Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions

Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematically particular nucleotides with different nucleotides. Among 347 unknown ESTs, 51 ESTs match mitogenome transcription, 17 and 2 ESTs are from nuclear chromosome non-coding regions, and uncharacterized nuclear genes. Identified ESTs mapped on 205 protein-coding genes, 10 genes had swinger RNAs in several biosamples. Whole cell transcriptome searches for 17 ESTs mapping on non-coding regions confirmed their transcription. The 10 swinger-transcribed genes identified more than once associate with cancer induction and progression, suggesting swinger transformation occurs mainly in highly transcribed genes. Swinger transformation is a unique method to identify noncanonical RNAs obtained from NGS, which identifies putative ncRNA transcribed regions. Results suggest that swinger transcription occurs in highly active genes in normal and genetically unstable cancer cells.