Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Troskie, RL., Jafrani, Y., Mercer, T.R. et al. Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biol 22, 146 (2021).
https://doi.org/10.1186/s13059-021-02369-0
Abstract
Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns. Some pseudogene transcripts have intact open reading frames and are translated in cultured cells, representing unannotated protein-coding genes. To assess the biological impact of noncoding pseudogenes, we CRISPR-Cas9 delete the nucleus-enriched pseudogene PDCL3P4 and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the human transcriptional landscape.
Acknowledgement
The authors thanked the University of Queensland Genome Innovation Hub for continuing support.
