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.

Ganesh Warthi,Hervé Seligmann,Pierre-Edouard Fournier

doi:10.3389/fgene.2020.00042

Abstract

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.

Highlights

Systematic nucleotide exchanges, called swinger transformations, systematically exchange specific nucleotides with other specific nucleotides during DNA replication and/or RNA transcription
Swinger-transformed sequences of these identified 347 Expressed sequence tags (ESTs) are in Supplementary Table 1
A ! T ! C ! G ! A transformed asymmetric swinger transformations account for 124 ESTs with 96.95% average percentage identity and 308 bp average alignment length

Summary

Introduction

Systematic nucleotide exchanges, called swinger transformations, systematically exchange specific nucleotides with other specific nucleotides during DNA replication and/or RNA transcription. Previous correlation analyses (Seligmann, 2013b; Seligmann, 2013c; Michel and Seligmann, 2014) show that the lengths and abundances of swinger RNAs are approximately proportional to rates calculated on the basis of corresponding single nucleotide misinsertions by the human mitochondrial gamma DNA polymerase (from Lee and Johnson, 2006). This suggests that swinger RNAs result from polymerizations where the polymerase is stabilized in the usually transient, unstable state that causes regular single nucleotide misinsertions

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Conclusion