RNAse protection assays to validate predicted fusion/chimeric transcripts.

<p>Each panel on top shows the autoradiographs of the probe that covers the predicted chimeric RNA fragment against human RNA from tissue pools detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028213#pone.0028213.s023" target="_blank">table S2</a>. In each panel, “+” and “−” indicate the tracks with presence and absence of input RNA, respectively. The RNA size ladder is shown on the left of the figure (unit: nucleotides). The bottom of the figure schematically shows the two components of each predicted chimeric transcript. For example, clone 7556-D12 contains 97 bases of an exon of gene TOP3D (designated A) joined to a 153-base exonic fragment of gene PIK4A (designated B); both fragments are in the same genome strand orientation (shown by arrows). In the top first panel corresponding to clone 7556-D12, the protected chimeric fragment in the RNA“+” lane is labeled A+B. The protected (non-chimeric) exons B and A are also shown. The other 2 validated chimeric fragments are shown in the second and third top panels. The fourth panel contains a control exon-exon junction of gene HIRA. The fifth panel contains a control actin gene fragment. A total of 3 out of 15 predicted and tested chimeric fragments were validated using this method. For more details on these experiments see Material and Methods, and for the genomic coordinates of the fragments see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028213#pone.0028213.s023" target="_blank">table S2</a>.