Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq

Ekaterina V Ilgisonis; Elena A Ponomarenko; Svetlana N Tarbeeva; Andrey V Lisitsa; Victor G Zgoda; Sergey P Radko; Alexander I Archakov

doi:10.3389/fmolb.2022.944639

Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq

Front Mol Biosci. 2022 Dec 5:9:944639. doi: 10.3389/fmolb.2022.944639. eCollection 2022.

Authors

Ekaterina V Ilgisonis¹, Elena A Ponomarenko¹, Svetlana N Tarbeeva¹, Andrey V Lisitsa¹, Victor G Zgoda¹, Sergey P Radko¹, Alexander I Archakov¹

Affiliation

¹ Institute of Biomedical Chemistry, Moscow, Russia.

Abstract

It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for various types of biological material was carried out, and the HepG2 cell line transcriptome was compared with the transcriptome of liver tissue cells. In addition, the contribution of variability in the coverage of expressed genes in human transcriptomes to the creation of a draft human transcriptome was evaluated. For human liver tissues, ONT makes an extremely insignificant contribution to the overall coverage of the transcriptome. Thus, to ensure maximum coverage of the liver tissue transcriptome, it is sufficient to apply only one technology: Illumina RNA-Seq (FPKM > 0).

Keywords: Illumina RNA-Seq; Oxford Nanopore Technologies MinION; human genome; qPCR; transcriptomics.