Figure 3.

Examples of genomic regions that were represented on tiling microarrays and subjected to gene expression profiling. A, C, and E represent generalized schematic examples of genomic regions that were tiled for further analysis. The heavy black horizontal arrows represent genomic sequence. The gray rectangles represent the region of genomic sequence represented in the microarray clone. The green arrows represent the location of BLASTX hits for homologues in other organisms. The blue squares represent individual tiling oligonucleotides that together represent the entire genomic region of interest. A is an example of a microarray clone that overlaps two homologues, C is an example of a microarray clone that has partial overlap with one homologue but contains sufficient sequence to potentially overlap a second unknown transcript as described in Results, and E represents a microarray clone with no overlap to any BLASTX hits. B, D, and F show examples of actual gene expression data for three specific genomic regions that correspond to the generalized categories depicted in A, C, and E, respectively. The top black line represents the genomic sequence with hatch marks every 100 base pairs, and the gray rectangles represent microarray clone sequence. The regions of BLASTX homology are labeled and shown in green (A. nidulans), yellow (S. cerevisiae), or red (S. pombe). Arrowheads reflect the direction of the BLASTX hit. The intensity units for each tile are graphed for both the minus and plus strands in the lower part of each figure. Cy5 signal (red) reflects the transcript profile in RNS stress, whereas Cy3 signal (green) reflects the transcript profile in the absence of RNS. B shows the gene expression data for H.c. FAT1, which is present on the plus strand. D shows the gene expression data for H.c. ATF1, which is present on the minus strand. F shows the gene expression data for the novel transcript NIT72, which is present on the plus strand. The boundaries of each of these three transcripts are delineated by vertical black arrows. G shows the tiling data for the control transcript AOX1 as described in the text. The known H. capsulatum AOX1 coding sequence (Johnson et al., 2003) is shown in yellow and intron sequences are represented as gaps between the yellow exons. The 5′ and 3′ UTR sequences from AOX1 clone 1 sequence are represented as gray boxes. The regions of the genomic sequence that are represented in the transcript (5′ UTR, 3′ UTR, and exons) are shaded in gray to emphasize the correspondence between these regions and the tiles that give a high intensity signal on the plus strand graph.