying this relaxed criterion, designed to mimic the effect of increased sequencing depth, resulted in 7,770 (50%) of the total 15,569 consensus −10 box sites being occupied at the fully mapped library size of ~6.6 million TEX+ reads (excluding rRNA). We also determined the degree to which −10 site occupancy by the accumulation of TEX+ reads contributes to TSS identification by mapping the relationship across different library sizes (Fig. 3A). The rate at which −10 boxes were found to become occupied mirrors almost exactly the call rate for TSSs, indicating that the identified TSSs and their distributions are largely functions of the presence of an appropriate initiation site combined with an appropriate sequencing depth. In contrast, equivalent numbers of randomly selected genomic positions show a significantly lower level of occupancy at each depth (P <2.2e-16, Pearson’s chi-square test).


Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.

Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ - MBio (2014)

(A) Line plots show the number of −10 box motifs showing RNAP occupancy at the indicated levels of sequence depth in M. bovis compared with randomly selected genomic sites. The dashed line shows the total number of actual TSS calls made with the available sequence data at each depth. (B) Expansion of TSSs within the upstream regions of orthologous genes in M. bovis. A histogram shows the density of TSSs upstream of orthologs with conserved TSSs (CPTs) in both species. The inset shows the distribution of nonprimary TSSs located within 500 nt of the TSP in both species. **, P < 0.005, Pearson’s chi-squared test.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4128351&req=5

fig3: (A) Line plots show the number of −10 box motifs showing RNAP occupancy at the indicated levels of sequence depth in M. bovis compared with randomly selected genomic sites. The dashed line shows the total number of actual TSS calls made with the available sequence data at each depth. (B) Expansion of TSSs within the upstream regions of orthologous genes in M. bovis. A histogram shows the density of TSSs upstream of orthologs with conserved TSSs (CPTs) in both species. The inset shows the distribution of nonprimary TSSs located within 500 nt of the TSP in both species. **, P < 0.005, Pearson’s chi-squared test.
Mentions: To explore the extent to which a genome’s density of −10 boxes correlates with promoter occupancy, we determined the number of consensus −10 sites in M. bovis being filled by at least 10 TEX+ reads, a number which is lower than the cutoff of 20 reads used for actual TSS calls, while maintaining a minimum TEX+/TEX− ratio of at least 2:1. Applying this relaxed criterion, designed to mimic the effect of increased sequencing depth, resulted in 7,770 (50%) of the total 15,569 consensus −10 box sites being occupied at the fully mapped library size of ~6.6 million TEX+ reads (excluding rRNA). We also determined the degree to which −10 site occupancy by the accumulation of TEX+ reads contributes to TSS identification by mapping the relationship across different library sizes (Fig. 3A). The rate at which −10 boxes were found to become occupied mirrors almost exactly the call rate for TSSs, indicating that the identified TSSs and their distributions are largely functions of the presence of an appropriate initiation site combined with an appropriate sequencing depth. In contrast, equivalent numbers of randomly selected genomic positions show a significantly lower level of occupancy at each depth (P <2.2e-16, Pearson’s chi-square test).

Bottom Line: A small number of studies have compared the primary transcriptomes of different bacterial species, but few have compared closely related species with clearly divergent evolutionary histories.We show that a species population history is reflected in its transcriptome and posit relaxed selection as the main driver of an abundance of canonical -10 promoter sites in M. bovis relative to M. marinum.Finally, through comparison of M. bovis and M. tuberculosis, we illustrate that single nucleotide polymorphism (SNP)-driven promoter differences likely underpin many of the transcriptional differences between M. tuberculosis complex lineages.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Cell Biology Centre, The University of Edinburgh, Edinburgh, United Kingdom.

Show MeSH
Related in: MedlinePlus