Bp chromosomes display distinct transcriptional landscapes.

<p>(A) Cumulative curves for expression of genes across the condition compendium. The graph represents the percentage of new genes expressed on Chr 1 (red) and Chr 2 (green) (y-axis) upon the successive addition of conditions (x-axis). This analysis was confined to Sanger genes to minimize annotation errors. (B) Chr 1 and Chr 2 exhibit constitutive and mosaic expression respectively. The graph relates the proportion of genes expressed on each chromosome (y-axis) under any particular number of conditions (x-axis). Chr 1 genes are expressed in most conditions (rightward upslope, red), while Chr 2 genes are expressed in specific conditions (leftward upslope, green). (C) Chr 1 genes exhibit higher expression levels than Chr 2 genes. Each dot represents the median expression of all detectably expressed genes on the respective chromosome, joined by the same condition. Chromosomal expression levels were compared using one-tailed paired t-test ().</p

Condition-specific deconvolution of QS mutants.

<p>(A) <i>pmlI</i> transcriptional network. The diagram shows genes differentially expressed in <i>pmlI</i>-disrupted mutants (>2-fold change), overlaid onto the condition-dependent network. Red and green spots represent up- and down-regulated genes. Yellow star - location of the <i>pmlI</i> gene. Genes coding for chemotaxis/mobility (violet-dotted line) and surface polysaccharide antigens (blue-dotted line) are shown. (B) Motility assays. The wild type parental strain Bp008 is motile, as shown by the more turbid medium. The QS mutant is non-motile and only grows along the line of inoculation. (C) Electron microscope photographs of the Bp capsule. The exopolysaccharide material typical of Bp capsule I (CPSI) is apparent in the parental strain Bp008 as shown by the black streaks surrounding the rod-shaped bacterium. In contrast, neither exopolysaccharide material nor capsule architecture is observable in the mutant. (D) Disruption of QS system results in altered bacterial phenotype. The wild type parental strain Bp008 exhibits a smooth colony phenotype when grown on agar plate whereas the QS mutant has a wrinkled phenotype.</p

Discovery of <i>cis</i>-regulatory motifs.

<p>Motifs were identified by analysing upstream sequences of constituent genes or operons in each cluster. The asterisk (*) indicates that the motif was detected using MEME and BioProspector. Tick symbols indicate that all cluster genes have a cognate homolog in the specified species (i.e. 100%), otherwise the proportion of homologs in that species is reported. Filled circles indicate that the discovered <i>cis</i>-motifs in Bp are significantly similar () to Bt or Bm. Motifs that match to known binding sites and corresponding binding proteins in other species are reported in the last column. Bt, <i>B. thailandensis</i>; Bm, <i>B. mallei</i>.</p

Co-expression network of Bp condition-dependent transcription.

<p>(A) Co-expression network. Nodes are individual genes, connected to one another by significant co-expression relationships (mutual information score ). The colours represent clusters over-represented in different Riley annotations, and their respective annotations are provided at the bottom. (B) Condition dependent cluster expression. The heat-map depicts representative clusters and patterns of expression across conditions. Gene expression levels were mean-normalized. (C) Inter-cluster relationships. The MRCN unit M036 consists of two clusters: C131 and C265, which include genes encoding proteins for degrading misfolded proteins and other genes with hypothetical functions. Thickness of edges represents the strength of the co-expression relationship between two genes. (D) Condition groups. The different condition-specific transcriptional profiles were clustered to one another based on similarities in expression of genes from the Bp core genome. Condition groups deemed to be stable by bootstrap assessment are marked in colors.</p

Expressed transcripts in the Bp condition compendium.

<p>High-resolution views of different genomic features are depicted. All transcripts depicted were expressed above the median cut-off threshold. (A) Transcriptional annotation of the <i>Burkholderia pseudomallei</i> K96243 reference genome. The transcriptome map is presented along the chromosomal coordinates in a strand-specific manner, with the outermost track composed of Sanger annotated genes (orange), followed by novel genes (green), the Bp operons (purple) and finally the non-coding RNAs (ncRNAs; red). In all tracks, predicted genomic features that do not have an associated transcript in this study are colored in grey. The genes, operons and ncRNAs are arranged in a strand-specific manner by visualizing them in either the forward (+) or the reverse (−) tracks. The black vertical lines indicate the start/stop sites of the circular chromosomes. (B) Sanger genes and novel genes. Expressed strand-specific transcripts are presented as blue bars along the forward and reverse strands. Transcript boundaries correspond to predicted start and stop coordinates of Sanger annotated genes and FGENESB novel genes. (C) Differential expression of a Bp operon. Expression of a predicted flagella operon (<i>BPSL0026 – BPSL0032</i>) in a specific condition (taurine exposure). (D) Antisense transcription. <i>BPSL0095</i>, a gene coding for hypothetical protein exhibits antisense transcription upon exposure to human serum.</p

Identification of Bp ncRNAs.

<p>(A) Condition-dependence of ncRNA expression. The heat-map depicts 766 identified ncRNAs and their patterns of expression across the condition compendium. Red depicts high expression, and green depicts low expression. (B) <i>BPNC10061R</i> expression is triggered by sorbitol. <i>BPNC10061R</i> is highly expressed under condition of osmotic stress (2M Sorbitol) compared to desiccation. (C) Secondary structure and species conservation of <i>BPNC10061R</i>. Consensus sequences homologous to <i>BPNC10061R</i> are found in <i>B. mallei</i>, <i>B. cenocepacia</i> and <i>B. thailandensis</i> strains. The sequences were aligned, and corresponding secondary structures were predicted.</p

Supplementary Tables 1 through 13 from Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma

Supplementary Table 1: Clinicopathological Parameters of samples used Supplementary Table 2: Read Mapping Statistics of NanoChIP-seq Libraries Supplementary Table 3: Non coding RNAs associated with Somatic Promoters Supplementary Table 4: Alternative Promoters Supplementary Table 5: Spectral Counts from CRC samples of N terminal peptides predicted to be gained in GC Supplementary Table 6: HLA prediction of GC samples Supplementary Table 7: Recurrent N terminal sequences with high affinity to MHC Class I Supplementary Table 8: P values of Wilcoxon test between ACRG samples with high and low somatic promoter usage Supplementary Table 9: HLA types of healthy PBMC donors Supplementary Table 10: Peptide pools for alternative promoters Supplementary Table 11: Cytokine Responses of N terminal Peptides Supplementary Table 12: Somatic Promoters Overlapping EZH2/SUZ12 Binding Sites Supplementary Table 13: RACE Primers</p

Supplementary Text, Supplementary Figures 1 through 13, Supplementary Methods from Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma

Supplementary text S1. Supplementary Figure 1: Chromatin Profiles of Primary GC. Supplementary Figure 2: Epithelial features of GC promoters. Supplementary Figure 3: GC Somatic Promoter Features. Supplementary Figure 4: Association of Somatic Promoters with Gene Expression in GC and Other Tumor Types. Supplementary Figure 5: Changes in DNA methylation at CpG island containing promoters. Supplementary Figure 6: Expression distribution of alternative and canonical isoforms. Supplementary Figure 7: Characterization of RASA3 Isoform. Supplementary Figure 8: Characterization of MET Isoforms. Supplementary Figure 9: Immunogenicity of N-terminal peptides. Supplementary Figure 10: Immunogenicity Assay and Nanostring Profiling. Supplementary Figure 11: Functional Assessment of Peptide Immunogenicity. Supplementary Figure 12: EZH2 Inhibition. Supplementary Figure 13: Unannotated somatic promoters.</p

Tables S1-S16 from <i>VHL</i> Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma

Supplementary tables</p

Figure S1-9; Supplementary methods from <i>VHL</i> Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma

Supplementary methods. Supplementary Figures 1-9</p