The Proportionality Critique Still Stands

Transcriptome data comparison. Comparison of genes reported as temperature-dependent in a DNA microarray [52] and asRNAs we identified opposite to them. (XLSX 11 kb

Additional file 10: Table S3. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

Genes with antisense and 5′ UTR sRNAs. The table contains information about all of the genes with antisense and 5′ UTR sRNAs associated with them. Gene ontology terms (GO terms) for biological processes (BP) are also given for each gene. The column titled, “Norgard FoldChange” contains the fold-change of that particular gene as reported by Revel et al. [52] via microarray after a temperature shift. (XLSX 221 kb

Additional file 12: Figure S8. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

Manual curation of peaks. Intragenic RNA peaks called in genes bb0311 and bb0312 were manually curated based on the coverage patterns. The deep-sequencing results are displayed as described in the caption of Additional file 4: Figure S2. The - strand coverage is shown in blue. Note that the y-axis scale is different between the peak calling libraries (peak) and the biological replicates used for differential expression analyses (23 °C and 37 °C). The genomic context is illustrated below the coverage maps: black arrows indicate the annotated genes; the yellow box indicates the region called as a small intraRNA by our peak caller. The peaks appear to be broad and similar in height across the gene, suggesting they are degradation products of the mRNA, not stable sRNAs. (PDF 2229 kb

Additional file 2: of Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

Configuration file used to benchmark Bowtie2 and demonstrates the simplicity of benchmarking 34 parameters using Teaser. (TXT 442 bytes

Table_1_The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi.xlsx

<p>The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by Rel_Bbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that Rel_Bbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were Rel_Bbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. Rel_Bbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.</p

Table_3_The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi.XLSX

<p>The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by Rel_Bbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that Rel_Bbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were Rel_Bbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. Rel_Bbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.</p

Additional file 15: Table S5. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

Oligonucleotides used in this study. Sequences and names of all oligonucleotides used in this study. (DOCX 15 kb

Image_2_The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi.TIFF

<p>The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by Rel_Bbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that Rel_Bbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were Rel_Bbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. Rel_Bbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.</p

Additional file 1: of Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

Detailed results shown in the Figures. In addition, it describes the report that is generated by Teaser. (DOCX 1789 kb

Table_2_The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi.XLSX

<p>The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by Rel_Bbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that Rel_Bbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were Rel_Bbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. Rel_Bbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.</p